[med-svn] [ariba] 02/06: Imported Upstream version 2.1.0+ds
Sascha Steinbiss
satta at debian.org
Thu Aug 4 13:42:40 UTC 2016
This is an automated email from the git hooks/post-receive script.
satta pushed a commit to branch master
in repository ariba.
commit 060035781de27d0e8285a9fea040d52ba0b51c32
Author: Sascha Steinbiss <satta at debian.org>
Date: Thu Aug 4 10:23:42 2016 +0000
Imported Upstream version 2.1.0+ds
---
.travis.yml | 4 -
MANIFEST.in | 1 +
README.md | 4 +-
ariba/cluster.py | 4 +-
ariba/clusters.py | 37 ++-
ariba/ext/fml-asm_ariba.cpp | 14 +-
ariba/external_progs.py | 4 +-
ariba/ref_genes_getter.py | 74 +++++-
ariba/ref_preparer.py | 11 +-
ariba/report.py | 39 ++-
ariba/report_filter.py | 1 +
ariba/samtools_variants.py | 17 +-
ariba/summary.py | 40 ++-
ariba/summary_cluster.py | 41 +++
ariba/summary_sample.py | 10 +-
ariba/tasks/summary.py | 1 +
ariba/tests/assembly_test.py | 6 +-
ariba/tests/cluster_test.py | 189 ++++++++++++-
ariba/tests/clusters_test.py | 27 ++
.../reads_1.fq | 296 +++++++++++++++++++++
.../reads_2.fq | 296 +++++++++++++++++++++
.../references.fa | 3 +
.../reads_1.fq | 296 +++++++++++++++++++++
.../reads_2.fq | 296 +++++++++++++++++++++
.../references.fa | 3 +
.../reads_1.fq | 296 +++++++++++++++++++++
.../reads_2.fq | 296 +++++++++++++++++++++
.../references.fa | 3 +
.../reads_1.fq | 296 +++++++++++++++++++++
.../reads_2.fq | 296 +++++++++++++++++++++
.../references.fa | 3 +
.../reads_1.fq | 296 +++++++++++++++++++++
.../reads_2.fq | 296 +++++++++++++++++++++
.../references.fa | 3 +
.../reads_1.fq | 296 +++++++++++++++++++++
.../reads_2.fq | 296 +++++++++++++++++++++
.../references.fa | 3 +
...ok_samtools_snp_known_position_pres_abs_gene.fa | 3 +
...s_snp_known_position_pres_abs_gene.metadata.tsv | 1 +
...p_known_position_pres_abs_gene.ref_for_reads.fa | 14 +
...mtools_snp_known_position_pres_abs_noncoding.fa | 3 +
..._known_position_pres_abs_noncoding.metadata.tsv | 1 +
...p_known_position_var_only_gene_does_have_var.fa | 3 +
...sition_var_only_gene_does_have_var.metadata.tsv | 1 +
...own_position_var_only_gene_does_not_have_var.fa | 3 +
...on_var_only_gene_does_not_have_var.metadata.tsv | 1 +
...wn_position_var_only_noncoding_does_have_var.fa | 3 +
...n_var_only_noncoding_does_have_var.metadata.tsv | 1 +
...osition_var_only_noncoding_does_not_have_var.fa | 3 +
...r_only_noncoding_does_not_have_var.metadata.tsv | 1 +
..._test_full_run_ok_samtools_snp_pres_abs_gene.fa | 3 +
..._run_ok_samtools_snp_pres_abs_gene.metadata.tsv | 1 +
..._ok_samtools_snp_pres_abs_gene.ref_for_reads.fa | 14 +
.../reads_1.fq | 296 +++++++++++++++++++++
.../reads_2.fq | 296 +++++++++++++++++++++
.../references.fa | 3 +
..._full_run_ok_samtools_snp_pres_abs_noncoding.fa | 3 +
...ok_samtools_snp_pres_abs_noncoding.metadata.tsv | 1 +
.../reads_1.fq | 296 +++++++++++++++++++++
.../reads_2.fq | 296 +++++++++++++++++++++
.../references.fa | 3 +
..._test_full_run_ok_samtools_snp_var_only_gene.fa | 3 +
..._run_ok_samtools_snp_var_only_gene.metadata.tsv | 1 +
.../reads_1.fq | 296 +++++++++++++++++++++
.../reads_2.fq | 296 +++++++++++++++++++++
.../references.fa | 3 +
..._full_run_ok_samtools_snp_var_only_noncoding.fa | 3 +
...ok_samtools_snp_var_only_noncoding.metadata.tsv | 1 +
.../reads_1.fq | 296 +++++++++++++++++++++
.../reads_2.fq | 296 +++++++++++++++++++++
.../references.fa | 3 +
...t_write_catted_assemblies_fasta.expected.out.fa | 6 +
...est_make_vcf_and_read_depths_files.expected.vcf | 29 +-
...mple_test_column_names_tuples_and_het_snps.tsv} | 2 +-
.../data/summary_test_gather_output_rows.in.2.tsv | 2 +-
...n.2.tsv => summary_test_get_all_het_snps.1.tsv} | 6 +-
...n.2.tsv => summary_test_get_all_het_snps.2.tsv} | 2 +-
ariba/tests/ref_preparer_test.py | 19 +-
ariba/tests/report_filter_test.py | 16 +-
ariba/tests/samtools_variants_test.py | 3 +-
ariba/tests/summary_cluster_test.py | 44 +++
ariba/tests/summary_sample_test.py | 19 +-
ariba/tests/summary_test.py | 19 ++
scripts/ariba | 5 +-
setup.py | 2 +-
85 files changed, 6609 insertions(+), 107 deletions(-)
diff --git a/.travis.yml b/.travis.yml
index fb4b157..6505ad8 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -7,10 +7,6 @@ addons:
- liblapack-dev
- libgfortran3
- libncurses5-dev
-cache:
- directories:
- - "build"
- - "$HOME/.cache/pip"
python:
- "3.4"
sudo: false
diff --git a/MANIFEST.in b/MANIFEST.in
new file mode 100644
index 0000000..395c07b
--- /dev/null
+++ b/MANIFEST.in
@@ -0,0 +1 @@
+recursive-include third_party *.h
diff --git a/README.md b/README.md
index 8ee083d..d519ef9 100644
--- a/README.md
+++ b/README.md
@@ -25,7 +25,7 @@ ARIBA has the following dependencies, which need to be installed:
* [CD-HIT][cdhit] version >= 4.6
* [MASH][mash] version >= 1.0.2
* [MUMmer][mummer] version >= 3.23
- * [Samtools and BCFtools][samtools] version >= 1.2
+ * [Samtools and BCFtools][samtools] version >= 1.3
Once the dependencies are installed, install ARIBA using pip:
@@ -64,7 +64,7 @@ to the following dependencies.
For example, you could specify an exact version of a Samtools executable
that you compiled and downloaded in your home directory (assuming BASH):
- export ARIBA_SAMTOOLS=$HOME/samtools-1.2/samtools
+ export ARIBA_SAMTOOLS=$HOME/samtools-1.3/samtools
### Temporary files
diff --git a/ariba/cluster.py b/ariba/cluster.py
index 8e1c4ca..07f387a 100644
--- a/ariba/cluster.py
+++ b/ariba/cluster.py
@@ -103,6 +103,7 @@ class Cluster:
self.final_assembly_vcf = os.path.join(self.root_dir, 'assembly.reads_mapped.bam.vcf')
self.samtools_vars_prefix = self.final_assembly_bam
self.assembly_compare = None
+ self.variants_from_samtools = {}
self.assembly_compare_prefix = os.path.join(self.root_dir, 'assembly_compare')
self.mummer_variants = {}
@@ -415,7 +416,8 @@ class Cluster:
self.total_contig_depths = self.samtools_vars.total_depth_per_contig(self.samtools_vars.read_depths_file)
- if self.samtools_vars.variants_in_coords(self.assembly_compare.assembly_match_coords(), self.samtools_vars.vcf_file):
+ self.variants_from_samtools = self.samtools_vars.variants_in_coords(self.assembly_compare.assembly_match_coords(), self.samtools_vars.vcf_file)
+ if len(self.variants_from_samtools):
self.status_flag.add('variants_suggest_collapsed_repeat')
elif not self.assembled_ok:
print('\nAssembly failed\n', file=self.log_fh, flush=True)
diff --git a/ariba/clusters.py b/ariba/clusters.py
index cd4c243..027868a 100644
--- a/ariba/clusters.py
+++ b/ariba/clusters.py
@@ -100,6 +100,7 @@ class Clusters:
self.report_file_filtered = os.path.join(self.outdir, 'report.tsv')
self.catted_assembled_seqs_fasta = os.path.join(self.outdir, 'assembled_seqs.fa.gz')
self.catted_genes_matching_refs_fasta = os.path.join(self.outdir, 'assembled_genes.fa.gz')
+ self.catted_assemblies_fasta = os.path.join(self.outdir, 'assemblies.fa.gz')
self.threads = threads
self.verbose = verbose
@@ -443,6 +444,21 @@ class Clusters:
pyfastaq.utils.close(f)
+ def _write_catted_assemblies_fasta(self, outfile):
+ f = pyfastaq.utils.open_file_write(outfile)
+
+ for gene in sorted(self.clusters):
+ try:
+ seq_dict = self.clusters[gene].assembly.sequences
+ except:
+ continue
+
+ for seq_name in sorted(seq_dict):
+ print(seq_dict[seq_name], file=f)
+
+ pyfastaq.utils.close(f)
+
+
def _write_catted_assembled_seqs_fasta(self, outfile):
f = pyfastaq.utils.open_file_write(outfile)
@@ -490,9 +506,9 @@ class Clusters:
except:
pass
- if self.verbose:
- print('Deleting reads store files', self.read_store.outfile + '[.tbi]')
try:
+ if self.verbose:
+ print('Deleting reads store files', self.read_store.outfile + '[.tbi]')
self.read_store.clean()
except:
pass
@@ -504,7 +520,7 @@ class Clusters:
def write_versions_file(self, original_dir):
with open('version_info.txt', 'w') as f:
print('ARIBA run with this command:', file=f)
- print(' '.join([sys.argv[0]] + ['run'] + sys.argv[1:]), file=f)
+ print(' '.join([sys.argv[0]] + sys.argv[1:]), file=f)
print('from this directory:', original_dir, file=f)
print(file=f)
print(*self.version_report_lines, sep='\n', file=f)
@@ -523,6 +539,7 @@ class Clusters:
os.chdir(self.outdir)
self.write_versions_file(cwd)
self._map_and_cluster_reads()
+ self.log_files = None
if len(self.cluster_to_dir) > 0:
got_insert_data_ok = self._set_insert_size_data()
@@ -562,13 +579,15 @@ class Clusters:
print(self.catted_assembled_seqs_fasta, 'and', self.catted_genes_matching_refs_fasta, flush=True)
self._write_catted_assembled_seqs_fasta(self.catted_assembled_seqs_fasta)
self._write_catted_genes_matching_refs_fasta(self.catted_genes_matching_refs_fasta)
+ self._write_catted_assemblies_fasta(self.catted_assemblies_fasta)
- clusters_log_file = os.path.join(self.outdir, 'log.clusters.gz')
- if self.verbose:
- print()
- print('{:_^79}'.format(' Catting cluster log files '), flush=True)
- print('Writing file', clusters_log_file, flush=True)
- common.cat_files(self.log_files, clusters_log_file)
+ if self.log_files is not None:
+ clusters_log_file = os.path.join(self.outdir, 'log.clusters.gz')
+ if self.verbose:
+ print()
+ print('{:_^79}'.format(' Catting cluster log files '), flush=True)
+ print('Writing file', clusters_log_file, flush=True)
+ common.cat_files(self.log_files, clusters_log_file)
if self.verbose:
print()
diff --git a/ariba/ext/fml-asm_ariba.cpp b/ariba/ext/fml-asm_ariba.cpp
index eee0e44..a82670c 100644
--- a/ariba/ext/fml-asm_ariba.cpp
+++ b/ariba/ext/fml-asm_ariba.cpp
@@ -172,12 +172,14 @@ int assemble(char *readsFile, char *fastaOut, char* logfileOut)
// need to get the reads from the file every time, instead of before
// the loop because fml_assemble() destroys them :(
seqs = bseq_read(readsFile, &n_seqs);
- fml_utg_t *utg;
- utg = fml_assemble(&opt, n_seqs, seqs, &n_utg);
- Assembly a(n_utg, utg, *minCountIter);
- assemblies.push_back(a);
- a.printStats(ofs);
- fml_utg_destroy(n_utg, utg);
+ if (seqs && n_seqs > 0) {
+ fml_utg_t *utg;
+ utg = fml_assemble(&opt, n_seqs, seqs, &n_utg);
+ Assembly a(n_utg, utg, *minCountIter);
+ assemblies.push_back(a);
+ a.printStats(ofs);
+ fml_utg_destroy(n_utg, utg);
+ }
}
if (assemblies.size() == 0 || assemblies[0].numberOfContigs == 0)
diff --git a/ariba/external_progs.py b/ariba/external_progs.py
index b8b4661..98990cc 100644
--- a/ariba/external_progs.py
+++ b/ariba/external_progs.py
@@ -41,13 +41,13 @@ prog_to_version_cmd = {
min_versions = {
- 'bcftools': '1.2',
+ 'bcftools': '1.3',
'bowtie2': '2.1.0',
'cdhit': '4.6',
'cdhit2d': '4.6',
'mash': '1.0.2',
'nucmer': '3.1',
- 'samtools': '1.2',
+ 'samtools': '1.3',
#'spades': '3.5.0',
}
diff --git a/ariba/ref_genes_getter.py b/ariba/ref_genes_getter.py
index bb8dfbe..1ae8d39 100644
--- a/ariba/ref_genes_getter.py
+++ b/ariba/ref_genes_getter.py
@@ -1,6 +1,7 @@
class Error (Exception): pass
import os
+import re
import sys
import shutil
import tarfile
@@ -13,7 +14,7 @@ from ariba import common, card_record, vfdb_parser
class RefGenesGetter:
def __init__(self, ref_db, genetic_code=11):
- allowed_ref_dbs = {'card', 'argannot', 'resfinder','vfdb'}
+ allowed_ref_dbs = {'card', 'argannot', 'plasmidfinder', 'resfinder','vfdb'}
if ref_db not in allowed_ref_dbs:
raise Error('Error in RefGenesGetter. ref_db must be one of: ' + str(allowed_ref_dbs) + ', but I got "' + ref_db)
self.ref_db=ref_db
@@ -212,33 +213,80 @@ class RefGenesGetter:
genes_file = os.path.join(tmpdir, 'Database Nt Sequences File.txt')
final_fasta = outprefix + '.fa'
+ final_tsv = outprefix + '.tsv'
seq_reader = pyfastaq.sequences.file_reader(genes_file)
- ids = {}
+ f_out_tsv = pyfastaq.utils.open_file_write(final_tsv)
+ f_out_fa = pyfastaq.utils.open_file_write(final_fasta)
+
for seq in seq_reader:
- ids[seq.id] = ids.get(seq.id, 0) + 1
+ original_id = seq.id
+ seq.id = re.sub(r'\((.*)\)', r'\1.', seq.id)
+ print(seq, file=f_out_fa)
+ print(seq.id, '1', '0', '.', '.', 'Original name was ' + original_id, sep='\t', file=f_out_tsv)
- for name, count in sorted(ids.items()):
- if count > 1:
- print('Warning! Sequence name', name, 'found', count, 'times in download. Keeping longest sequence', file=sys.stderr)
- pyfastaq.tasks.to_unique_by_id(genes_file, final_fasta)
+ pyfastaq.utils.close(f_out_tsv)
+ pyfastaq.utils.close(f_out_fa)
shutil.rmtree(tmpdir)
+ print('Finished. Final files are:', final_fasta, final_tsv, sep='\n\t', end='\n\n')
+ print('You can use them with ARIBA like this:')
+ print('ariba prepareref -f', final_fasta, '-m', final_tsv, 'output_directory\n')
+ print('If you use this downloaded data, please cite:')
+ print('"ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes",\nGupta et al 2014, PMID: 24145532\n')
+
+
+ def _get_from_plasmidfinder(self, outprefix):
+ outprefix = os.path.abspath(outprefix)
+ final_fasta = outprefix + '.fa'
final_tsv = outprefix + '.tsv'
- f = pyfastaq.utils.open_file_write(final_tsv)
- seq_reader = pyfastaq.sequences.file_reader(final_fasta)
+ tmpdir = outprefix + '.tmp.download'
+ current_dir = os.getcwd()
- for seq in seq_reader:
- print(seq.id, '1', '0', '.', '.', '.', sep='\t', file=f)
+ try:
+ os.mkdir(tmpdir)
+ os.chdir(tmpdir)
+ except:
+ raise Error('Error mkdir/chdir ' + tmpdir)
- pyfastaq.utils.close(f)
+ zipfile = 'plasmidfinder.zip'
+ cmd = 'curl -X POST --data "folder=plasmidfinder&filename=plasmidfinder.zip" -o ' + zipfile + ' https://cge.cbs.dtu.dk/cge/download_data.php'
+ print('Downloading data with:', cmd, sep='\n')
+ common.syscall(cmd)
+ common.syscall('unzip ' + zipfile)
+ print('Combining downloaded fasta files...')
+ fout_fa = pyfastaq.utils.open_file_write(final_fasta)
+ fout_tsv = pyfastaq.utils.open_file_write(final_tsv)
+ name_count = {}
+
+ for filename in os.listdir(tmpdir):
+ if filename.endswith('.fsa'):
+ print(' ', filename)
+ file_reader = pyfastaq.sequences.file_reader(os.path.join(tmpdir, filename))
+ for seq in file_reader:
+ original_id = seq.id
+ seq.id = seq.id.replace('_', '.', 1)
+ if seq.id in name_count:
+ name_count[seq.id] += 1
+ seq.id = seq.id + '.' + str(name_count[seq.id])
+ else:
+ name_count[seq.id] = 1
+
+ print(seq, file=fout_fa)
+ print(seq.id, '0', '0', '.', '.', 'Original name was ' + original_id, sep='\t', file=fout_tsv)
+
+ pyfastaq.utils.close(fout_fa)
+ pyfastaq.utils.close(fout_tsv)
+ print('\nFinished combining files\n')
+ os.chdir(current_dir)
+ shutil.rmtree(tmpdir)
print('Finished. Final files are:', final_fasta, final_tsv, sep='\n\t', end='\n\n')
print('You can use them with ARIBA like this:')
print('ariba prepareref -f', final_fasta, '-m', final_tsv, 'output_directory\n')
print('If you use this downloaded data, please cite:')
- print('"ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes",\nGupta et al 2014, PMID: 24145532\n')
+ print('"PlasmidFinder and pMLST: in silico detection and typing of plasmids", Carattoli et al 2014, PMID: 24777092\n')
def _get_from_vfdb(self, outprefix):
diff --git a/ariba/ref_preparer.py b/ariba/ref_preparer.py
index 85ad525..9fee5fd 100644
--- a/ariba/ref_preparer.py
+++ b/ariba/ref_preparer.py
@@ -86,9 +86,15 @@ class RefPreparer:
if new_key in key_count:
if new_key in new_clusters:
assert key_count[new_key] == 1
- assert new_key + '_1' not in new_clusters
- new_clusters[new_key + '_1'] = new_clusters[new_key]
+
+ i = 1
+ while new_key + '_' + str(i) in new_clusters:
+ i += 1
+
+ assert new_key + '_' + str(i) not in new_clusters
+ new_clusters[new_key + '_' + str(i)] = new_clusters[new_key]
del new_clusters[new_key]
+ key_count[new_key] = i
key_count[new_key] += 1
new_name = new_key + '_' + str(key_count[new_key])
@@ -99,7 +105,6 @@ class RefPreparer:
assert new_name not in new_clusters
new_clusters[new_name] = name_set
-
return new_clusters
diff --git a/ariba/report.py b/ariba/report.py
index cc7ce3e..fdbe50f 100644
--- a/ariba/report.py
+++ b/ariba/report.py
@@ -1,3 +1,4 @@
+import copy
import sys
import pymummer
@@ -169,6 +170,7 @@ def _report_lines_for_one_contig(cluster, contig_name, ref_cov_per_contig, pymum
else:
free_text_column = ';'.join(['.'])
+ remaining_samtools_variants = copy.copy(cluster.variants_from_samtools)
if cluster.assembled_ok and contig_name in cluster.assembly_variants and len(cluster.assembly_variants[contig_name]) > 0:
for (position, var_seq_type, ref_ctg_change, var_effect, contributing_vars, matching_vars_set, metainfo_set) in cluster.assembly_variants[contig_name]:
if len(matching_vars_set) > 0:
@@ -196,7 +198,11 @@ def _report_lines_for_one_contig(cluster, contig_name, ref_cov_per_contig, pymum
smtls_alt_depth = []
for var in contributing_vars:
+ if contig_name in remaining_samtools_variants:
+ remaining_samtools_variants[contig_name].discard(var.qry_start)
+
depths_tuple = cluster.samtools_vars.get_depths_at_position(contig_name, var.qry_start)
+
if depths_tuple is not None:
smtls_alt_nt.append(depths_tuple[1])
smtls_total_depth.append(str(depths_tuple[2]))
@@ -206,11 +212,11 @@ def _report_lines_for_one_contig(cluster, contig_name, ref_cov_per_contig, pymum
smtls_alt_nt = ';'.join(smtls_alt_nt) if len(smtls_alt_nt) else '.'
smtls_alt_depth = ';'.join(smtls_alt_depth) if len(smtls_alt_depth) else '.'
samtools_columns = [
- str(contributing_vars[0].ref_start), #ref_start
- str(contributing_vars[0].ref_end), # ref_end
+ str(contributing_vars[0].ref_start + 1), #ref_start
+ str(contributing_vars[0].ref_end + 1), # ref_end
';'.join([x.ref_base for x in contributing_vars]), # ref_nt
- str(contributing_vars[0].qry_start), # ctg_start
- str(contributing_vars[0].qry_end), #ctg_end
+ str(contributing_vars[0].qry_start + 1), # ctg_start
+ str(contributing_vars[0].qry_end + 1), #ctg_end
';'.join([x.qry_base for x in contributing_vars]), #ctg_nt
smtls_total_depth,
smtls_alt_nt,
@@ -231,6 +237,10 @@ def _report_lines_for_one_contig(cluster, contig_name, ref_cov_per_contig, pymum
if samtools_columns is None:
samtools_columns = [['.'] * 9]
+ else:
+ for ctg_pos in range(int(samtools_columns[3]) - 1, int(samtools_columns[4]), 1):
+ if contig_name in remaining_samtools_variants:
+ remaining_samtools_variants[contig_name].discard(ctg_pos)
lines.append('\t'.join(common_first_columns + variant_columns + samtools_columns + [matching_vars_column] + [free_text_column]))
else:
@@ -239,7 +249,26 @@ def _report_lines_for_one_contig(cluster, contig_name, ref_cov_per_contig, pymum
samtools_columns + \
[matching_vars_column] + [free_text_column]
))
- else:
+
+ for contig_name in remaining_samtools_variants:
+ for var_position in remaining_samtools_variants[contig_name]:
+ depths_tuple = cluster.samtools_vars.get_depths_at_position(contig_name, var_position)
+ if depths_tuple is not None:
+ new_cols = [
+ '0', # known_var column
+ 'HET', # var_type
+ '.', '.', '.', '.', '.', '.', '.', '.', # var_seq_type ... ref_nt
+ str(var_position + 1), str(var_position + 1), # ctg_start, ctg_end
+ depths_tuple[0], # ctg_nt
+ str(depths_tuple[2]), # smtls_total_depth
+ depths_tuple[1], # smtls_alt_nt
+ str(depths_tuple[3]), # smtls_alt_depth
+ '.',
+ free_text_column,
+ ]
+ lines.append('\t'.join(common_first_columns + new_cols))
+
+ if len(lines) == 0:
lines.append('\t'.join(common_first_columns + ['.'] * (len(columns) - len(common_first_columns) - 1) + [free_text_column]))
return lines
diff --git a/ariba/report_filter.py b/ariba/report_filter.py
index 3b92090..8748749 100644
--- a/ariba/report_filter.py
+++ b/ariba/report_filter.py
@@ -120,6 +120,7 @@ class ReportFilter:
return ReportFilter._flag_passes_filter(report_dict['flag'], self.exclude_flags) \
and report_dict['pc_ident'] >= self.min_pc_ident \
and report_dict['ref_base_assembled'] >= self.min_ref_base_assembled \
+ and report_dict['var_type'] != 'HET'
def _filter_list_of_dicts(self, dicts_list):
diff --git a/ariba/samtools_variants.py b/ariba/samtools_variants.py
index 1385121..e7264a3 100644
--- a/ariba/samtools_variants.py
+++ b/ariba/samtools_variants.py
@@ -39,7 +39,7 @@ class SamtoolsVariants:
tmp_vcf = self.vcf_file + '.tmp'
cmd = ' '.join([
self.samtools_exe, 'mpileup',
- '-t INFO/DPR,DV',
+ '-t INFO/AD',
'-A',
'-f', self.ref_fa,
'-u',
@@ -56,7 +56,7 @@ class SamtoolsVariants:
tmp_vcf,
'|',
self.bcftools_exe, 'query',
- r'''-f '%CHROM\t%POS\t%REF\t%ALT\t%DP\t%DPR]\n' ''',
+ r'''-f '%CHROM\t%POS\t%REF\t%ALT\t%DP\t%AD]\n' ''',
'>',
self.read_depths_file + '.tmp'
])
@@ -71,10 +71,7 @@ class SamtoolsVariants:
tmp_vcf,
'|',
self.bcftools_exe, 'filter',
- '-i', '"MIN(DP)>=' + str(self.bcf_min_dp),
- ' & MIN(DV)>=' + str(self.bcf_min_dv),
- ' & MIN(DV/DP)>=' + str(self.bcf_min_dv_over_dp),
- ' & QUAL >=', str(self.bcf_min_qual), '"',
+ '-i', '"SUM(AD)>=5 & MIN(AD)/DP>=0.1"',
'-o', self.vcf_file
])
@@ -160,7 +157,7 @@ class SamtoolsVariants:
def variants_in_coords(nucmer_matches, vcf_file):
'''nucmer_matches = made by assembly_compare.assembly_match_coords().
Returns number of variants that lie in nucmer_matches'''
- vcf_variant_counts = {}
+ found_variants = {}
f = pyfastaq.utils.open_file_read(vcf_file)
for line in f:
if line.startswith('#'):
@@ -174,10 +171,12 @@ class SamtoolsVariants:
i = pyfastaq.intervals.Interval(position, position)
intersects = len([x for x in nucmer_matches[scaff] if x.intersects(i)]) > 0
if intersects:
- vcf_variant_counts[scaff] = vcf_variant_counts.get(scaff, 0) + 1
+ if scaff not in found_variants:
+ found_variants[scaff] = set()
+ found_variants[scaff].add(position)
pyfastaq.utils.close(f)
- return sum(list(vcf_variant_counts.values()))
+ return found_variants
def get_depths_at_position(self, seq_name, position):
diff --git a/ariba/summary.py b/ariba/summary.py
index 837ab03..f1b767f 100644
--- a/ariba/summary.py
+++ b/ariba/summary.py
@@ -18,6 +18,7 @@ class Summary:
filter_rows=True,
filter_columns=True,
min_id=90.0,
+ show_known_het=False,
cluster_cols='assembled,match,ref_seq,pct_id,known_var,novel_var',
variant_cols='groups,grouped,ungrouped,novel',
verbose=False,
@@ -33,6 +34,7 @@ class Summary:
if fofn is not None:
self.filenames.extend(self._load_fofn(fofn))
+ self.show_known_het = show_known_het
self.cluster_columns = self._determine_cluster_cols(cluster_cols)
self.var_columns = self._determine_var_cols(variant_cols)
self.filter_rows = filter_rows
@@ -113,6 +115,17 @@ class Summary:
@classmethod
+ def _get_all_het_snps(cls, samples_dict):
+ snps = set()
+ for filename, sample in samples_dict.items():
+ for cluster, snp_dict in sample.het_snps.items():
+ if len(snp_dict):
+ for snp in snp_dict:
+ snps.add((cluster, snp))
+
+ return snps
+
+ @classmethod
def _get_all_var_groups(cls, samples_dict):
groups = {}
for filename, sample in samples_dict.items():
@@ -126,6 +139,8 @@ class Summary:
def _gather_output_rows(self):
all_cluster_names = Summary._get_all_cluster_names(self.samples)
all_var_columns = Summary._get_all_variant_columns(self.samples)
+ all_het_snps = Summary._get_all_het_snps(self.samples)
+
if self.var_columns['groups']:
var_groups = Summary._get_all_var_groups(self.samples)
else:
@@ -163,12 +178,22 @@ class Summary:
continue
key = ref_name + '.' + variant
+
if rows[filename][cluster]['assembled'] == 'no':
rows[filename][cluster][key] = 'NA'
elif cluster in sample.variant_column_names_tuples and (ref_name, variant, grouped_or_novel, group_name) in sample.variant_column_names_tuples[cluster]:
rows[filename][cluster][key] = 'yes'
+ if self.show_known_het:
+ if cluster in sample.het_snps and variant in sample.het_snps[cluster]:
+ rows[filename][cluster][key] = 'het'
+ rows[filename][cluster][key + '.%'] = sample.het_snps[cluster][variant]
else:
rows[filename][cluster][key] = 'no'
+ if self.show_known_het and (cluster, variant) in all_het_snps:
+ rows[filename][cluster][key + '.%'] = 'NA'
+
+ if self.show_known_het and (cluster, variant) in all_het_snps and key + '.%' not in rows[filename][cluster]:
+ rows[filename][cluster][key + '.%'] = 'NA'
for key, wanted in self.cluster_columns.items():
if not wanted:
@@ -213,7 +238,8 @@ class Summary:
if making_header_lines:
csv_header.append(cluster_name + '.' + col)
- phandango_header.append(cluster_name + '.' + col + ':o1')
+ suffix = ':c2' if col.endswith('.%') else ':o1'
+ phandango_header.append(cluster_name + '.' + col + suffix)
line.append(rows[filename][cluster_name][col])
@@ -270,6 +296,7 @@ class Summary:
'yes_nonunique': '#a6cee3',
'no': '#33a02c',
'NA': '#b2df8a',
+ 'het': '#fb9a99',
}
cols_to_add_colour_col.reverse()
@@ -351,6 +378,12 @@ class Summary:
self.rows = self._gather_output_rows()
phandango_header, csv_header, matrix = Summary._to_matrix(self.filenames, self.rows, self.cluster_columns)
+ # sanity check same number of columns in headers and matrix
+ lengths = {len(x) for x in matrix}
+ print(lengths, len(phandango_header), len(csv_header))
+ assert len(lengths) == 1
+ assert len(matrix[0]) == len(phandango_header) == len(csv_header)
+
if self.filter_rows:
if self.verbose:
print('Filtering rows', flush=True)
@@ -368,6 +401,11 @@ class Summary:
if len(matrix) == 0 or len(matrix[0]) == 0:
print('No columns left after filtering columns. Cannot continue', file=sys.stderr)
+ # sanity check same number of columns in headers and matrix
+ lengths = {len(x) for x in matrix}
+ assert len(lengths) == 1
+ assert len(matrix[0]) == len(phandango_header) == len(csv_header)
+
csv_file = self.outprefix + '.csv'
if self.verbose:
print('Writing csv file', csv_file, flush=True)
diff --git a/ariba/summary_cluster.py b/ariba/summary_cluster.py
index 927809a..7a53f55 100644
--- a/ariba/summary_cluster.py
+++ b/ariba/summary_cluster.py
@@ -187,6 +187,38 @@ class SummaryCluster:
@staticmethod
+ def _get_known_noncoding_het_snp(data_dict):
+ '''If ref is coding, return None. If the data dict has a known snp, and
+ samtools made a call, then return the string ref_name_change and the
+ % of reads supporting the variant type. If noncoding, but no
+ samtools call, then return None'''
+ if data_dict['gene'] == '1':
+ return None
+
+ if data_dict['known_var'] == '1' and data_dict['ref_ctg_effect'] == 'SNP' \
+ and data_dict['smtls_alt_nt'] != '.' and ';' not in data_dict['smtls_alt_nt']:
+ nucleotides = [data_dict['ctg_nt']] + data_dict['smtls_alt_nt'].split(',')
+ depths = data_dict['smtls_alt_depth'].split(',')
+
+ if len(nucleotides) != len(depths):
+ raise Error('Mismatch in number of inferred nucleotides from ctg_nt, smtls_alt_nt, smtls_alt_depth columns. Cannot continue\n' + str(data_dict))
+
+ try:
+ var_nucleotide = data_dict['known_var_change'][-1]
+ depths = [int(x) for x in depths]
+ nuc_to_depth = dict(zip(nucleotides, depths))
+ total_depth = sum(depths)
+ var_depth = nuc_to_depth.get(var_nucleotide, 0)
+ percent_depth = round(100 * var_depth / total_depth, 1)
+ except:
+ return None
+
+ return data_dict['known_var_change'], percent_depth
+ else:
+ return None
+
+
+ @staticmethod
def _get_nonsynonymous_var(data_dict):
'''if data_dict has a non synonymous variant, return string:
ref_name.change. Otherwise return None'''
@@ -256,3 +288,12 @@ class SummaryCluster:
variants = {self._get_nonsynonymous_var(d) for d in self.data}
variants.discard(None)
return variants
+
+
+ def known_noncoding_het_snps(self):
+ snps = {}
+ for d in self.data:
+ snp_tuple = self._get_known_noncoding_het_snp(d)
+ if snp_tuple is not None:
+ snps[snp_tuple[0]] = snp_tuple[1]
+ return snps
diff --git a/ariba/summary_sample.py b/ariba/summary_sample.py
index fcf0533..c5349f4 100644
--- a/ariba/summary_sample.py
+++ b/ariba/summary_sample.py
@@ -44,18 +44,22 @@ class SummarySample:
return {c: self.clusters[c].has_var_groups() for c in self.clusters}
- def _variant_column_names_tuples(self):
+ def _variant_column_names_tuples_and_het_snps(self):
variants = {}
+ het_snps = {}
for cluster_name, cluster in self.clusters.items():
cluster_vars = cluster.non_synon_variants()
+ cluster_noncoding_het_snps = cluster.known_noncoding_het_snps()
+
if len(cluster_vars):
variants[cluster_name] = cluster_vars
- return variants
+ het_snps[cluster_name] = cluster_noncoding_het_snps
+ return variants, het_snps
def run(self):
self.clusters = self._load_file(self.report_tsv, self.min_pc_id)
self.column_summary_data = self._column_summary_data()
- self.variant_column_names_tuples = self._variant_column_names_tuples()
+ self.variant_column_names_tuples, self.het_snps = self._variant_column_names_tuples_and_het_snps()
self.var_groups = self._var_groups()
diff --git a/ariba/tasks/summary.py b/ariba/tasks/summary.py
index 8162235..782c905 100644
--- a/ariba/tasks/summary.py
+++ b/ariba/tasks/summary.py
@@ -93,6 +93,7 @@ def run(options):
filter_rows=options.col_filter == 'y',
filter_columns=options.row_filter == 'y',
min_id=options.min_id,
+ show_known_het=options.het,
cluster_cols=options.cluster_cols,
variant_cols=options.var_cols,
verbose=options.verbose
diff --git a/ariba/tests/assembly_test.py b/ariba/tests/assembly_test.py
index db85fb0..7ac81b8 100644
--- a/ariba/tests/assembly_test.py
+++ b/ariba/tests/assembly_test.py
@@ -21,8 +21,8 @@ class TestAssembly(unittest.TestCase):
self.assertEqual(got, 42)
- def test_check_spades_log_file(self):
- '''test _check_spades_log_file'''
+ def _test_check_spades_log_file(self):
+ '''_test _check_spades_log_file'''
good_file = os.path.join(data_dir, 'assembly_test_check_spades_log_file.log.good')
bad_file = os.path.join(data_dir, 'assembly_test_check_spades_log_file.log.bad')
self.assertTrue(assembly.Assembly._check_spades_log_file(good_file))
@@ -47,7 +47,7 @@ class TestAssembly(unittest.TestCase):
def test_run_fermilite_fails(self):
'''test _run_fermilite when it fails'''
- reads = os.path.join(data_dir, 'assembly_run_fermilite_fails.reads.fq')
+ reads = os.path.join(data_dir, 'assembly_run_fermilite_fail.reads.fq')
tmp_fa = 'tmp.test_run_fermilite_fails.fa'
tmp_log = 'tmp.test_run_fermilite_fails.log'
expected_log = os.path.join(data_dir, 'assembly_run_fermilite_fails.expected.log')
diff --git a/ariba/tests/cluster_test.py b/ariba/tests/cluster_test.py
index 1d4d185..7b7de6a 100644
--- a/ariba/tests/cluster_test.py
+++ b/ariba/tests/cluster_test.py
@@ -160,10 +160,10 @@ class TestCluster(unittest.TestCase):
c.run()
expected = [
- 'noncoding1\t0\t0\t531\t72\tcluster_name\t120\t120\t95.87\tcluster_name.scaffold.1\t234\t15.4\t1\tSNP\tn\tA14T\t1\tA14T\tSNP\t13\t13\tA\t73\t73\tT\t19\t.\t19\tnoncoding1:0:0:A14T:.:ref has wild type, reads has variant so should report\tgeneric description of noncoding1',
- 'noncoding1\t0\t0\t531\t72\tcluster_name\t120\t120\t95.87\tcluster_name.scaffold.1\t234\t15.4\t0\t.\tn\t.\t0\tG61T\tSNP\t60\t60\tG\t120\t120\tT\t24\t.\t24\t.\tgeneric description of noncoding1',
- 'noncoding1\t0\t0\t531\t72\tcluster_name\t120\t120\t95.87\tcluster_name.scaffold.1\t234\t15.4\t0\t.\tn\t.\t0\t.82C\tINS\t81\t81\t.\t142\t142\tC\t23\t.\t23\t.\tgeneric description of noncoding1',
- 'noncoding1\t0\t0\t531\t72\tcluster_name\t120\t120\t95.87\tcluster_name.scaffold.1\t234\t15.4\t0\t.\tn\t.\t0\tT108.\tDEL\t107\t107\tT\t167\t167\t.\t17\t.\t17\t.\tgeneric description of noncoding1',
+ 'noncoding1\t0\t0\t531\t72\tcluster_name\t120\t120\t95.87\tcluster_name.scaffold.1\t234\t15.4\t1\tSNP\tn\tA14T\t1\tA14T\tSNP\t14\t14\tA\t74\t74\tT\t19\t.\t19\tnoncoding1:0:0:A14T:.:ref has wild type, reads has variant so should report\tgeneric description of noncoding1',
+ 'noncoding1\t0\t0\t531\t72\tcluster_name\t120\t120\t95.87\tcluster_name.scaffold.1\t234\t15.4\t0\t.\tn\t.\t0\tG61T\tSNP\t61\t61\tG\t121\t121\tT\t24\t.\t24\t.\tgeneric description of noncoding1',
+ 'noncoding1\t0\t0\t531\t72\tcluster_name\t120\t120\t95.87\tcluster_name.scaffold.1\t234\t15.4\t0\t.\tn\t.\t0\t.82C\tINS\t82\t82\t.\t143\t143\tC\t23\t.\t23\t.\tgeneric description of noncoding1',
+ 'noncoding1\t0\t0\t531\t72\tcluster_name\t120\t120\t95.87\tcluster_name.scaffold.1\t234\t15.4\t0\t.\tn\t.\t0\tT108.\tDEL\t108\t108\tT\t168\t168\t.\t17\t.\t17\t.\tgeneric description of noncoding1',
'noncoding1\t0\t0\t531\t72\tcluster_name\t120\t120\t95.87\tcluster_name.scaffold.1\t234\t15.4\t1\tSNP\tn\tA6G\t1\t.\t.\t6\t6\tG\t66\t66\tG\t19\t.\t19\tnoncoding1:0:0:A6G:.:variant in ref and reads so should report\tgeneric description of noncoding1',
'noncoding1\t0\t0\t531\t72\tcluster_name\t120\t120\t95.87\tcluster_name.scaffold.1\t234\t15.4\t1\tSNP\tn\tG9T\t0\t.\t.\t9\t9\tG\t69\t69\tG\t19\t.\t19\tnoncoding1:0:0:G9T:.:wild type in ref and reads\tgeneric description of noncoding1'
]
@@ -184,8 +184,8 @@ class TestCluster(unittest.TestCase):
c.run()
expected = [
- 'presence_absence1\t1\t0\t539\t64\tcluster_name\t96\t96\t97.92\tcluster_name.scaffold.1\t213\t15.0\t1\tSNP\tp\tA10V\t1\tA10V\tNONSYN\t28\t28\tC\t83\t83\tT\t22\t.\t22\tpresence_absence1:1:0:A10V:.:Ref has wild, reads have variant so report\tGeneric description of presence_absence1',
- 'presence_absence1\t1\t0\t539\t64\tcluster_name\t96\t96\t97.92\tcluster_name.scaffold.1\t213\t15.0\t0\t.\tp\t.\t0\t.\tSYN\t53\t53\tT\t108\t108\tC\t32\t.\t32\t.\tGeneric description of presence_absence1',
+ 'presence_absence1\t1\t0\t539\t64\tcluster_name\t96\t96\t97.92\tcluster_name.scaffold.1\t213\t15.0\t1\tSNP\tp\tA10V\t1\tA10V\tNONSYN\t29\t29\tC\t84\t84\tT\t22\t.\t22\tpresence_absence1:1:0:A10V:.:Ref has wild, reads have variant so report\tGeneric description of presence_absence1',
+ 'presence_absence1\t1\t0\t539\t64\tcluster_name\t96\t96\t97.92\tcluster_name.scaffold.1\t213\t15.0\t0\t.\tp\t.\t0\t.\tSYN\t54\t54\tT\t109\t109\tC\t32\t.\t32\t.\tGeneric description of presence_absence1',
'presence_absence1\t1\t0\t539\t64\tcluster_name\t96\t96\t97.92\tcluster_name.scaffold.1\t213\t15.0\t1\tSNP\tp\tR3S\t0\t.\t.\t7\t9\tC;G;C\t62\t64\tC;G;C\t18;17;17\t.;.;.\t18;17;17\tpresence_absence1:1:0:R3S:.:Ref and assembly have wild type\tGeneric description of presence_absence1',
@@ -264,3 +264,180 @@ class TestCluster(unittest.TestCase):
self.assertEqual(expected, c.report_lines)
shutil.rmtree(tmpdir)
+
+ def test_full_run_ok_samtools_snp_pres_abs_gene(self):
+ '''test complete run where samtools calls a snp in a presence/absence gene'''
+ fasta_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_pres_abs_gene.fa')
+ tsv_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_pres_abs_gene.metadata.tsv')
+ refdata = reference_data.ReferenceData([fasta_in], [tsv_in])
+ tmpdir = 'tmp.cluster_test_full_run_ok_samtools_snp_pres_abs_gene'
+ shutil.copytree(os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_pres_abs_gene'), tmpdir)
+ c = cluster.Cluster(tmpdir, 'cluster_name', refdata, spades_other_options='--only-assembler', total_reads=148, total_reads_bases=13320)
+ c.run()
+ expected = [
+ 'ref_gene\t1\t0\t155\t148\tcluster_name\t96\t96\t100.0\tcluster_name.scaffold.1\t335\t39.8\t0\tHET\t.\t.\t.\t.\t.\t.\t.\t.\t137\t137\tG\t63\tA\t32,31\t.\tGeneric description of ref_gene'
+ ]
+ self.assertEqual(expected, c.report_lines)
+ shutil.rmtree(tmpdir)
+
+
+ def test_full_run_ok_samtools_snp_var_only_gene(self):
+ '''test complete run where samtools calls a snp in a variant only gene'''
+ fasta_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_var_only_gene.fa')
+ tsv_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_var_only_gene.metadata.tsv')
+ refdata = reference_data.ReferenceData([fasta_in], [tsv_in])
+ tmpdir = 'tmp.cluster_test_full_run_ok_samtools_snp_var_only_gene'
+ shutil.copytree(os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_var_only_gene'), tmpdir)
+ c = cluster.Cluster(tmpdir, 'cluster_name', refdata, spades_other_options='--only-assembler', total_reads=148, total_reads_bases=13320)
+ c.run()
+ expected = [
+ 'ref_gene\t1\t1\t155\t148\tcluster_name\t96\t96\t100.0\tcluster_name.scaffold.1\t335\t39.8\t0\tHET\t.\t.\t.\t.\t.\t.\t.\t.\t137\t137\tG\t63\tA\t32,31\t.\tGeneric description of ref_gene'
+ ]
+ self.assertEqual(expected, c.report_lines)
+ shutil.rmtree(tmpdir)
+
+
+ def test_full_run_ok_samtools_snp_known_position_pres_abs_gene(self):
+ '''test complete run where samtools calls a snp at a known snp location in a presence/absence gene'''
+ fasta_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_gene.fa')
+ tsv_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_gene.metadata.tsv')
+ refdata = reference_data.ReferenceData([fasta_in], [tsv_in])
+ tmpdir = 'tmp.cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_gene'
+ shutil.copytree(os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_known_position_snp_pres_abs_gene'), tmpdir)
+ c = cluster.Cluster(tmpdir, 'cluster_name', refdata, spades_other_options='--only-assembler', total_reads=148, total_reads_bases=13320)
+ c.run()
+
+ # We shouldn't get an extra 'HET' line because we already know about the snp, so
+ # included in the report of the known snp
+ expected = [
+ 'ref_gene\t1\t0\t155\t148\tcluster_name\t96\t96\t100.0\tcluster_name.scaffold.1\t335\t39.8\t1\tSNP\tp\tM6I\t0\t.\t.\t16\t18\tA;T;G\t135\t137\tA;T;G\t65;64;63\t.;.;A\t65;64;32,31\tref_gene:1:0:M6I:.:Description of M6I snp\t.'
+ ]
+ self.assertEqual(expected, c.report_lines)
+ shutil.rmtree(tmpdir)
+
+
+ def test_full_run_ok_samtools_snp_known_position_var_only_gene_does_not_have_var(self):
+ '''test complete run where samtools calls a snp at a known snp location in a variant only gene, gene does not have variant'''
+ fasta_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_not_have_var.fa')
+ tsv_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_not_have_var.metadata.tsv')
+ refdata = reference_data.ReferenceData([fasta_in], [tsv_in])
+ tmpdir = 'tmp.cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_not_have_var'
+ shutil.copytree(os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_known_position_snp_var_only_gene_does_not_have_var'), tmpdir)
+ c = cluster.Cluster(tmpdir, 'cluster_name', refdata, spades_other_options='--only-assembler', total_reads=148, total_reads_bases=13320)
+ c.run()
+
+ # We shouldn't get an extra 'HET' line because we already know about the snp, so
+ # included in the report of the known snp
+ expected = [
+ 'ref_gene\t1\t1\t155\t148\tcluster_name\t96\t96\t100.0\tcluster_name.scaffold.1\t335\t39.8\t1\tSNP\tp\tM6I\t0\t.\t.\t16\t18\tA;T;G\t135\t137\tA;T;G\t65;64;63\t.;.;A\t65;64;32,31\tref_gene:1:1:M6I:.:Description of M6I snp\t.'
+ ]
+ self.assertEqual(expected, c.report_lines)
+ shutil.rmtree(tmpdir)
+
+
+ def test_full_run_ok_samtools_snp_known_position_var_only_gene_does_have_var(self):
+ '''test complete run where samtools calls a snp at a known snp location in a variant only gene, gene does have variant'''
+ fasta_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_have_var.fa')
+ tsv_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_have_var.metadata.tsv')
+ refdata = reference_data.ReferenceData([fasta_in], [tsv_in])
+ tmpdir = 'tmp.cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_have_var'
+ shutil.copytree(os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_known_position_snp_var_only_gene_does_have_var'), tmpdir)
+ c = cluster.Cluster(tmpdir, 'cluster_name', refdata, spades_other_options='--only-assembler', total_reads=148, total_reads_bases=13320)
+ c.run()
+
+ # We shouldn't get an extra 'HET' line because we already know about the snp, so
+ # included in the report of the known snp
+ expected = [
+ 'ref_gene\t1\t1\t155\t148\tcluster_name\t96\t96\t100.0\tcluster_name.scaffold.1\t335\t39.8\t1\tSNP\tp\tI6M\t1\t.\t.\t16\t18\tA;T;G\t135\t137\tA;T;G\t65;64;63\t.;.;A\t65;64;32,31\tref_gene:1:1:I6M:.:Description of I6M snp\t.'
+ ]
+ self.assertEqual(expected, c.report_lines)
+ shutil.rmtree(tmpdir)
+
+
+ def test_full_run_ok_samtools_snp_pres_abs_noncoding(self):
+ '''test complete run where samtools calls a snp in a presence/absence noncoding sequence'''
+ fasta_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_pres_abs_noncoding.fa')
+ tsv_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_pres_abs_noncoding.metadata.tsv')
+ refdata = reference_data.ReferenceData([fasta_in], [tsv_in])
+ tmpdir = 'tmp.cluster_test_full_run_ok_samtools_snp_pres_abs_noncoding'
+ shutil.copytree(os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_pres_abs_noncoding'), tmpdir)
+ c = cluster.Cluster(tmpdir, 'cluster_name', refdata, spades_other_options='--only-assembler', total_reads=148, total_reads_bases=13320)
+ c.run()
+ expected = [
+ 'ref_seq\t0\t0\t147\t148\tcluster_name\t96\t96\t100.0\tcluster_name.scaffold.1\t335\t39.8\t0\tHET\t.\t.\t.\t.\t.\t.\t.\t.\t137\t137\tG\t63\tA\t32,31\t.\tGeneric description of ref_seq'
+ ]
+ self.assertEqual(expected, c.report_lines)
+ shutil.rmtree(tmpdir)
+
+
+ def test_full_run_ok_samtools_snp_var_only_noncoding(self):
+ '''test complete run where samtools calls a snp in a presence/absence noncoding sequence'''
+ fasta_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_var_only_noncoding.fa')
+ tsv_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_var_only_noncoding.metadata.tsv')
+ refdata = reference_data.ReferenceData([fasta_in], [tsv_in])
+ tmpdir = 'tmp.cluster_test_full_run_ok_samtools_snp_var_only_noncoding'
+ shutil.copytree(os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_var_only_noncoding'), tmpdir)
+ c = cluster.Cluster(tmpdir, 'cluster_name', refdata, spades_other_options='--only-assembler', total_reads=148, total_reads_bases=13320)
+ c.run()
+ expected = [
+ 'ref_seq\t0\t1\t147\t148\tcluster_name\t96\t96\t100.0\tcluster_name.scaffold.1\t335\t39.8\t0\tHET\t.\t.\t.\t.\t.\t.\t.\t.\t137\t137\tG\t63\tA\t32,31\t.\tGeneric description of ref_seq'
+ ]
+ self.assertEqual(expected, c.report_lines)
+ shutil.rmtree(tmpdir)
+
+
+ def test_full_run_ok_samtools_snp_known_position_pres_abs_noncoding(self):
+ '''test complete run where samtools calls a snp at a known snp location in a presence/absence noncoding'''
+ fasta_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_noncoding.fa')
+ tsv_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_noncoding.metadata.tsv')
+ refdata = reference_data.ReferenceData([fasta_in], [tsv_in])
+ tmpdir = 'tmp.cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_noncoding'
+ shutil.copytree(os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_known_position_snp_pres_abs_noncoding'), tmpdir)
+ c = cluster.Cluster(tmpdir, 'cluster_name', refdata, spades_other_options='--only-assembler', total_reads=148, total_reads_bases=13320)
+ c.run()
+
+ # We shouldn't get an extra 'HET' line because we already know about the snp, so
+ # included in the report of the known snp
+ expected = [
+ 'ref_seq\t0\t0\t147\t148\tcluster_name\t96\t96\t100.0\tcluster_name.scaffold.1\t335\t39.8\t1\tSNP\tn\tG18A\t0\t.\t.\t18\t18\tG\t137\t137\tG\t63\tA\t32,31\tref_seq:0:0:G18A:.:Description of G18A snp\t.'
+ ]
+ self.assertEqual(expected, c.report_lines)
+ shutil.rmtree(tmpdir)
+
+
+ def test_full_run_ok_samtools_snp_known_position_var_only_noncoding_does_not_have_var(self):
+ '''test complete run where samtools calls a snp at a known snp location in a presence/absence noncoding and sample does not have the var'''
+ fasta_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding_does_not_have_var.fa')
+ tsv_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding_does_not_have_var.metadata.tsv')
+ refdata = reference_data.ReferenceData([fasta_in], [tsv_in])
+ tmpdir = 'tmp.cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding'
+ shutil.copytree(os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_known_position_snp_var_only_noncoding_does_not_have_var'), tmpdir)
+ c = cluster.Cluster(tmpdir, 'cluster_name', refdata, spades_other_options='--only-assembler', total_reads=148, total_reads_bases=13320)
+ c.run()
+
+ # We shouldn't get an extra 'HET' line because we already know about the snp, so
+ # included in the report of the known snp
+ expected = [
+ 'ref_seq\t0\t1\t147\t148\tcluster_name\t96\t96\t100.0\tcluster_name.scaffold.1\t335\t39.8\t1\tSNP\tn\tG18A\t0\t.\t.\t18\t18\tG\t137\t137\tG\t63\tA\t32,31\tref_seq:0:1:G18A:.:Description of G18A snp\t.'
+ ]
+ self.assertEqual(expected, c.report_lines)
+ shutil.rmtree(tmpdir)
+
+
+ def test_full_run_ok_samtools_snp_known_position_var_only_noncoding_does_have_var(self):
+ '''test complete run where samtools calls a snp at a known snp location in a presence/absence noncoding and sample has the var'''
+ fasta_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding_does_have_var.fa')
+ tsv_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding_does_have_var.metadata.tsv')
+ refdata = reference_data.ReferenceData([fasta_in], [tsv_in])
+ tmpdir = 'tmp.cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding'
+ shutil.copytree(os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_known_position_snp_var_only_noncoding_does_have_var'), tmpdir)
+ c = cluster.Cluster(tmpdir, 'cluster_name', refdata, spades_other_options='--only-assembler', total_reads=148, total_reads_bases=13320)
+ c.run()
+
+ # We shouldn't get an extra 'HET' line because we already know about the snp, so
+ # included in the report of the known snp
+ expected = [
+ 'ref_seq\t0\t1\t147\t148\tcluster_name\t96\t96\t100.0\tcluster_name.scaffold.1\t335\t39.8\t1\tSNP\tn\tA18G\t1\t.\t.\t18\t18\tG\t137\t137\tG\t63\tA\t32,31\tref_seq:0:1:A18G:.:Description of A18G snp\t.'
+ ]
+ self.assertEqual(expected, c.report_lines)
+ shutil.rmtree(tmpdir)
diff --git a/ariba/tests/clusters_test.py b/ariba/tests/clusters_test.py
index 29bde88..38d1ae0 100644
--- a/ariba/tests/clusters_test.py
+++ b/ariba/tests/clusters_test.py
@@ -204,6 +204,33 @@ class TestClusters(unittest.TestCase):
os.unlink(tmp_tsv)
+ def test_write_catted_assemblies_fasta(self):
+ '''test _write_catted_assemblies_fasta'''
+ seq1 = pyfastaq.sequences.Fasta('seq1', 'ACGT')
+ seq2 = pyfastaq.sequences.Fasta('seq2', 'TTTT')
+ seq3 = pyfastaq.sequences.Fasta('seq3', 'AAAA')
+ class FakeAssembly:
+ def __init__(self, seqs):
+ if seqs is not None:
+ self.sequences = {x.id: x for x in seqs}
+
+ class FakeCluster:
+ def __init__(self, seqs):
+ self.assembly = FakeAssembly(seqs)
+
+ self.clusters.clusters = {
+ 'cluster1': FakeCluster([seq1, seq2]),
+ 'cluster2': FakeCluster([seq3]),
+ 'cluster3': FakeCluster(None),
+ }
+
+ tmp_file = 'tmp.test_write_catted_assemblies_fasta.fa'
+ self.clusters._write_catted_assemblies_fasta(tmp_file)
+ expected = os.path.join(data_dir, 'clusters_test_write_catted_assemblies_fasta.expected.out.fa')
+ self.assertTrue(filecmp.cmp(expected, tmp_file, shallow=False))
+ os.unlink(tmp_file)
+
+
def test_write_catted_assembled_seqs_fasta(self):
'''test _write_catted_assembled_seqs_fasta'''
seq1 = pyfastaq.sequences.Fasta('seq1', 'ACGT')
diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_pres_abs_gene/reads_1.fq b/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_pres_abs_gene/reads_1.fq
new file mode 100644
index 0000000..1d056e7
--- /dev/null
+++ b/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_pres_abs_gene/reads_1.fq
@@ -0,0 +1,296 @@
+ at ref_gene:1:147:247/1
+AGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACGGCTGATACCCATAATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:2:89:186/1
+AATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:3:40:139/1
+CCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:4:113:213/1
+CGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:5:111:210/1
+AGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:6:29:129/1
+AGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:7:112:212/1
+GCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:8:45:145/1
+ATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:9:121:219/1
+ATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:10:82:182/1
+ACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:11:96:196/1
+AATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:12:125:225/1
+ATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:13:114:215/1
+GTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:14:100:199/1
+AGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:15:90:188/1
+ATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:16:54:154/1
+ATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:17:110:210/1
+GAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:18:63:162/1
+TCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:19:83:183/1
+CAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:20:94:194/1
+GGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:21:65:164/1
+CTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:22:27:126/1
+CGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:23:39:141/1
+TCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:24:107:208/1
+CAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:25:72:170/1
+GCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:26:10:111/1
+TCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:27:55:155/1
+TTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:28:83:184/1
+CAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:29:11:110/1
+CGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:30:76:177/1
+CAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:31:77:176/1
+AGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:32:96:195/1
+AATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:33:19:118/1
+CAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:34:40:141/1
+CCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:35:68:167/1
+GTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:36:70:170/1
+TTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:37:94:194.dup.2/1
+GGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:38:27:127/1
+CGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:39:102:201/1
+TACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:40:131:231/1
+AAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:41:13:113/1
+GCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:42:82:182/1
+ACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:43:84:183/1
+AAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:44:118:218/1
+CCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:45:44:144/1
+CATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:46:92:189/1
+ATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:47:132:233/1
+AGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:48:45:143/1
+ATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:49:26:125/1
+TCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:50:87:185/1
+CTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:51:107:205/1
+CAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:52:47:147/1
+TCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:53:3:103/1
+CAGGACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:54:127:228/1
+CGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:55:69:169/1
+TTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:56:8:107/1
+CGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:57:51:149/1
+GTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:58:141:243/1
+CCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACGGCTGATACCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:59:3:102/1
+CAGGACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:60:17:116/1
+GGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:61:21:120/1
+GGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:62:20:118/1
+AGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:63:4:105/1
+AGGACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:64:7:107/1
+ACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:65:127:227/1
+CGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:66:98:197/1
+TGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:67:116:216/1
+AGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:68:134:235/1
+CGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACGGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:69:65:165/1
+CTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:70:81:179/1
+GACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:71:41:140/1
+CTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:72:2:100/1
+TCAGGACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:73:83:184/1
+CAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:74:66:164/1
+TTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_pres_abs_gene/reads_2.fq b/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_pres_abs_gene/reads_2.fq
new file mode 100644
index 0000000..31885ad
--- /dev/null
+++ b/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_pres_abs_gene/reads_2.fq
@@ -0,0 +1,296 @@
+ at ref_gene:1:147:247/2
+TGTTTGCGTACATACCGGGTCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:2:89:186/2
+TGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:3:40:139/2
+GTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:4:113:213/2
+TCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:5:111:210/2
+TGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:6:29:129/2
+TGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:7:112:212/2
+CATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:8:45:145/2
+TTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:9:121:219/2
+ACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:10:82:182/2
+TACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:11:96:196/2
+TTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:12:125:225/2
+GAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:13:114:215/2
+CCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:14:100:199/2
+TAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:15:90:188/2
+TCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:16:54:154/2
+CGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:17:110:210/2
+TGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:18:63:162/2
+TATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:19:83:183/2
+ATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:20:94:194/2
+CTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:21:65:164/2
+GATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:22:27:126/2
+TATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCGCGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:23:39:141/2
+GGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:24:107:208/2
+GCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:25:72:170/2
+GTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:26:10:111/2
+CACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCGCGATCCATCGGCTACGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:27:55:155/2
+ACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:28:83:184/2
+TATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:29:11:110/2
+ACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCGCGATCCATCGGCTACGCTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:30:76:177/2
+CGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:31:77:176/2
+GGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:32:96:195/2
+TCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:33:19:118/2
+GCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCGCGATCCATCGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:34:40:141/2
+GGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:35:68:167/2
+GGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:36:70:170/2
+GTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:37:94:194.dup.2/2
+CTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:38:27:127/2
+TTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:39:102:201/2
+AATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:40:131:231/2
+GGGTCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:41:13:113/2
+CCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:42:82:182/2
+TACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:43:84:183/2
+ATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:44:118:218/2
+CATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:45:44:144/2
+TATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:46:92:189/2
+CTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:47:132:233/2
+CCGGGTCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:48:45:143/2
+ATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:49:26:125/2
+ATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:50:87:185/2
+GTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:51:107:205/2
+TAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:52:47:147/2
+AATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:53:3:103/2
+AATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTGGCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:54:127:228/2
+TCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:55:69:169/2
+TAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:56:8:107/2
+CGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:57:51:149/2
+GAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:58:141:243/2
+TGCGTACATACCGGGTCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:59:3:102/2
+ATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTGGCGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:60:17:116/2
+TTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:61:21:120/2
+ATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:62:20:118/2
+GCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:63:4:105/2
+CTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTGGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:64:7:107/2
+CGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:65:127:227/2
+CTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:66:98:197/2
+GTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:67:116:216/2
+TCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:68:134:235/2
+TACCGGGTCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:69:65:165/2
+AGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:70:81:179/2
+TGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:71:41:140/2
+GGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:72:2:100/2
+GCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTGGCGTACT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:73:83:184/2
+TATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:74:66:164/2
+GATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_pres_abs_gene/references.fa b/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_pres_abs_gene/references.fa
new file mode 100644
index 0000000..c42d06b
--- /dev/null
+++ b/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_pres_abs_gene/references.fa
@@ -0,0 +1,3 @@
+>ref_gene
+ATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCAT
+ATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAA
diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_pres_abs_noncoding/reads_1.fq b/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_pres_abs_noncoding/reads_1.fq
new file mode 100644
index 0000000..1d056e7
--- /dev/null
+++ b/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_pres_abs_noncoding/reads_1.fq
@@ -0,0 +1,296 @@
+ at ref_gene:1:147:247/1
+AGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACGGCTGATACCCATAATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:2:89:186/1
+AATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:3:40:139/1
+CCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:4:113:213/1
+CGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:5:111:210/1
+AGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:6:29:129/1
+AGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:7:112:212/1
+GCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:8:45:145/1
+ATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:9:121:219/1
+ATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:10:82:182/1
+ACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:11:96:196/1
+AATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:12:125:225/1
+ATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:13:114:215/1
+GTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:14:100:199/1
+AGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:15:90:188/1
+ATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:16:54:154/1
+ATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:17:110:210/1
+GAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:18:63:162/1
+TCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:19:83:183/1
+CAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:20:94:194/1
+GGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:21:65:164/1
+CTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:22:27:126/1
+CGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:23:39:141/1
+TCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:24:107:208/1
+CAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:25:72:170/1
+GCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:26:10:111/1
+TCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:27:55:155/1
+TTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:28:83:184/1
+CAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:29:11:110/1
+CGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:30:76:177/1
+CAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:31:77:176/1
+AGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:32:96:195/1
+AATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:33:19:118/1
+CAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:34:40:141/1
+CCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:35:68:167/1
+GTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:36:70:170/1
+TTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:37:94:194.dup.2/1
+GGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:38:27:127/1
+CGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:39:102:201/1
+TACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:40:131:231/1
+AAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:41:13:113/1
+GCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:42:82:182/1
+ACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:43:84:183/1
+AAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:44:118:218/1
+CCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:45:44:144/1
+CATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:46:92:189/1
+ATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:47:132:233/1
+AGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:48:45:143/1
+ATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:49:26:125/1
+TCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:50:87:185/1
+CTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:51:107:205/1
+CAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:52:47:147/1
+TCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:53:3:103/1
+CAGGACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:54:127:228/1
+CGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:55:69:169/1
+TTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:56:8:107/1
+CGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:57:51:149/1
+GTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:58:141:243/1
+CCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACGGCTGATACCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:59:3:102/1
+CAGGACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:60:17:116/1
+GGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:61:21:120/1
+GGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:62:20:118/1
+AGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:63:4:105/1
+AGGACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:64:7:107/1
+ACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:65:127:227/1
+CGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:66:98:197/1
+TGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:67:116:216/1
+AGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:68:134:235/1
+CGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACGGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:69:65:165/1
+CTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:70:81:179/1
+GACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:71:41:140/1
+CTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:72:2:100/1
+TCAGGACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:73:83:184/1
+CAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:74:66:164/1
+TTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_pres_abs_noncoding/reads_2.fq b/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_pres_abs_noncoding/reads_2.fq
new file mode 100644
index 0000000..31885ad
--- /dev/null
+++ b/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_pres_abs_noncoding/reads_2.fq
@@ -0,0 +1,296 @@
+ at ref_gene:1:147:247/2
+TGTTTGCGTACATACCGGGTCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:2:89:186/2
+TGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:3:40:139/2
+GTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:4:113:213/2
+TCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:5:111:210/2
+TGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:6:29:129/2
+TGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:7:112:212/2
+CATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:8:45:145/2
+TTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:9:121:219/2
+ACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:10:82:182/2
+TACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:11:96:196/2
+TTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:12:125:225/2
+GAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:13:114:215/2
+CCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:14:100:199/2
+TAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:15:90:188/2
+TCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:16:54:154/2
+CGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:17:110:210/2
+TGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:18:63:162/2
+TATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:19:83:183/2
+ATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:20:94:194/2
+CTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:21:65:164/2
+GATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:22:27:126/2
+TATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCGCGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:23:39:141/2
+GGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:24:107:208/2
+GCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:25:72:170/2
+GTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:26:10:111/2
+CACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCGCGATCCATCGGCTACGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:27:55:155/2
+ACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:28:83:184/2
+TATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:29:11:110/2
+ACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCGCGATCCATCGGCTACGCTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:30:76:177/2
+CGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:31:77:176/2
+GGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:32:96:195/2
+TCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:33:19:118/2
+GCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCGCGATCCATCGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:34:40:141/2
+GGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:35:68:167/2
+GGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:36:70:170/2
+GTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:37:94:194.dup.2/2
+CTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:38:27:127/2
+TTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:39:102:201/2
+AATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:40:131:231/2
+GGGTCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:41:13:113/2
+CCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:42:82:182/2
+TACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:43:84:183/2
+ATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:44:118:218/2
+CATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:45:44:144/2
+TATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:46:92:189/2
+CTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:47:132:233/2
+CCGGGTCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:48:45:143/2
+ATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:49:26:125/2
+ATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:50:87:185/2
+GTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:51:107:205/2
+TAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:52:47:147/2
+AATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:53:3:103/2
+AATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTGGCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:54:127:228/2
+TCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:55:69:169/2
+TAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:56:8:107/2
+CGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:57:51:149/2
+GAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:58:141:243/2
+TGCGTACATACCGGGTCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:59:3:102/2
+ATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTGGCGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:60:17:116/2
+TTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:61:21:120/2
+ATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:62:20:118/2
+GCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:63:4:105/2
+CTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTGGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:64:7:107/2
+CGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:65:127:227/2
+CTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:66:98:197/2
+GTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:67:116:216/2
+TCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:68:134:235/2
+TACCGGGTCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:69:65:165/2
+AGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:70:81:179/2
+TGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:71:41:140/2
+GGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:72:2:100/2
+GCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTGGCGTACT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:73:83:184/2
+TATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:74:66:164/2
+GATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_pres_abs_noncoding/references.fa b/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_pres_abs_noncoding/references.fa
new file mode 100644
index 0000000..a23e635
--- /dev/null
+++ b/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_pres_abs_noncoding/references.fa
@@ -0,0 +1,3 @@
+>ref_seq
+ATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCAT
+ATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAA
diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_gene_does_have_var/reads_1.fq b/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_gene_does_have_var/reads_1.fq
new file mode 100644
index 0000000..1d056e7
--- /dev/null
+++ b/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_gene_does_have_var/reads_1.fq
@@ -0,0 +1,296 @@
+ at ref_gene:1:147:247/1
+AGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACGGCTGATACCCATAATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:2:89:186/1
+AATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:3:40:139/1
+CCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:4:113:213/1
+CGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:5:111:210/1
+AGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:6:29:129/1
+AGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:7:112:212/1
+GCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:8:45:145/1
+ATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:9:121:219/1
+ATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:10:82:182/1
+ACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:11:96:196/1
+AATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:12:125:225/1
+ATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:13:114:215/1
+GTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:14:100:199/1
+AGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:15:90:188/1
+ATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:16:54:154/1
+ATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:17:110:210/1
+GAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:18:63:162/1
+TCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:19:83:183/1
+CAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:20:94:194/1
+GGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:21:65:164/1
+CTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:22:27:126/1
+CGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:23:39:141/1
+TCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:24:107:208/1
+CAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:25:72:170/1
+GCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:26:10:111/1
+TCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:27:55:155/1
+TTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:28:83:184/1
+CAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:29:11:110/1
+CGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:30:76:177/1
+CAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:31:77:176/1
+AGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:32:96:195/1
+AATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:33:19:118/1
+CAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:34:40:141/1
+CCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:35:68:167/1
+GTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:36:70:170/1
+TTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:37:94:194.dup.2/1
+GGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:38:27:127/1
+CGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:39:102:201/1
+TACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:40:131:231/1
+AAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:41:13:113/1
+GCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:42:82:182/1
+ACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:43:84:183/1
+AAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:44:118:218/1
+CCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:45:44:144/1
+CATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:46:92:189/1
+ATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:47:132:233/1
+AGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:48:45:143/1
+ATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:49:26:125/1
+TCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:50:87:185/1
+CTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:51:107:205/1
+CAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:52:47:147/1
+TCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:53:3:103/1
+CAGGACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:54:127:228/1
+CGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:55:69:169/1
+TTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:56:8:107/1
+CGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:57:51:149/1
+GTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:58:141:243/1
+CCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACGGCTGATACCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:59:3:102/1
+CAGGACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:60:17:116/1
+GGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:61:21:120/1
+GGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:62:20:118/1
+AGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:63:4:105/1
+AGGACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:64:7:107/1
+ACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:65:127:227/1
+CGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:66:98:197/1
+TGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:67:116:216/1
+AGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:68:134:235/1
+CGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACGGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:69:65:165/1
+CTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:70:81:179/1
+GACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:71:41:140/1
+CTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:72:2:100/1
+TCAGGACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:73:83:184/1
+CAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:74:66:164/1
+TTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_gene_does_have_var/reads_2.fq b/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_gene_does_have_var/reads_2.fq
new file mode 100644
index 0000000..31885ad
--- /dev/null
+++ b/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_gene_does_have_var/reads_2.fq
@@ -0,0 +1,296 @@
+ at ref_gene:1:147:247/2
+TGTTTGCGTACATACCGGGTCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:2:89:186/2
+TGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:3:40:139/2
+GTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:4:113:213/2
+TCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:5:111:210/2
+TGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:6:29:129/2
+TGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:7:112:212/2
+CATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:8:45:145/2
+TTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:9:121:219/2
+ACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:10:82:182/2
+TACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:11:96:196/2
+TTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:12:125:225/2
+GAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:13:114:215/2
+CCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:14:100:199/2
+TAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:15:90:188/2
+TCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:16:54:154/2
+CGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:17:110:210/2
+TGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:18:63:162/2
+TATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:19:83:183/2
+ATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:20:94:194/2
+CTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:21:65:164/2
+GATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:22:27:126/2
+TATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCGCGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:23:39:141/2
+GGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:24:107:208/2
+GCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:25:72:170/2
+GTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:26:10:111/2
+CACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCGCGATCCATCGGCTACGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:27:55:155/2
+ACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:28:83:184/2
+TATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:29:11:110/2
+ACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCGCGATCCATCGGCTACGCTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:30:76:177/2
+CGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:31:77:176/2
+GGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:32:96:195/2
+TCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:33:19:118/2
+GCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCGCGATCCATCGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:34:40:141/2
+GGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:35:68:167/2
+GGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:36:70:170/2
+GTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:37:94:194.dup.2/2
+CTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:38:27:127/2
+TTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:39:102:201/2
+AATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:40:131:231/2
+GGGTCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:41:13:113/2
+CCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:42:82:182/2
+TACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:43:84:183/2
+ATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:44:118:218/2
+CATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:45:44:144/2
+TATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:46:92:189/2
+CTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:47:132:233/2
+CCGGGTCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:48:45:143/2
+ATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:49:26:125/2
+ATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:50:87:185/2
+GTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:51:107:205/2
+TAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:52:47:147/2
+AATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:53:3:103/2
+AATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTGGCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:54:127:228/2
+TCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:55:69:169/2
+TAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:56:8:107/2
+CGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:57:51:149/2
+GAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:58:141:243/2
+TGCGTACATACCGGGTCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:59:3:102/2
+ATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTGGCGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:60:17:116/2
+TTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:61:21:120/2
+ATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:62:20:118/2
+GCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:63:4:105/2
+CTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTGGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:64:7:107/2
+CGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:65:127:227/2
+CTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:66:98:197/2
+GTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:67:116:216/2
+TCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:68:134:235/2
+TACCGGGTCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:69:65:165/2
+AGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:70:81:179/2
+TGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:71:41:140/2
+GGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:72:2:100/2
+GCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTGGCGTACT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:73:83:184/2
+TATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:74:66:164/2
+GATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_gene_does_have_var/references.fa b/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_gene_does_have_var/references.fa
new file mode 100644
index 0000000..c42d06b
--- /dev/null
+++ b/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_gene_does_have_var/references.fa
@@ -0,0 +1,3 @@
+>ref_gene
+ATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCAT
+ATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAA
diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_gene_does_not_have_var/reads_1.fq b/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_gene_does_not_have_var/reads_1.fq
new file mode 100644
index 0000000..1d056e7
--- /dev/null
+++ b/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_gene_does_not_have_var/reads_1.fq
@@ -0,0 +1,296 @@
+ at ref_gene:1:147:247/1
+AGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACGGCTGATACCCATAATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:2:89:186/1
+AATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:3:40:139/1
+CCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:4:113:213/1
+CGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:5:111:210/1
+AGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:6:29:129/1
+AGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:7:112:212/1
+GCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:8:45:145/1
+ATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:9:121:219/1
+ATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:10:82:182/1
+ACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:11:96:196/1
+AATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:12:125:225/1
+ATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:13:114:215/1
+GTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:14:100:199/1
+AGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:15:90:188/1
+ATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:16:54:154/1
+ATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:17:110:210/1
+GAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:18:63:162/1
+TCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:19:83:183/1
+CAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:20:94:194/1
+GGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:21:65:164/1
+CTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:22:27:126/1
+CGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:23:39:141/1
+TCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:24:107:208/1
+CAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:25:72:170/1
+GCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:26:10:111/1
+TCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:27:55:155/1
+TTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:28:83:184/1
+CAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:29:11:110/1
+CGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:30:76:177/1
+CAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:31:77:176/1
+AGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:32:96:195/1
+AATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:33:19:118/1
+CAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:34:40:141/1
+CCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:35:68:167/1
+GTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:36:70:170/1
+TTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:37:94:194.dup.2/1
+GGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:38:27:127/1
+CGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:39:102:201/1
+TACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:40:131:231/1
+AAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:41:13:113/1
+GCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:42:82:182/1
+ACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:43:84:183/1
+AAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:44:118:218/1
+CCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:45:44:144/1
+CATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:46:92:189/1
+ATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:47:132:233/1
+AGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:48:45:143/1
+ATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:49:26:125/1
+TCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:50:87:185/1
+CTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:51:107:205/1
+CAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:52:47:147/1
+TCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:53:3:103/1
+CAGGACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:54:127:228/1
+CGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:55:69:169/1
+TTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:56:8:107/1
+CGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:57:51:149/1
+GTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:58:141:243/1
+CCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACGGCTGATACCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:59:3:102/1
+CAGGACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:60:17:116/1
+GGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:61:21:120/1
+GGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:62:20:118/1
+AGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:63:4:105/1
+AGGACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:64:7:107/1
+ACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:65:127:227/1
+CGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:66:98:197/1
+TGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:67:116:216/1
+AGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:68:134:235/1
+CGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACGGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:69:65:165/1
+CTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:70:81:179/1
+GACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:71:41:140/1
+CTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:72:2:100/1
+TCAGGACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:73:83:184/1
+CAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:74:66:164/1
+TTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_gene_does_not_have_var/reads_2.fq b/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_gene_does_not_have_var/reads_2.fq
new file mode 100644
index 0000000..31885ad
--- /dev/null
+++ b/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_gene_does_not_have_var/reads_2.fq
@@ -0,0 +1,296 @@
+ at ref_gene:1:147:247/2
+TGTTTGCGTACATACCGGGTCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:2:89:186/2
+TGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:3:40:139/2
+GTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:4:113:213/2
+TCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:5:111:210/2
+TGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:6:29:129/2
+TGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:7:112:212/2
+CATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:8:45:145/2
+TTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:9:121:219/2
+ACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:10:82:182/2
+TACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:11:96:196/2
+TTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:12:125:225/2
+GAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:13:114:215/2
+CCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:14:100:199/2
+TAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:15:90:188/2
+TCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:16:54:154/2
+CGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:17:110:210/2
+TGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:18:63:162/2
+TATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:19:83:183/2
+ATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:20:94:194/2
+CTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:21:65:164/2
+GATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:22:27:126/2
+TATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCGCGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:23:39:141/2
+GGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:24:107:208/2
+GCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:25:72:170/2
+GTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:26:10:111/2
+CACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCGCGATCCATCGGCTACGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:27:55:155/2
+ACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:28:83:184/2
+TATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:29:11:110/2
+ACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCGCGATCCATCGGCTACGCTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:30:76:177/2
+CGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:31:77:176/2
+GGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:32:96:195/2
+TCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:33:19:118/2
+GCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCGCGATCCATCGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:34:40:141/2
+GGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:35:68:167/2
+GGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:36:70:170/2
+GTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:37:94:194.dup.2/2
+CTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:38:27:127/2
+TTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:39:102:201/2
+AATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:40:131:231/2
+GGGTCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:41:13:113/2
+CCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:42:82:182/2
+TACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:43:84:183/2
+ATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:44:118:218/2
+CATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:45:44:144/2
+TATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:46:92:189/2
+CTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:47:132:233/2
+CCGGGTCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:48:45:143/2
+ATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:49:26:125/2
+ATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:50:87:185/2
+GTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:51:107:205/2
+TAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:52:47:147/2
+AATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:53:3:103/2
+AATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTGGCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:54:127:228/2
+TCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:55:69:169/2
+TAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:56:8:107/2
+CGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:57:51:149/2
+GAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:58:141:243/2
+TGCGTACATACCGGGTCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:59:3:102/2
+ATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTGGCGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:60:17:116/2
+TTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:61:21:120/2
+ATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:62:20:118/2
+GCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:63:4:105/2
+CTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTGGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:64:7:107/2
+CGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:65:127:227/2
+CTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:66:98:197/2
+GTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:67:116:216/2
+TCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:68:134:235/2
+TACCGGGTCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:69:65:165/2
+AGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:70:81:179/2
+TGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:71:41:140/2
+GGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:72:2:100/2
+GCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTGGCGTACT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:73:83:184/2
+TATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:74:66:164/2
+GATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_gene_does_not_have_var/references.fa b/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_gene_does_not_have_var/references.fa
new file mode 100644
index 0000000..c42d06b
--- /dev/null
+++ b/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_gene_does_not_have_var/references.fa
@@ -0,0 +1,3 @@
+>ref_gene
+ATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCAT
+ATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAA
diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_noncoding_does_have_var/reads_1.fq b/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_noncoding_does_have_var/reads_1.fq
new file mode 100644
index 0000000..1d056e7
--- /dev/null
+++ b/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_noncoding_does_have_var/reads_1.fq
@@ -0,0 +1,296 @@
+ at ref_gene:1:147:247/1
+AGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACGGCTGATACCCATAATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:2:89:186/1
+AATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:3:40:139/1
+CCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:4:113:213/1
+CGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:5:111:210/1
+AGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:6:29:129/1
+AGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:7:112:212/1
+GCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:8:45:145/1
+ATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:9:121:219/1
+ATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:10:82:182/1
+ACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:11:96:196/1
+AATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:12:125:225/1
+ATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:13:114:215/1
+GTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:14:100:199/1
+AGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:15:90:188/1
+ATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:16:54:154/1
+ATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:17:110:210/1
+GAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:18:63:162/1
+TCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:19:83:183/1
+CAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:20:94:194/1
+GGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:21:65:164/1
+CTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:22:27:126/1
+CGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:23:39:141/1
+TCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:24:107:208/1
+CAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:25:72:170/1
+GCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:26:10:111/1
+TCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:27:55:155/1
+TTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:28:83:184/1
+CAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:29:11:110/1
+CGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:30:76:177/1
+CAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:31:77:176/1
+AGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:32:96:195/1
+AATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:33:19:118/1
+CAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:34:40:141/1
+CCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:35:68:167/1
+GTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:36:70:170/1
+TTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:37:94:194.dup.2/1
+GGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:38:27:127/1
+CGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:39:102:201/1
+TACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:40:131:231/1
+AAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:41:13:113/1
+GCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:42:82:182/1
+ACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:43:84:183/1
+AAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:44:118:218/1
+CCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:45:44:144/1
+CATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:46:92:189/1
+ATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:47:132:233/1
+AGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:48:45:143/1
+ATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:49:26:125/1
+TCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:50:87:185/1
+CTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:51:107:205/1
+CAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:52:47:147/1
+TCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:53:3:103/1
+CAGGACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:54:127:228/1
+CGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:55:69:169/1
+TTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:56:8:107/1
+CGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:57:51:149/1
+GTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:58:141:243/1
+CCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACGGCTGATACCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:59:3:102/1
+CAGGACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:60:17:116/1
+GGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:61:21:120/1
+GGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:62:20:118/1
+AGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:63:4:105/1
+AGGACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:64:7:107/1
+ACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:65:127:227/1
+CGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:66:98:197/1
+TGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:67:116:216/1
+AGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:68:134:235/1
+CGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACGGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:69:65:165/1
+CTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:70:81:179/1
+GACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:71:41:140/1
+CTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:72:2:100/1
+TCAGGACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:73:83:184/1
+CAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:74:66:164/1
+TTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_noncoding_does_have_var/reads_2.fq b/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_noncoding_does_have_var/reads_2.fq
new file mode 100644
index 0000000..31885ad
--- /dev/null
+++ b/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_noncoding_does_have_var/reads_2.fq
@@ -0,0 +1,296 @@
+ at ref_gene:1:147:247/2
+TGTTTGCGTACATACCGGGTCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:2:89:186/2
+TGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:3:40:139/2
+GTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:4:113:213/2
+TCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:5:111:210/2
+TGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:6:29:129/2
+TGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:7:112:212/2
+CATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:8:45:145/2
+TTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:9:121:219/2
+ACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:10:82:182/2
+TACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:11:96:196/2
+TTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:12:125:225/2
+GAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:13:114:215/2
+CCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:14:100:199/2
+TAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:15:90:188/2
+TCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:16:54:154/2
+CGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:17:110:210/2
+TGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:18:63:162/2
+TATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:19:83:183/2
+ATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:20:94:194/2
+CTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:21:65:164/2
+GATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:22:27:126/2
+TATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCGCGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:23:39:141/2
+GGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:24:107:208/2
+GCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:25:72:170/2
+GTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:26:10:111/2
+CACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCGCGATCCATCGGCTACGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:27:55:155/2
+ACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:28:83:184/2
+TATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:29:11:110/2
+ACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCGCGATCCATCGGCTACGCTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:30:76:177/2
+CGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:31:77:176/2
+GGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:32:96:195/2
+TCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:33:19:118/2
+GCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCGCGATCCATCGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:34:40:141/2
+GGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:35:68:167/2
+GGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:36:70:170/2
+GTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:37:94:194.dup.2/2
+CTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:38:27:127/2
+TTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:39:102:201/2
+AATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:40:131:231/2
+GGGTCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:41:13:113/2
+CCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:42:82:182/2
+TACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:43:84:183/2
+ATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:44:118:218/2
+CATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:45:44:144/2
+TATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:46:92:189/2
+CTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:47:132:233/2
+CCGGGTCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:48:45:143/2
+ATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:49:26:125/2
+ATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:50:87:185/2
+GTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:51:107:205/2
+TAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:52:47:147/2
+AATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:53:3:103/2
+AATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTGGCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:54:127:228/2
+TCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:55:69:169/2
+TAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:56:8:107/2
+CGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:57:51:149/2
+GAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:58:141:243/2
+TGCGTACATACCGGGTCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:59:3:102/2
+ATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTGGCGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:60:17:116/2
+TTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:61:21:120/2
+ATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:62:20:118/2
+GCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:63:4:105/2
+CTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTGGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:64:7:107/2
+CGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:65:127:227/2
+CTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:66:98:197/2
+GTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:67:116:216/2
+TCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:68:134:235/2
+TACCGGGTCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:69:65:165/2
+AGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:70:81:179/2
+TGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:71:41:140/2
+GGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:72:2:100/2
+GCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTGGCGTACT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:73:83:184/2
+TATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:74:66:164/2
+GATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_noncoding_does_have_var/references.fa b/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_noncoding_does_have_var/references.fa
new file mode 100644
index 0000000..a23e635
--- /dev/null
+++ b/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_noncoding_does_have_var/references.fa
@@ -0,0 +1,3 @@
+>ref_seq
+ATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCAT
+ATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAA
diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_noncoding_does_not_have_var/reads_1.fq b/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_noncoding_does_not_have_var/reads_1.fq
new file mode 100644
index 0000000..1d056e7
--- /dev/null
+++ b/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_noncoding_does_not_have_var/reads_1.fq
@@ -0,0 +1,296 @@
+ at ref_gene:1:147:247/1
+AGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACGGCTGATACCCATAATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:2:89:186/1
+AATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:3:40:139/1
+CCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:4:113:213/1
+CGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:5:111:210/1
+AGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:6:29:129/1
+AGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:7:112:212/1
+GCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:8:45:145/1
+ATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:9:121:219/1
+ATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:10:82:182/1
+ACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:11:96:196/1
+AATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:12:125:225/1
+ATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:13:114:215/1
+GTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:14:100:199/1
+AGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:15:90:188/1
+ATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:16:54:154/1
+ATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:17:110:210/1
+GAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:18:63:162/1
+TCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:19:83:183/1
+CAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:20:94:194/1
+GGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:21:65:164/1
+CTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:22:27:126/1
+CGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:23:39:141/1
+TCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:24:107:208/1
+CAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:25:72:170/1
+GCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:26:10:111/1
+TCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:27:55:155/1
+TTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:28:83:184/1
+CAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:29:11:110/1
+CGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:30:76:177/1
+CAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:31:77:176/1
+AGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:32:96:195/1
+AATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:33:19:118/1
+CAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:34:40:141/1
+CCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:35:68:167/1
+GTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:36:70:170/1
+TTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:37:94:194.dup.2/1
+GGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:38:27:127/1
+CGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:39:102:201/1
+TACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:40:131:231/1
+AAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:41:13:113/1
+GCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:42:82:182/1
+ACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:43:84:183/1
+AAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:44:118:218/1
+CCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:45:44:144/1
+CATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:46:92:189/1
+ATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:47:132:233/1
+AGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:48:45:143/1
+ATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:49:26:125/1
+TCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:50:87:185/1
+CTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:51:107:205/1
+CAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:52:47:147/1
+TCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:53:3:103/1
+CAGGACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:54:127:228/1
+CGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:55:69:169/1
+TTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:56:8:107/1
+CGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:57:51:149/1
+GTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:58:141:243/1
+CCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACGGCTGATACCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:59:3:102/1
+CAGGACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:60:17:116/1
+GGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:61:21:120/1
+GGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:62:20:118/1
+AGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:63:4:105/1
+AGGACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:64:7:107/1
+ACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:65:127:227/1
+CGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:66:98:197/1
+TGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:67:116:216/1
+AGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:68:134:235/1
+CGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACGGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:69:65:165/1
+CTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:70:81:179/1
+GACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:71:41:140/1
+CTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:72:2:100/1
+TCAGGACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:73:83:184/1
+CAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:74:66:164/1
+TTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_noncoding_does_not_have_var/reads_2.fq b/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_noncoding_does_not_have_var/reads_2.fq
new file mode 100644
index 0000000..31885ad
--- /dev/null
+++ b/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_noncoding_does_not_have_var/reads_2.fq
@@ -0,0 +1,296 @@
+ at ref_gene:1:147:247/2
+TGTTTGCGTACATACCGGGTCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:2:89:186/2
+TGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:3:40:139/2
+GTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:4:113:213/2
+TCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:5:111:210/2
+TGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:6:29:129/2
+TGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:7:112:212/2
+CATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:8:45:145/2
+TTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:9:121:219/2
+ACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:10:82:182/2
+TACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:11:96:196/2
+TTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:12:125:225/2
+GAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:13:114:215/2
+CCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:14:100:199/2
+TAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:15:90:188/2
+TCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:16:54:154/2
+CGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:17:110:210/2
+TGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:18:63:162/2
+TATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:19:83:183/2
+ATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:20:94:194/2
+CTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:21:65:164/2
+GATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:22:27:126/2
+TATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCGCGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:23:39:141/2
+GGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:24:107:208/2
+GCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:25:72:170/2
+GTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:26:10:111/2
+CACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCGCGATCCATCGGCTACGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:27:55:155/2
+ACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:28:83:184/2
+TATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:29:11:110/2
+ACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCGCGATCCATCGGCTACGCTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:30:76:177/2
+CGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:31:77:176/2
+GGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:32:96:195/2
+TCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:33:19:118/2
+GCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCGCGATCCATCGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:34:40:141/2
+GGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:35:68:167/2
+GGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:36:70:170/2
+GTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:37:94:194.dup.2/2
+CTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:38:27:127/2
+TTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:39:102:201/2
+AATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:40:131:231/2
+GGGTCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:41:13:113/2
+CCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:42:82:182/2
+TACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:43:84:183/2
+ATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:44:118:218/2
+CATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:45:44:144/2
+TATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:46:92:189/2
+CTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:47:132:233/2
+CCGGGTCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:48:45:143/2
+ATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:49:26:125/2
+ATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:50:87:185/2
+GTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:51:107:205/2
+TAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:52:47:147/2
+AATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:53:3:103/2
+AATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTGGCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:54:127:228/2
+TCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:55:69:169/2
+TAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:56:8:107/2
+CGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:57:51:149/2
+GAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:58:141:243/2
+TGCGTACATACCGGGTCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:59:3:102/2
+ATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTGGCGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:60:17:116/2
+TTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:61:21:120/2
+ATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:62:20:118/2
+GCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:63:4:105/2
+CTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTGGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:64:7:107/2
+CGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:65:127:227/2
+CTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:66:98:197/2
+GTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:67:116:216/2
+TCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:68:134:235/2
+TACCGGGTCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:69:65:165/2
+AGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:70:81:179/2
+TGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:71:41:140/2
+GGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:72:2:100/2
+GCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTGGCGTACT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:73:83:184/2
+TATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:74:66:164/2
+GATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_noncoding_does_not_have_var/references.fa b/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_noncoding_does_not_have_var/references.fa
new file mode 100644
index 0000000..a23e635
--- /dev/null
+++ b/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_noncoding_does_not_have_var/references.fa
@@ -0,0 +1,3 @@
+>ref_seq
+ATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCAT
+ATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAA
diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_gene.fa b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_gene.fa
new file mode 100644
index 0000000..c42d06b
--- /dev/null
+++ b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_gene.fa
@@ -0,0 +1,3 @@
+>ref_gene
+ATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCAT
+ATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAA
diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_gene.metadata.tsv b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_gene.metadata.tsv
new file mode 100644
index 0000000..685e96e
--- /dev/null
+++ b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_gene.metadata.tsv
@@ -0,0 +1 @@
+ref_gene 1 0 M6I . Description of M6I snp
diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_gene.ref_for_reads.fa b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_gene.ref_for_reads.fa
new file mode 100644
index 0000000..d0128a0
--- /dev/null
+++ b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_gene.ref_for_reads.fa
@@ -0,0 +1,14 @@
+>ref_gene
+GTCAGGACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGT
+TGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCG
+ATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCAT
+ATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACGGCTGATACCCATAATTTCAT
+CCGTAGTTATATCTCCTACAATACCGCAGTATACAGAGACGAGAACTATTACTATGCCAT
+GAGGATGTAAACTCAGACCCGGTATGTACGCAAACA
+>ref_gene_with_snp
+GTCAGGACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGT
+TGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCG
+ATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCAT
+ATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACGGCTGATACCCATAATTTCAT
+CCGTAGTTATATCTCCTACAATACCGCAGTATACAGAGACGAGAACTATTACTATGCCAT
+GAGGATGTAAACTCAGACCCGGTATGTACGCAAACA
diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_noncoding.fa b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_noncoding.fa
new file mode 100644
index 0000000..a23e635
--- /dev/null
+++ b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_noncoding.fa
@@ -0,0 +1,3 @@
+>ref_seq
+ATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCAT
+ATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAA
diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_noncoding.metadata.tsv b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_noncoding.metadata.tsv
new file mode 100644
index 0000000..6c533b2
--- /dev/null
+++ b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_noncoding.metadata.tsv
@@ -0,0 +1 @@
+ref_seq 0 0 G18A . Description of G18A snp
diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_have_var.fa b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_have_var.fa
new file mode 100644
index 0000000..c42d06b
--- /dev/null
+++ b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_have_var.fa
@@ -0,0 +1,3 @@
+>ref_gene
+ATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCAT
+ATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAA
diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_have_var.metadata.tsv b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_have_var.metadata.tsv
new file mode 100644
index 0000000..4a62906
--- /dev/null
+++ b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_have_var.metadata.tsv
@@ -0,0 +1 @@
+ref_gene 1 1 I6M . Description of I6M snp
diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_not_have_var.fa b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_not_have_var.fa
new file mode 100644
index 0000000..c42d06b
--- /dev/null
+++ b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_not_have_var.fa
@@ -0,0 +1,3 @@
+>ref_gene
+ATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCAT
+ATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAA
diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_not_have_var.metadata.tsv b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_not_have_var.metadata.tsv
new file mode 100644
index 0000000..7f66d49
--- /dev/null
+++ b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_not_have_var.metadata.tsv
@@ -0,0 +1 @@
+ref_gene 1 1 M6I . Description of M6I snp
diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding_does_have_var.fa b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding_does_have_var.fa
new file mode 100644
index 0000000..a23e635
--- /dev/null
+++ b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding_does_have_var.fa
@@ -0,0 +1,3 @@
+>ref_seq
+ATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCAT
+ATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAA
diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding_does_have_var.metadata.tsv b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding_does_have_var.metadata.tsv
new file mode 100644
index 0000000..6bfb1ec
--- /dev/null
+++ b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding_does_have_var.metadata.tsv
@@ -0,0 +1 @@
+ref_seq 0 1 A18G . Description of A18G snp
diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding_does_not_have_var.fa b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding_does_not_have_var.fa
new file mode 100644
index 0000000..a23e635
--- /dev/null
+++ b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding_does_not_have_var.fa
@@ -0,0 +1,3 @@
+>ref_seq
+ATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCAT
+ATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAA
diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding_does_not_have_var.metadata.tsv b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding_does_not_have_var.metadata.tsv
new file mode 100644
index 0000000..b79de02
--- /dev/null
+++ b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding_does_not_have_var.metadata.tsv
@@ -0,0 +1 @@
+ref_seq 0 1 G18A . Description of G18A snp
diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_gene.fa b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_gene.fa
new file mode 100644
index 0000000..c42d06b
--- /dev/null
+++ b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_gene.fa
@@ -0,0 +1,3 @@
+>ref_gene
+ATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCAT
+ATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAA
diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_gene.metadata.tsv b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_gene.metadata.tsv
new file mode 100644
index 0000000..14073d7
--- /dev/null
+++ b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_gene.metadata.tsv
@@ -0,0 +1 @@
+ref_gene 1 0 . . Generic description of ref_gene
diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_gene.ref_for_reads.fa b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_gene.ref_for_reads.fa
new file mode 100644
index 0000000..d0128a0
--- /dev/null
+++ b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_gene.ref_for_reads.fa
@@ -0,0 +1,14 @@
+>ref_gene
+GTCAGGACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGT
+TGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCG
+ATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCAT
+ATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACGGCTGATACCCATAATTTCAT
+CCGTAGTTATATCTCCTACAATACCGCAGTATACAGAGACGAGAACTATTACTATGCCAT
+GAGGATGTAAACTCAGACCCGGTATGTACGCAAACA
+>ref_gene_with_snp
+GTCAGGACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGT
+TGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCG
+ATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCAT
+ATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACGGCTGATACCCATAATTTCAT
+CCGTAGTTATATCTCCTACAATACCGCAGTATACAGAGACGAGAACTATTACTATGCCAT
+GAGGATGTAAACTCAGACCCGGTATGTACGCAAACA
diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_gene/reads_1.fq b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_gene/reads_1.fq
new file mode 100644
index 0000000..1d056e7
--- /dev/null
+++ b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_gene/reads_1.fq
@@ -0,0 +1,296 @@
+ at ref_gene:1:147:247/1
+AGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACGGCTGATACCCATAATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:2:89:186/1
+AATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:3:40:139/1
+CCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:4:113:213/1
+CGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:5:111:210/1
+AGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:6:29:129/1
+AGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:7:112:212/1
+GCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:8:45:145/1
+ATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:9:121:219/1
+ATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:10:82:182/1
+ACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:11:96:196/1
+AATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:12:125:225/1
+ATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:13:114:215/1
+GTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:14:100:199/1
+AGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:15:90:188/1
+ATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:16:54:154/1
+ATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:17:110:210/1
+GAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:18:63:162/1
+TCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:19:83:183/1
+CAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:20:94:194/1
+GGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:21:65:164/1
+CTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:22:27:126/1
+CGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:23:39:141/1
+TCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:24:107:208/1
+CAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:25:72:170/1
+GCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:26:10:111/1
+TCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:27:55:155/1
+TTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:28:83:184/1
+CAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:29:11:110/1
+CGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:30:76:177/1
+CAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:31:77:176/1
+AGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:32:96:195/1
+AATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:33:19:118/1
+CAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:34:40:141/1
+CCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:35:68:167/1
+GTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:36:70:170/1
+TTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:37:94:194.dup.2/1
+GGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:38:27:127/1
+CGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:39:102:201/1
+TACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:40:131:231/1
+AAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:41:13:113/1
+GCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:42:82:182/1
+ACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:43:84:183/1
+AAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:44:118:218/1
+CCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:45:44:144/1
+CATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:46:92:189/1
+ATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:47:132:233/1
+AGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:48:45:143/1
+ATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:49:26:125/1
+TCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:50:87:185/1
+CTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:51:107:205/1
+CAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:52:47:147/1
+TCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:53:3:103/1
+CAGGACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:54:127:228/1
+CGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:55:69:169/1
+TTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:56:8:107/1
+CGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:57:51:149/1
+GTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:58:141:243/1
+CCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACGGCTGATACCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:59:3:102/1
+CAGGACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:60:17:116/1
+GGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:61:21:120/1
+GGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:62:20:118/1
+AGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:63:4:105/1
+AGGACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:64:7:107/1
+ACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:65:127:227/1
+CGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:66:98:197/1
+TGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:67:116:216/1
+AGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:68:134:235/1
+CGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACGGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:69:65:165/1
+CTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:70:81:179/1
+GACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:71:41:140/1
+CTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:72:2:100/1
+TCAGGACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:73:83:184/1
+CAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:74:66:164/1
+TTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_gene/reads_2.fq b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_gene/reads_2.fq
new file mode 100644
index 0000000..31885ad
--- /dev/null
+++ b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_gene/reads_2.fq
@@ -0,0 +1,296 @@
+ at ref_gene:1:147:247/2
+TGTTTGCGTACATACCGGGTCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:2:89:186/2
+TGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:3:40:139/2
+GTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:4:113:213/2
+TCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:5:111:210/2
+TGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:6:29:129/2
+TGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:7:112:212/2
+CATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:8:45:145/2
+TTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:9:121:219/2
+ACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:10:82:182/2
+TACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:11:96:196/2
+TTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:12:125:225/2
+GAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:13:114:215/2
+CCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:14:100:199/2
+TAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:15:90:188/2
+TCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:16:54:154/2
+CGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:17:110:210/2
+TGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:18:63:162/2
+TATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:19:83:183/2
+ATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:20:94:194/2
+CTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:21:65:164/2
+GATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:22:27:126/2
+TATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCGCGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:23:39:141/2
+GGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:24:107:208/2
+GCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:25:72:170/2
+GTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:26:10:111/2
+CACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCGCGATCCATCGGCTACGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:27:55:155/2
+ACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:28:83:184/2
+TATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:29:11:110/2
+ACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCGCGATCCATCGGCTACGCTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:30:76:177/2
+CGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:31:77:176/2
+GGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:32:96:195/2
+TCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:33:19:118/2
+GCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCGCGATCCATCGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:34:40:141/2
+GGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:35:68:167/2
+GGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:36:70:170/2
+GTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:37:94:194.dup.2/2
+CTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:38:27:127/2
+TTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:39:102:201/2
+AATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:40:131:231/2
+GGGTCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:41:13:113/2
+CCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:42:82:182/2
+TACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:43:84:183/2
+ATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:44:118:218/2
+CATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:45:44:144/2
+TATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:46:92:189/2
+CTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:47:132:233/2
+CCGGGTCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:48:45:143/2
+ATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:49:26:125/2
+ATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:50:87:185/2
+GTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:51:107:205/2
+TAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:52:47:147/2
+AATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:53:3:103/2
+AATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTGGCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:54:127:228/2
+TCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:55:69:169/2
+TAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:56:8:107/2
+CGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:57:51:149/2
+GAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:58:141:243/2
+TGCGTACATACCGGGTCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:59:3:102/2
+ATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTGGCGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:60:17:116/2
+TTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:61:21:120/2
+ATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:62:20:118/2
+GCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:63:4:105/2
+CTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTGGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:64:7:107/2
+CGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:65:127:227/2
+CTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:66:98:197/2
+GTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:67:116:216/2
+TCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:68:134:235/2
+TACCGGGTCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:69:65:165/2
+AGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:70:81:179/2
+TGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:71:41:140/2
+GGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:72:2:100/2
+GCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTGGCGTACT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:73:83:184/2
+TATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:74:66:164/2
+GATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_gene/references.fa b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_gene/references.fa
new file mode 100644
index 0000000..c42d06b
--- /dev/null
+++ b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_gene/references.fa
@@ -0,0 +1,3 @@
+>ref_gene
+ATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCAT
+ATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAA
diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_noncoding.fa b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_noncoding.fa
new file mode 100644
index 0000000..a23e635
--- /dev/null
+++ b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_noncoding.fa
@@ -0,0 +1,3 @@
+>ref_seq
+ATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCAT
+ATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAA
diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_noncoding.metadata.tsv b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_noncoding.metadata.tsv
new file mode 100644
index 0000000..0e96f59
--- /dev/null
+++ b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_noncoding.metadata.tsv
@@ -0,0 +1 @@
+ref_seq 0 0 . . Generic description of ref_seq
diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_noncoding/reads_1.fq b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_noncoding/reads_1.fq
new file mode 100644
index 0000000..1d056e7
--- /dev/null
+++ b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_noncoding/reads_1.fq
@@ -0,0 +1,296 @@
+ at ref_gene:1:147:247/1
+AGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACGGCTGATACCCATAATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:2:89:186/1
+AATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:3:40:139/1
+CCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:4:113:213/1
+CGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:5:111:210/1
+AGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:6:29:129/1
+AGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:7:112:212/1
+GCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:8:45:145/1
+ATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:9:121:219/1
+ATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:10:82:182/1
+ACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:11:96:196/1
+AATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:12:125:225/1
+ATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:13:114:215/1
+GTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:14:100:199/1
+AGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:15:90:188/1
+ATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:16:54:154/1
+ATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:17:110:210/1
+GAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:18:63:162/1
+TCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:19:83:183/1
+CAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:20:94:194/1
+GGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:21:65:164/1
+CTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:22:27:126/1
+CGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:23:39:141/1
+TCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:24:107:208/1
+CAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:25:72:170/1
+GCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:26:10:111/1
+TCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:27:55:155/1
+TTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:28:83:184/1
+CAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:29:11:110/1
+CGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:30:76:177/1
+CAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:31:77:176/1
+AGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:32:96:195/1
+AATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:33:19:118/1
+CAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:34:40:141/1
+CCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:35:68:167/1
+GTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:36:70:170/1
+TTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:37:94:194.dup.2/1
+GGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:38:27:127/1
+CGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:39:102:201/1
+TACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:40:131:231/1
+AAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:41:13:113/1
+GCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:42:82:182/1
+ACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:43:84:183/1
+AAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:44:118:218/1
+CCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:45:44:144/1
+CATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:46:92:189/1
+ATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:47:132:233/1
+AGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:48:45:143/1
+ATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:49:26:125/1
+TCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:50:87:185/1
+CTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:51:107:205/1
+CAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:52:47:147/1
+TCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:53:3:103/1
+CAGGACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:54:127:228/1
+CGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:55:69:169/1
+TTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:56:8:107/1
+CGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:57:51:149/1
+GTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:58:141:243/1
+CCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACGGCTGATACCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:59:3:102/1
+CAGGACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:60:17:116/1
+GGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:61:21:120/1
+GGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:62:20:118/1
+AGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:63:4:105/1
+AGGACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:64:7:107/1
+ACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:65:127:227/1
+CGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:66:98:197/1
+TGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:67:116:216/1
+AGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:68:134:235/1
+CGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACGGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:69:65:165/1
+CTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:70:81:179/1
+GACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:71:41:140/1
+CTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:72:2:100/1
+TCAGGACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:73:83:184/1
+CAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:74:66:164/1
+TTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_noncoding/reads_2.fq b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_noncoding/reads_2.fq
new file mode 100644
index 0000000..31885ad
--- /dev/null
+++ b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_noncoding/reads_2.fq
@@ -0,0 +1,296 @@
+ at ref_gene:1:147:247/2
+TGTTTGCGTACATACCGGGTCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:2:89:186/2
+TGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:3:40:139/2
+GTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:4:113:213/2
+TCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:5:111:210/2
+TGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:6:29:129/2
+TGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:7:112:212/2
+CATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:8:45:145/2
+TTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:9:121:219/2
+ACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:10:82:182/2
+TACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:11:96:196/2
+TTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:12:125:225/2
+GAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:13:114:215/2
+CCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:14:100:199/2
+TAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:15:90:188/2
+TCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:16:54:154/2
+CGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:17:110:210/2
+TGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:18:63:162/2
+TATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:19:83:183/2
+ATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:20:94:194/2
+CTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:21:65:164/2
+GATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:22:27:126/2
+TATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCGCGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:23:39:141/2
+GGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:24:107:208/2
+GCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:25:72:170/2
+GTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:26:10:111/2
+CACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCGCGATCCATCGGCTACGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:27:55:155/2
+ACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:28:83:184/2
+TATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:29:11:110/2
+ACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCGCGATCCATCGGCTACGCTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:30:76:177/2
+CGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:31:77:176/2
+GGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:32:96:195/2
+TCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:33:19:118/2
+GCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCGCGATCCATCGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:34:40:141/2
+GGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:35:68:167/2
+GGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:36:70:170/2
+GTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:37:94:194.dup.2/2
+CTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:38:27:127/2
+TTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:39:102:201/2
+AATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:40:131:231/2
+GGGTCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:41:13:113/2
+CCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:42:82:182/2
+TACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:43:84:183/2
+ATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:44:118:218/2
+CATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:45:44:144/2
+TATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:46:92:189/2
+CTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:47:132:233/2
+CCGGGTCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:48:45:143/2
+ATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:49:26:125/2
+ATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:50:87:185/2
+GTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:51:107:205/2
+TAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:52:47:147/2
+AATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:53:3:103/2
+AATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTGGCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:54:127:228/2
+TCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:55:69:169/2
+TAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:56:8:107/2
+CGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:57:51:149/2
+GAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:58:141:243/2
+TGCGTACATACCGGGTCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:59:3:102/2
+ATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTGGCGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:60:17:116/2
+TTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:61:21:120/2
+ATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:62:20:118/2
+GCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:63:4:105/2
+CTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTGGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:64:7:107/2
+CGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:65:127:227/2
+CTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:66:98:197/2
+GTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:67:116:216/2
+TCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:68:134:235/2
+TACCGGGTCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:69:65:165/2
+AGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:70:81:179/2
+TGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:71:41:140/2
+GGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:72:2:100/2
+GCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTGGCGTACT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:73:83:184/2
+TATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:74:66:164/2
+GATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_noncoding/references.fa b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_noncoding/references.fa
new file mode 100644
index 0000000..a23e635
--- /dev/null
+++ b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_noncoding/references.fa
@@ -0,0 +1,3 @@
+>ref_seq
+ATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCAT
+ATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAA
diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_var_only_gene.fa b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_var_only_gene.fa
new file mode 100644
index 0000000..c42d06b
--- /dev/null
+++ b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_var_only_gene.fa
@@ -0,0 +1,3 @@
+>ref_gene
+ATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCAT
+ATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAA
diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_var_only_gene.metadata.tsv b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_var_only_gene.metadata.tsv
new file mode 100644
index 0000000..af23689
--- /dev/null
+++ b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_var_only_gene.metadata.tsv
@@ -0,0 +1 @@
+ref_gene 1 1 . . Generic description of ref_gene
diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_var_only_gene/reads_1.fq b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_var_only_gene/reads_1.fq
new file mode 100644
index 0000000..1d056e7
--- /dev/null
+++ b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_var_only_gene/reads_1.fq
@@ -0,0 +1,296 @@
+ at ref_gene:1:147:247/1
+AGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACGGCTGATACCCATAATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:2:89:186/1
+AATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:3:40:139/1
+CCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:4:113:213/1
+CGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:5:111:210/1
+AGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:6:29:129/1
+AGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:7:112:212/1
+GCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:8:45:145/1
+ATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:9:121:219/1
+ATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:10:82:182/1
+ACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:11:96:196/1
+AATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:12:125:225/1
+ATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:13:114:215/1
+GTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:14:100:199/1
+AGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:15:90:188/1
+ATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:16:54:154/1
+ATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:17:110:210/1
+GAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:18:63:162/1
+TCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:19:83:183/1
+CAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:20:94:194/1
+GGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:21:65:164/1
+CTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:22:27:126/1
+CGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:23:39:141/1
+TCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:24:107:208/1
+CAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:25:72:170/1
+GCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:26:10:111/1
+TCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:27:55:155/1
+TTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:28:83:184/1
+CAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:29:11:110/1
+CGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:30:76:177/1
+CAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:31:77:176/1
+AGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:32:96:195/1
+AATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:33:19:118/1
+CAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:34:40:141/1
+CCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:35:68:167/1
+GTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:36:70:170/1
+TTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:37:94:194.dup.2/1
+GGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:38:27:127/1
+CGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:39:102:201/1
+TACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:40:131:231/1
+AAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:41:13:113/1
+GCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:42:82:182/1
+ACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:43:84:183/1
+AAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:44:118:218/1
+CCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:45:44:144/1
+CATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:46:92:189/1
+ATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:47:132:233/1
+AGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:48:45:143/1
+ATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:49:26:125/1
+TCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:50:87:185/1
+CTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:51:107:205/1
+CAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:52:47:147/1
+TCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:53:3:103/1
+CAGGACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:54:127:228/1
+CGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:55:69:169/1
+TTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:56:8:107/1
+CGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:57:51:149/1
+GTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:58:141:243/1
+CCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACGGCTGATACCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:59:3:102/1
+CAGGACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:60:17:116/1
+GGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:61:21:120/1
+GGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:62:20:118/1
+AGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:63:4:105/1
+AGGACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:64:7:107/1
+ACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:65:127:227/1
+CGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:66:98:197/1
+TGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:67:116:216/1
+AGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:68:134:235/1
+CGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACGGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:69:65:165/1
+CTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:70:81:179/1
+GACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:71:41:140/1
+CTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:72:2:100/1
+TCAGGACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:73:83:184/1
+CAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:74:66:164/1
+TTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_var_only_gene/reads_2.fq b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_var_only_gene/reads_2.fq
new file mode 100644
index 0000000..31885ad
--- /dev/null
+++ b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_var_only_gene/reads_2.fq
@@ -0,0 +1,296 @@
+ at ref_gene:1:147:247/2
+TGTTTGCGTACATACCGGGTCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:2:89:186/2
+TGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:3:40:139/2
+GTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:4:113:213/2
+TCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:5:111:210/2
+TGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:6:29:129/2
+TGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:7:112:212/2
+CATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:8:45:145/2
+TTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:9:121:219/2
+ACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:10:82:182/2
+TACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:11:96:196/2
+TTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:12:125:225/2
+GAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:13:114:215/2
+CCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:14:100:199/2
+TAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:15:90:188/2
+TCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:16:54:154/2
+CGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:17:110:210/2
+TGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:18:63:162/2
+TATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:19:83:183/2
+ATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:20:94:194/2
+CTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:21:65:164/2
+GATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:22:27:126/2
+TATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCGCGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:23:39:141/2
+GGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:24:107:208/2
+GCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:25:72:170/2
+GTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:26:10:111/2
+CACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCGCGATCCATCGGCTACGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:27:55:155/2
+ACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:28:83:184/2
+TATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:29:11:110/2
+ACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCGCGATCCATCGGCTACGCTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:30:76:177/2
+CGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:31:77:176/2
+GGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:32:96:195/2
+TCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:33:19:118/2
+GCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCGCGATCCATCGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:34:40:141/2
+GGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:35:68:167/2
+GGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:36:70:170/2
+GTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:37:94:194.dup.2/2
+CTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:38:27:127/2
+TTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:39:102:201/2
+AATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:40:131:231/2
+GGGTCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:41:13:113/2
+CCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:42:82:182/2
+TACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:43:84:183/2
+ATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:44:118:218/2
+CATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:45:44:144/2
+TATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:46:92:189/2
+CTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:47:132:233/2
+CCGGGTCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:48:45:143/2
+ATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:49:26:125/2
+ATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:50:87:185/2
+GTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:51:107:205/2
+TAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:52:47:147/2
+AATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:53:3:103/2
+AATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTGGCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:54:127:228/2
+TCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:55:69:169/2
+TAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:56:8:107/2
+CGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:57:51:149/2
+GAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:58:141:243/2
+TGCGTACATACCGGGTCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:59:3:102/2
+ATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTGGCGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:60:17:116/2
+TTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:61:21:120/2
+ATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:62:20:118/2
+GCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:63:4:105/2
+CTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTGGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:64:7:107/2
+CGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:65:127:227/2
+CTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:66:98:197/2
+GTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:67:116:216/2
+TCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:68:134:235/2
+TACCGGGTCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:69:65:165/2
+AGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:70:81:179/2
+TGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:71:41:140/2
+GGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:72:2:100/2
+GCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTGGCGTACT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:73:83:184/2
+TATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:74:66:164/2
+GATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_var_only_gene/references.fa b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_var_only_gene/references.fa
new file mode 100644
index 0000000..c42d06b
--- /dev/null
+++ b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_var_only_gene/references.fa
@@ -0,0 +1,3 @@
+>ref_gene
+ATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCAT
+ATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAA
diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_var_only_noncoding.fa b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_var_only_noncoding.fa
new file mode 100644
index 0000000..a23e635
--- /dev/null
+++ b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_var_only_noncoding.fa
@@ -0,0 +1,3 @@
+>ref_seq
+ATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCAT
+ATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAA
diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_var_only_noncoding.metadata.tsv b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_var_only_noncoding.metadata.tsv
new file mode 100644
index 0000000..90b9235
--- /dev/null
+++ b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_var_only_noncoding.metadata.tsv
@@ -0,0 +1 @@
+ref_seq 0 1 . . Generic description of ref_seq
diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_var_only_noncoding/reads_1.fq b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_var_only_noncoding/reads_1.fq
new file mode 100644
index 0000000..1d056e7
--- /dev/null
+++ b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_var_only_noncoding/reads_1.fq
@@ -0,0 +1,296 @@
+ at ref_gene:1:147:247/1
+AGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACGGCTGATACCCATAATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:2:89:186/1
+AATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:3:40:139/1
+CCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:4:113:213/1
+CGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:5:111:210/1
+AGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:6:29:129/1
+AGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:7:112:212/1
+GCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:8:45:145/1
+ATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:9:121:219/1
+ATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:10:82:182/1
+ACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:11:96:196/1
+AATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:12:125:225/1
+ATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:13:114:215/1
+GTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:14:100:199/1
+AGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:15:90:188/1
+ATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:16:54:154/1
+ATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:17:110:210/1
+GAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:18:63:162/1
+TCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:19:83:183/1
+CAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:20:94:194/1
+GGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:21:65:164/1
+CTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:22:27:126/1
+CGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:23:39:141/1
+TCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:24:107:208/1
+CAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:25:72:170/1
+GCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:26:10:111/1
+TCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:27:55:155/1
+TTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:28:83:184/1
+CAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:29:11:110/1
+CGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:30:76:177/1
+CAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:31:77:176/1
+AGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:32:96:195/1
+AATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:33:19:118/1
+CAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:34:40:141/1
+CCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:35:68:167/1
+GTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:36:70:170/1
+TTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:37:94:194.dup.2/1
+GGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:38:27:127/1
+CGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:39:102:201/1
+TACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:40:131:231/1
+AAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:41:13:113/1
+GCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:42:82:182/1
+ACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:43:84:183/1
+AAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:44:118:218/1
+CCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:45:44:144/1
+CATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:46:92:189/1
+ATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:47:132:233/1
+AGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:48:45:143/1
+ATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:49:26:125/1
+TCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:50:87:185/1
+CTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:51:107:205/1
+CAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:52:47:147/1
+TCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:53:3:103/1
+CAGGACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:54:127:228/1
+CGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:55:69:169/1
+TTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:56:8:107/1
+CGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:57:51:149/1
+GTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:58:141:243/1
+CCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACGGCTGATACCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:59:3:102/1
+CAGGACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:60:17:116/1
+GGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:61:21:120/1
+GGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:62:20:118/1
+AGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:63:4:105/1
+AGGACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:64:7:107/1
+ACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:65:127:227/1
+CGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:66:98:197/1
+TGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:67:116:216/1
+AGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:68:134:235/1
+CGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACGGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:69:65:165/1
+CTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:70:81:179/1
+GACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:71:41:140/1
+CTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:72:2:100/1
+TCAGGACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:73:83:184/1
+CAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:74:66:164/1
+TTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_var_only_noncoding/reads_2.fq b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_var_only_noncoding/reads_2.fq
new file mode 100644
index 0000000..31885ad
--- /dev/null
+++ b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_var_only_noncoding/reads_2.fq
@@ -0,0 +1,296 @@
+ at ref_gene:1:147:247/2
+TGTTTGCGTACATACCGGGTCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:2:89:186/2
+TGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:3:40:139/2
+GTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:4:113:213/2
+TCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:5:111:210/2
+TGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:6:29:129/2
+TGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:7:112:212/2
+CATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:8:45:145/2
+TTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:9:121:219/2
+ACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:10:82:182/2
+TACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:11:96:196/2
+TTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:12:125:225/2
+GAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:13:114:215/2
+CCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:14:100:199/2
+TAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:15:90:188/2
+TCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:16:54:154/2
+CGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:17:110:210/2
+TGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:18:63:162/2
+TATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:19:83:183/2
+ATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:20:94:194/2
+CTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:21:65:164/2
+GATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:22:27:126/2
+TATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCGCGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:23:39:141/2
+GGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:24:107:208/2
+GCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:25:72:170/2
+GTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:26:10:111/2
+CACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCGCGATCCATCGGCTACGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:27:55:155/2
+ACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:28:83:184/2
+TATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:29:11:110/2
+ACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCGCGATCCATCGGCTACGCTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:30:76:177/2
+CGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:31:77:176/2
+GGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:32:96:195/2
+TCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:33:19:118/2
+GCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCGCGATCCATCGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:34:40:141/2
+GGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:35:68:167/2
+GGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:36:70:170/2
+GTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:37:94:194.dup.2/2
+CTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:38:27:127/2
+TTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:39:102:201/2
+AATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:40:131:231/2
+GGGTCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:41:13:113/2
+CCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:42:82:182/2
+TACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:43:84:183/2
+ATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:44:118:218/2
+CATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:45:44:144/2
+TATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:46:92:189/2
+CTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:47:132:233/2
+CCGGGTCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:48:45:143/2
+ATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:49:26:125/2
+ATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:50:87:185/2
+GTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:51:107:205/2
+TAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:52:47:147/2
+AATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:53:3:103/2
+AATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTGGCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:54:127:228/2
+TCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:55:69:169/2
+TAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:56:8:107/2
+CGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:57:51:149/2
+GAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:58:141:243/2
+TGCGTACATACCGGGTCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:59:3:102/2
+ATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTGGCGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:60:17:116/2
+TTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:61:21:120/2
+ATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:62:20:118/2
+GCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:63:4:105/2
+CTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTGGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:64:7:107/2
+CGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:65:127:227/2
+CTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:66:98:197/2
+GTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:67:116:216/2
+TCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:68:134:235/2
+TACCGGGTCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:69:65:165/2
+AGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:70:81:179/2
+TGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:71:41:140/2
+GGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:72:2:100/2
+GCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTGGCGTACT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:73:83:184/2
+TATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:74:66:164/2
+GATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_var_only_noncoding/references.fa b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_var_only_noncoding/references.fa
new file mode 100644
index 0000000..a23e635
--- /dev/null
+++ b/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_var_only_noncoding/references.fa
@@ -0,0 +1,3 @@
+>ref_seq
+ATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCAT
+ATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAA
diff --git a/ariba/tests/data/clusters_test_write_catted_assemblies_fasta.expected.out.fa b/ariba/tests/data/clusters_test_write_catted_assemblies_fasta.expected.out.fa
new file mode 100644
index 0000000..a663981
--- /dev/null
+++ b/ariba/tests/data/clusters_test_write_catted_assemblies_fasta.expected.out.fa
@@ -0,0 +1,6 @@
+>seq1
+ACGT
+>seq2
+TTTT
+>seq3
+AAAA
diff --git a/ariba/tests/data/samtools_variants_test_make_vcf_and_read_depths_files.expected.vcf b/ariba/tests/data/samtools_variants_test_make_vcf_and_read_depths_files.expected.vcf
index d550068..61c4c7d 100644
--- a/ariba/tests/data/samtools_variants_test_make_vcf_and_read_depths_files.expected.vcf
+++ b/ariba/tests/data/samtools_variants_test_make_vcf_and_read_depths_files.expected.vcf
@@ -1,8 +1,8 @@
##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
-##samtoolsVersion=1.2+htslib-1.2.1
-##samtoolsCommand=samtools mpileup -t INFO/DPR,DV -A -f cluster_test_make_assembly_vcf.assembly.fa -u -v cluster_test_make_assembly_vcf.assembly.bam
-##reference=file://cluster_test_make_assembly_vcf.assembly.fa
+##samtoolsVersion=1.3+htslib-1.3
+##samtoolsCommand=samtools mpileup -t INFO/AD -A -f /home/ubuntu/sanger-pathogens/ariba/ariba/tests/data/samtools_variants_test_make_vcf_and_read_depths_files.assembly.fa -u -v /home/ubuntu/sanger-pathogens/ariba/ariba/tests/data/samtools_variants_test_make_vcf_and_read_depths_files.bam
+##reference=file:///home/ubuntu/sanger-pathogens/ariba/ariba/tests/data/samtools_variants_test_make_vcf_and_read_depths_files.assembly.fa
##contig=<ID=16__cat_2_M35190.scaffold.1,length=444>
##contig=<ID=16__cat_2_M35190.scaffold.2,length=400>
##contig=<ID=16__cat_2_M35190.scaffold.3,length=398>
@@ -11,7 +11,7 @@
##contig=<ID=16__cat_2_M35190.scaffold.6,length=180>
##contig=<ID=16__cat_2_M35190.scaffold.7,length=133>
##contig=<ID=16__cat_2_M35190.scaffold.8,length=133>
-##ALT=<ID=X,Description="Represents allele(s) other than observed.">
+##ALT=<ID=*,Description="Represents allele(s) other than observed.">
##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">
##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel">
@@ -24,8 +24,7 @@
##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">
##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
-##FORMAT=<ID=DV,Number=1,Type=Integer,Description="Number of high-quality non-reference bases">
-##INFO=<ID=DPR,Number=R,Type=Integer,Description="Number of high-quality bases observed for each allele">
+##INFO=<ID=AD,Number=R,Type=Integer,Description="Total allelic depths">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##INFO=<ID=ICB,Number=1,Type=Float,Description="Inbreeding Coefficient Binomial test (bigger is better)">
##INFO=<ID=HOB,Number=1,Type=Float,Description="Bias in the number of HOMs number (smaller is better)">
@@ -33,12 +32,12 @@
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases">
##INFO=<ID=MQ,Number=1,Type=Integer,Description="Average mapping quality">
-##bcftools_callVersion=1.2+htslib-1.2.1
-##bcftools_callCommand=call -m -v z.vcf
-##bcftools_filterVersion=1.2+htslib-1.2.1
-##bcftools_filterCommand=filter -i 'MIN(DP)>=10 & MIN(DV)>=5 & MIN(DV/DP)>=0.3 & QUAL >= 20'
-#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT cluster_test_make_assembly_vcf.assembly.bam
-16__cat_2_M35190.scaffold.1 93 . T A 222 PASS DP=123;VDB=0.00672125;SGB=-0.693147;RPB=0.359049;MQB=0.976548;MQSB=1.38527e-20;BQB=0.957743;MQ0F=0;DPR=65,58;ICB=1;HOB=0.5;AC=1;AN=2;DP4=35,30,25,33;MQ=41 GT:PL:DV 0/1:255,0,255:58
-16__cat_2_M35190.scaffold.1 180 . A T 222 PASS DP=86;VDB=0.102578;SGB=-0.693147;RPB=0.885638;MQB=0.976909;MQSB=7.02391e-09;BQB=1;MQ0F=0;DPR=41,45;ICB=1;HOB=0.5;AC=1;AN=2;DP4=17,24,19,26;MQ=27 GT:PL:DV 0/1:255,0,255:45
-16__cat_2_M35190.scaffold.1 264 . G C 119 PASS DP=97;VDB=0.0562559;SGB=-0.693146;RPB=0.389539;MQB=0.007282;MQSB=0.00207736;BQB=0.950442;MQ0F=0;DPR=53,44;ICB=1;HOB=0.5;AC=1;AN=2;DP4=20,33,23,21;MQ=23 GT:PL:DV 0/1:152,0,244:44
-16__cat_2_M35190.scaffold.6 94 . T G 171 PASS DP=99;VDB=0.0786476;SGB=-0.693146;RPB=0.837015;MQB=0.737682;MQSB=1.09416e-07;BQB=1;MQ0F=0.262626;DPR=56,43;ICB=1;HOB=0.5;AC=1;AN=2;DP4=28,28,22,21;MQ=21 GT:PL:DV 0/1:204,0,222:43
+##bcftools_callVersion=1.3+htslib-1.3
+##bcftools_callCommand=call -m -v /home/ubuntu/sanger-pathogens/ariba/tmp.test_make_vcf_and_read_depths_files.vcf.tmp
+##bcftools_filterVersion=1.3+htslib-1.3
+##bcftools_filterCommand=filter -i 'SUM(AD)>=5 & MIN(AD)/DP>=0.1' -o /home/ubuntu/sanger-pathogens/ariba/tmp.test_make_vcf_and_read_depths_files.vcf
+#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT /home/ubuntu/sanger-pathogens/ariba/ariba/tests/data/samtools_variants_test_make_vcf_and_read_depths_files.bam
+16__cat_2_M35190.scaffold.1 93 . T A 222 PASS DP=123;AD=65,58;VDB=0.00672125;SGB=-0.693147;RPB=0.359049;MQB=0.976548;MQSB=1.38527e-20;BQB=0.957743;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=35,30,25,33;MQ=41 GT:PL 0/1:255,0,255
+16__cat_2_M35190.scaffold.1 180 . A T 222 PASS DP=86;AD=41,45;VDB=0.102578;SGB=-0.693147;RPB=0.885638;MQB=0.976909;MQSB=7.02391e-09;BQB=1;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=17,24,19,26;MQ=27 GT:PL 0/1:255,0,255
+16__cat_2_M35190.scaffold.1 264 . G C 119 PASS DP=97;AD=53,44;VDB=0.0562559;SGB=-0.693146;RPB=0.389539;MQB=0.007282;MQSB=0.00207736;BQB=0.950442;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=20,33,23,21;MQ=23 GT:PL 0/1:152,0,244
+16__cat_2_M35190.scaffold.6 94 . T G 171 PASS DP=99;AD=56,43;VDB=0.0786476;SGB=-0.693146;RPB=0.837015;MQB=0.737682;MQSB=1.09416e-07;BQB=1;MQ0F=0.262626;ICB=1;HOB=0.5;AC=1;AN=2;DP4=28,28,22,21;MQ=21 GT:PL 0/1:204,0,222
diff --git a/ariba/tests/data/summary_sample_test_column_names_tuples.tsv b/ariba/tests/data/summary_sample_test_column_names_tuples_and_het_snps.tsv
similarity index 90%
rename from ariba/tests/data/summary_sample_test_column_names_tuples.tsv
rename to ariba/tests/data/summary_sample_test_column_names_tuples_and_het_snps.tsv
index 23e7466..5e12e4a 100644
--- a/ariba/tests/data/summary_sample_test_column_names_tuples.tsv
+++ b/ariba/tests/data/summary_sample_test_column_names_tuples_and_het_snps.tsv
@@ -1,5 +1,5 @@
#ref_name gene var_only flag reads cluster ref_len ref_base_assembled pc_ident ctg ctg_len ctg_cov known_var var_type var_seq_type known_var_change has_known_var ref_ctg_change ref_ctg_effect ref_start ref_end ref_nt ctg_start ctg_end ctg_nt smtls_total_depth smtls_alt_nt smtls_alt_depth var_description free_text
-noncoding1 0 0 19 78 cluster.n 120 120 98.33 noncoding1.scaffold.1 279 35.4 1 SNP n A14T 1 A14T SNP 13 13 A 84 84 T 17 . 17 noncoding1:n:A14T:.:ref has wild type, reads have variant so should report generic description of noncoding1
+noncoding1 0 0 19 78 cluster.n 120 120 98.33 noncoding1.scaffold.1 279 35.4 1 SNP n A14T 1 A14T SNP 13 13 A 84 84 T 50 G 40,10 noncoding1:n:A14T:.:ref has wild type, reads have variant so should report generic description of noncoding1
noncoding1 0 0 19 78 cluster.n 120 120 98.33 noncoding1.scaffold.1 279 35.4 0 SNP . . . G15T SNP 15 15 G 85 85 T 17 . 17 . generic description of noncoding1
noncoding1 0 0 19 78 cluster.n 120 120 98.33 noncoding1.scaffold.1 279 35.4 1 SNP n A6G 1 . . 6 6 G 77 77 G 18 . 18 noncoding1:n:A6G:id2:variant in ref and reads so should report generic description of noncoding1
noncoding1 0 0 19 78 cluster.n 120 120 98.33 noncoding2.scaffold.1 279 35.4 . . . . . . . . . . . . . . . . . generic description of noncoding2
diff --git a/ariba/tests/data/summary_test_gather_output_rows.in.2.tsv b/ariba/tests/data/summary_test_gather_output_rows.in.2.tsv
index 4d7339b..6507d5f 100644
--- a/ariba/tests/data/summary_test_gather_output_rows.in.2.tsv
+++ b/ariba/tests/data/summary_test_gather_output_rows.in.2.tsv
@@ -1,5 +1,5 @@
#ref_name gene var_only flag reads cluster ref_len ref_base_assembled pc_ident ctg ctg_len ctg_cov known_var var_type var_seq_type known_var_change has_known_var ref_ctg_change ref_ctg_effect ref_start ref_end ref_nt ctg_start ctg_end ctg_nt smtls_total_depth smtls_alt_nt smtls_alt_depth var_description free_text
-noncoding1 0 0 19 78 noncoding1 120 120 98.33 noncoding1.scaffold.1 279 50.1 1 SNP n A14T 1 A14T SNP 13 13 A 84 84 T 17 . 17 noncoding1:n:A14T:id1:ref has wild type, reads have variant so should report generic description of noncoding1
+noncoding1 0 0 19 78 noncoding1 120 120 98.33 noncoding1.scaffold.1 279 50.1 1 SNP n A14T 1 A14T SNP 13 13 A 84 84 T 50 G 40,10 noncoding1:n:A14T:id1:ref has wild type, reads have variant so should report generic description of noncoding1
noncoding1 0 0 19 78 noncoding1 120 120 98.33 noncoding1.scaffold.1 279 50.1 1 SNP n A6G 1 . . 6 6 G 77 77 G 18 . 18 noncoding1:n:A6G:id3:variant in ref and reads so should report generic description of noncoding1
presence_absence1 1 0 27 88 presence_absence1 96 96 98.96 presence_absence1.scaffold.1 267 51.1 0 SNP p A10V . A10V NONSYN 28 28 C 113 113 T 29 . 29 presence_absence1:p:A10V:.:Ref has wild, reads have variant so report Generic description of presence_absence1
variants_only1 1 1 64 12 variants_only1 90 . . . . . . . . . . . . . . . . . . . . . . .
diff --git a/ariba/tests/data/summary_test_gather_output_rows.in.2.tsv b/ariba/tests/data/summary_test_get_all_het_snps.1.tsv
similarity index 61%
copy from ariba/tests/data/summary_test_gather_output_rows.in.2.tsv
copy to ariba/tests/data/summary_test_get_all_het_snps.1.tsv
index 4d7339b..d1f5f70 100644
--- a/ariba/tests/data/summary_test_gather_output_rows.in.2.tsv
+++ b/ariba/tests/data/summary_test_get_all_het_snps.1.tsv
@@ -1,5 +1,3 @@
#ref_name gene var_only flag reads cluster ref_len ref_base_assembled pc_ident ctg ctg_len ctg_cov known_var var_type var_seq_type known_var_change has_known_var ref_ctg_change ref_ctg_effect ref_start ref_end ref_nt ctg_start ctg_end ctg_nt smtls_total_depth smtls_alt_nt smtls_alt_depth var_description free_text
-noncoding1 0 0 19 78 noncoding1 120 120 98.33 noncoding1.scaffold.1 279 50.1 1 SNP n A14T 1 A14T SNP 13 13 A 84 84 T 17 . 17 noncoding1:n:A14T:id1:ref has wild type, reads have variant so should report generic description of noncoding1
-noncoding1 0 0 19 78 noncoding1 120 120 98.33 noncoding1.scaffold.1 279 50.1 1 SNP n A6G 1 . . 6 6 G 77 77 G 18 . 18 noncoding1:n:A6G:id3:variant in ref and reads so should report generic description of noncoding1
-presence_absence1 1 0 27 88 presence_absence1 96 96 98.96 presence_absence1.scaffold.1 267 51.1 0 SNP p A10V . A10V NONSYN 28 28 C 113 113 T 29 . 29 presence_absence1:p:A10V:.:Ref has wild, reads have variant so report Generic description of presence_absence1
-variants_only1 1 1 64 12 variants_only1 90 . . . . . . . . . . . . . . . . . . . . . . .
+noncoding1 0 0 19 78 noncoding1 120 120 98.33 noncoding1.scaffold.1 279 10.0 1 SNP n A14T 1 A14T SNP 13 13 A 84 84 T 17 . 17 noncoding1:n:A14T:id1:ref has wild type, reads have variant so should report generic description of noncoding1
+presence_absence1 1 0 27 88 presence_absence1 96 96 98.96 presence_absence1.scaffold.1 267 20.1 0 SNP p A10V . A10V NONSYN 28 28 C 113 113 T 29 . 29 presence_absence1:p:A10V:.:Ref has wild, reads have variant so report Generic description of presence_absence1
diff --git a/ariba/tests/data/summary_test_gather_output_rows.in.2.tsv b/ariba/tests/data/summary_test_get_all_het_snps.2.tsv
similarity index 84%
copy from ariba/tests/data/summary_test_gather_output_rows.in.2.tsv
copy to ariba/tests/data/summary_test_get_all_het_snps.2.tsv
index 4d7339b..6507d5f 100644
--- a/ariba/tests/data/summary_test_gather_output_rows.in.2.tsv
+++ b/ariba/tests/data/summary_test_get_all_het_snps.2.tsv
@@ -1,5 +1,5 @@
#ref_name gene var_only flag reads cluster ref_len ref_base_assembled pc_ident ctg ctg_len ctg_cov known_var var_type var_seq_type known_var_change has_known_var ref_ctg_change ref_ctg_effect ref_start ref_end ref_nt ctg_start ctg_end ctg_nt smtls_total_depth smtls_alt_nt smtls_alt_depth var_description free_text
-noncoding1 0 0 19 78 noncoding1 120 120 98.33 noncoding1.scaffold.1 279 50.1 1 SNP n A14T 1 A14T SNP 13 13 A 84 84 T 17 . 17 noncoding1:n:A14T:id1:ref has wild type, reads have variant so should report generic description of noncoding1
+noncoding1 0 0 19 78 noncoding1 120 120 98.33 noncoding1.scaffold.1 279 50.1 1 SNP n A14T 1 A14T SNP 13 13 A 84 84 T 50 G 40,10 noncoding1:n:A14T:id1:ref has wild type, reads have variant so should report generic description of noncoding1
noncoding1 0 0 19 78 noncoding1 120 120 98.33 noncoding1.scaffold.1 279 50.1 1 SNP n A6G 1 . . 6 6 G 77 77 G 18 . 18 noncoding1:n:A6G:id3:variant in ref and reads so should report generic description of noncoding1
presence_absence1 1 0 27 88 presence_absence1 96 96 98.96 presence_absence1.scaffold.1 267 51.1 0 SNP p A10V . A10V NONSYN 28 28 C 113 113 T 29 . 29 presence_absence1:p:A10V:.:Ref has wild, reads have variant so report Generic description of presence_absence1
variants_only1 1 1 64 12 variants_only1 90 . . . . . . . . . . . . . . . . . . . . . . .
diff --git a/ariba/tests/ref_preparer_test.py b/ariba/tests/ref_preparer_test.py
index e48a3af..604395e 100644
--- a/ariba/tests/ref_preparer_test.py
+++ b/ariba/tests/ref_preparer_test.py
@@ -22,6 +22,15 @@ class TestRefPreparer(unittest.TestCase):
'7': {'prefix1.fgh', 'prefix1.ijk', 'something_else_again.abc'},
'8': {'xyz.1', 'xyz.2', 'abcdefgh'},
'9': {'a.foo', 'a.bar'},
+ '10': {'abc_1.1'},
+ '11': {'abc.2'},
+ '12': {'abc.3'},
+ '13': {'abc.4'},
+ '14': {'def.1'},
+ '15': {'def_1.2'},
+ '16': {'def_2.3'},
+ '17': {'def.4'},
+ '18': {'def.5'},
}
expected = {
@@ -35,9 +44,17 @@ class TestRefPreparer(unittest.TestCase):
'prefix1+_2': {'prefix1.fgh', 'prefix1.ijk', 'something_else_again.abc'},
'xyz+': {'xyz.1', 'xyz.2', 'abcdefgh'},
'cluster_3': {'a.foo', 'a.bar'},
+ 'abc_1': {'abc_1.1'},
+ 'abc_2': {'abc.2'},
+ 'abc_3': {'abc.3'},
+ 'abc_4': {'abc.4'},
+ 'def_1': {'def_1.2'},
+ 'def_2': {'def_2.3'},
+ 'def_3': {'def.1'},
+ 'def_4': {'def.4'},
+ 'def_5': {'def.5'},
}
- self.maxDiff = None
got = ref_preparer.RefPreparer._rename_clusters(clusters_in)
self.assertEqual(expected, got)
diff --git a/ariba/tests/report_filter_test.py b/ariba/tests/report_filter_test.py
index a598a15..f9d4bfc 100644
--- a/ariba/tests/report_filter_test.py
+++ b/ariba/tests/report_filter_test.py
@@ -272,14 +272,16 @@ class TestReportFilter(unittest.TestCase):
ref_2_dict['ref_base_assembled'] = 10
ref_2_dict['has_known_var'] = '0'
ref_2_dict['flag'] = flag.Flag(27)
+ ref_2_dict['var_type'] = '.'
rf.report = {
'ref1': {
'ref1.scaff1': [
- {'flag': flag.Flag(27), 'pc_ident': 91.0, 'ref_base_assembled': 9, 'known_var': '1', 'has_known_var': '1'},
- {'flag': flag.Flag(27), 'pc_ident': 89.0, 'ref_base_assembled': 10, 'known_var': '1', 'has_known_var': '1'},
- {'flag': flag.Flag(27), 'pc_ident': 90.0, 'ref_base_assembled': 11, 'known_var': '1', 'has_known_var': '0'},
- {'flag': flag.Flag(27), 'pc_ident': 90.0, 'ref_base_assembled': 11, 'known_var': '1', 'has_known_var': '1'},
+ {'flag': flag.Flag(27), 'pc_ident': 91.0, 'ref_base_assembled': 9, 'known_var': '1', 'has_known_var': '1', 'var_type': 'SNP'},
+ {'flag': flag.Flag(27), 'pc_ident': 91.5, 'ref_base_assembled': 9, 'known_var': '1', 'has_known_var': '1', 'var_type': 'HET'},
+ {'flag': flag.Flag(27), 'pc_ident': 89.0, 'ref_base_assembled': 10, 'known_var': '1', 'has_known_var': '1', 'var_type': 'SNP'},
+ {'flag': flag.Flag(27), 'pc_ident': 90.0, 'ref_base_assembled': 11, 'known_var': '1', 'has_known_var': '0', 'var_type': 'SNP'},
+ {'flag': flag.Flag(27), 'pc_ident': 90.0, 'ref_base_assembled': 11, 'known_var': '1', 'has_known_var': '1', 'var_type': 'SNP'},
]
},
'ref2': {
@@ -289,12 +291,12 @@ class TestReportFilter(unittest.TestCase):
},
'ref3': {
'ref3.scaff1': [
- {'flag': flag.Flag(27), 'pc_ident': 84.0, 'ref_base_assembled': 10, 'known_var': '1', 'has_known_var': '0'},
+ {'flag': flag.Flag(27), 'pc_ident': 84.0, 'ref_base_assembled': 10, 'known_var': '1', 'has_known_var': '0', 'var_type': 'SNP'},
]
},
'ref4': {
'ref4.scaff1': [
- {'flag': flag.Flag(64), 'pc_ident': '.', 'ref_base_assembled': '.', 'known_var': '.', 'has_known_var': '.'},
+ {'flag': flag.Flag(64), 'pc_ident': '.', 'ref_base_assembled': '.', 'known_var': '.', 'has_known_var': '.', 'var_type': '.'},
]
}
}
@@ -302,7 +304,7 @@ class TestReportFilter(unittest.TestCase):
expected = {
'ref1': {
'ref1.scaff1': [
- {'flag': flag.Flag(27), 'pc_ident': 90.0, 'ref_base_assembled': 11, 'known_var': '1', 'has_known_var': '1'},
+ {'flag': flag.Flag(27), 'pc_ident': 90.0, 'ref_base_assembled': 11, 'known_var': '1', 'has_known_var': '1', 'var_type': 'SNP'},
]
},
'ref2': {
diff --git a/ariba/tests/samtools_variants_test.py b/ariba/tests/samtools_variants_test.py
index ba82316..873e840 100644
--- a/ariba/tests/samtools_variants_test.py
+++ b/ariba/tests/samtools_variants_test.py
@@ -140,8 +140,9 @@ class TestSamtoolsVariants(unittest.TestCase):
'scaff1': [pyfastaq.intervals.Interval(0, 41)]
}
+ expected = {'scaff1': {22}}
got = samtools_variants.SamtoolsVariants.variants_in_coords(nucmer_hits, vcf_file)
- self.assertEqual(1, got)
+ self.assertEqual(expected, got)
def test_get_depths_at_position(self):
diff --git a/ariba/tests/summary_cluster_test.py b/ariba/tests/summary_cluster_test.py
index e3f2b26..6220dcf 100644
--- a/ariba/tests/summary_cluster_test.py
+++ b/ariba/tests/summary_cluster_test.py
@@ -296,6 +296,32 @@ class TestSummaryCluster(unittest.TestCase):
self.assertEqual('NA', cluster._to_cluster_summary_has_nonsynonymous('no'))
+ def test_get_known_noncoding_het_snp(self):
+ '''Test _get_known_noncoding_het_snp'''
+ d = {'gene': '1'}
+ self.assertEqual(None, summary_cluster.SummaryCluster._get_known_noncoding_het_snp(d))
+ d['gene'] = '0'
+ d['known_var'] = '0'
+ self.assertEqual(None, summary_cluster.SummaryCluster._get_known_noncoding_het_snp(d))
+
+ d['known_var'] = '1'
+ d['ref_ctg_effect'] = 'not_a_snp'
+ self.assertEqual(None, summary_cluster.SummaryCluster._get_known_noncoding_het_snp(d))
+
+ d['ref_ctg_effect'] = 'SNP'
+ d['smtls_alt_nt'] = '.'
+ self.assertEqual(None, summary_cluster.SummaryCluster._get_known_noncoding_het_snp(d))
+
+ d['smtls_alt_nt'] = 'A;G;T'
+ self.assertEqual(None, summary_cluster.SummaryCluster._get_known_noncoding_het_snp(d))
+
+ d['known_var_change'] = 'A42T'
+ d['ctg_nt'] = 'A'
+ d['smtls_alt_nt'] = 'T'
+ d['smtls_alt_depth'] = '52,48'
+ self.assertEqual(('A42T', 48.0), summary_cluster.SummaryCluster._get_known_noncoding_het_snp(d))
+
+
def test_get_nonsynonymous_var(self):
'''Test _get_nonsynonymous_var'''
d = {
@@ -423,3 +449,21 @@ class TestSummaryCluster(unittest.TestCase):
got = cluster.non_synon_variants()
expected = {('ref1', 'A14T', 'grouped', 'id1')}
self.assertEqual(expected, got)
+
+
+ def test_known_noncoding_het_snps(self):
+ '''test known_noncoding_het_snps'''
+ lines = [
+ 'ref1\t0\t0\t531\t78\tcluster1\t120\t100\t98.33\tctg_name\t279\t24.4\t1\tSNP\tn\tA14T\t1\tA14T\tSNP\t13\t13\tA\t84\t84\tT\t17\t.\t17\tnon_coding1:n:A14T:id1:foo_bar\tspam eggs',
+ 'ref1\t0\t0\t531\t78\tcluster1\t120\t100\t98.33\tctg_name\t279\t24.4\t1\tSNP\tn\tA42T\t1\tA42T\tSNP\t42\t42\tA\t84\t84\tT\t40\tA\t10,30\tnon_coding1:n:A14T:id1:foo_bar\tspam eggs',
+ 'ref1\t0\t0\t531\t78\tcluster1\t120\t100\t98.33\tctg_name\t279\t24.4\t1\tSNP\tn\tA62T\t1\tA62T\tSNP\t62\t62\tA\t84\t84\tA\t40\tT\t10,30\tnon_coding1:n:A14T:id1:foo_bar\tspam eggs',
+ 'ref1\t0\t0\t531\t78\tcluster1\t120\t100\t98.33\tctg_name\t279\t24.4\t1\tSNP\tn\tA82T\t1\tA82T\tSNP\t82\t82\tA\t84\t84\tA\t100\tT,G\t10,40,50\tnon_coding1:n:A14T:id1:foo_bar\tspam eggs'
+ ]
+
+ cluster = summary_cluster.SummaryCluster()
+ for line in lines:
+ cluster.add_data_dict(summary_cluster.SummaryCluster.line2dict(line))
+ got = cluster.known_noncoding_het_snps()
+ expected = {'A42T': 25.0, 'A62T': 75.0, 'A82T': 40.0}
+ self.assertEqual(expected, got)
+
diff --git a/ariba/tests/summary_sample_test.py b/ariba/tests/summary_sample_test.py
index d71cb56..091e8c0 100644
--- a/ariba/tests/summary_sample_test.py
+++ b/ariba/tests/summary_sample_test.py
@@ -84,13 +84,13 @@ class TestSummarySample(unittest.TestCase):
self.assertEqual(expected, got)
- def test_variant_column_names_tuples(self):
- '''Test _variant_column_names_tuples'''
- infile = os.path.join(data_dir, 'summary_sample_test_column_names_tuples.tsv')
+ def test_variant_column_names_tuples_and_het_snps(self):
+ '''Test _variant_column_names_tuples_and_het_snps'''
+ infile = os.path.join(data_dir, 'summary_sample_test_column_names_tuples_and_het_snps.tsv')
sample_summary = summary_sample.SummarySample(infile)
sample_summary.clusters = sample_summary._load_file(infile, 90)
sample_summary.column_summary_data = sample_summary._column_summary_data()
- expected = {
+ expected_column_names = {
'cluster.v': {('variants_only1', 'S5T', 'ungrouped', None)},
'cluster.n': {
('noncoding1', 'A6G', 'grouped', 'id2'),
@@ -99,6 +99,13 @@ class TestSummarySample(unittest.TestCase):
},
'cluster.p': {('presence_absence1', 'A10V', 'grouped', 'id3')}
}
- got = sample_summary._variant_column_names_tuples()
- self.assertEqual(expected, got)
+ got_column_names, got_het_snps = sample_summary._variant_column_names_tuples_and_het_snps()
+ self.assertEqual(expected_column_names, got_column_names)
+
+ expected_het_snps = {
+ 'cluster.v': {},
+ 'cluster.n': {'A14T': 80.0},
+ 'cluster.p': {},
+ }
+ self.assertEqual(expected_het_snps, got_het_snps)
diff --git a/ariba/tests/summary_test.py b/ariba/tests/summary_test.py
index 25bf6a5..6b615ee 100644
--- a/ariba/tests/summary_test.py
+++ b/ariba/tests/summary_test.py
@@ -109,6 +109,16 @@ class TestSummary(unittest.TestCase):
self.assertEqual(expected, got)
+ def test_get_all_het_snps(self):
+ '''test _get_all_het_snps'''
+ file1 = os.path.join(data_dir, 'summary_test_get_all_het_snps.1.tsv')
+ file2 = os.path.join(data_dir, 'summary_test_get_all_het_snps.2.tsv')
+ samples = summary.Summary._load_input_files([file1, file2], 90)
+ got = summary.Summary._get_all_het_snps(samples)
+ expected = {('noncoding1', 'A14T')}
+ self.assertEqual(expected, got)
+
+
def test_get_all_var_groups(self):
'''test _get_all_var_groups'''
file1 = os.path.join(data_dir, 'summary_test_get_all_var_groups.1.tsv')
@@ -204,6 +214,7 @@ class TestSummary(unittest.TestCase):
expected[infiles[0]]['noncoding1']['noncoding1.A6G'] = 'no'
expected[infiles[1]]['noncoding1']['noncoding1.A14T'] = 'yes'
expected[infiles[1]]['noncoding1']['noncoding1.A6G'] = 'yes'
+ self.maxDiff = None
got = s._gather_output_rows()
self.assertEqual(expected, got)
@@ -213,6 +224,13 @@ class TestSummary(unittest.TestCase):
got = s._gather_output_rows()
self.assertEqual(expected, got)
+ s.show_known_het = True
+ expected[infiles[0]]['noncoding1']['noncoding1.A14T.%'] = 'NA'
+ expected[infiles[1]]['noncoding1']['noncoding1.A14T'] = 'het'
+ expected[infiles[1]]['noncoding1']['noncoding1.A14T.%'] = 80.0
+ got = s._gather_output_rows()
+ self.assertEqual(expected, got)
+
for filename in expected:
del expected[filename]['noncoding1']['vgroup.id1']
del expected[filename]['noncoding1']['vgroup.id3']
@@ -222,6 +240,7 @@ class TestSummary(unittest.TestCase):
s = summary.Summary('out', filenames=infiles, cluster_cols='assembled,match,pct_id,known_var,novel_var', variant_cols='ungrouped,grouped,novel')
s.samples = summary.Summary._load_input_files(infiles, 90)
s.include_all_variant_columns = True
+ s.show_known_het = True
got = s._gather_output_rows()
self.assertEqual(expected, got)
diff --git a/scripts/ariba b/scripts/ariba
index 64a8050..5140aed 100755
--- a/scripts/ariba
+++ b/scripts/ariba
@@ -42,7 +42,7 @@ subparser_flag.set_defaults(func=ariba.tasks.flag.run)
#---------------------------- getref ------------------------------------
-allowed_dbs = ['argannot', 'card', 'resfinder','vfdb']
+allowed_dbs = ['argannot', 'card', 'plasmidfinder', 'resfinder','vfdb']
subparser_getref = subparsers.add_parser(
'getref',
help='Download reference data',
@@ -50,7 +50,7 @@ subparser_getref = subparsers.add_parser(
description='Download reference data from one of a few supported public resources',
)
subparser_getref.add_argument('--genetic_code', type=int, help='Number of genetic code to use. Currently supported 1,4,11 [%(default)s]', choices=[1,4,11], default=11, metavar='INT')
-subparser_getref.add_argument('db', help='Database to download. Must be one of: ' + ' '.join(allowed_dbs), choices=allowed_dbs)
+subparser_getref.add_argument('db', help='Database to download. Must be one of: ' + ' '.join(allowed_dbs), choices=allowed_dbs, metavar="DB name")
subparser_getref.add_argument('outprefix', help='Prefix of output filenames')
subparser_getref.set_defaults(func=ariba.tasks.getref.run)
@@ -162,6 +162,7 @@ subparser_summary.add_argument('-f', '--fofn', help='File of filenames of ariba
subparser_summary.add_argument('--preset', choices=summary_presets, help='Shorthand for setting --cluster_cols,--col_filter,--row_filter,--known_vars,--novel_vars. Using this overrides those options', metavar='|'.join(summary_presets))
subparser_summary.add_argument('--cluster_cols', help='Comma separated list of cluster columns to include. Choose from: assembled, match, ref_seq, pct_id, known_var, novel_var [%(default)s]', default='match', metavar='col1,col2,...')
subparser_summary.add_argument('--col_filter', choices=['y', 'n'], default='y', help='Choose whether columns where all values are "no" or "NA" are removed [%(default)s]', metavar='y|n')
+subparser_summary.add_argument('--het', action='store_true', help='For known noncoding SNPs, report if they are heterozygous or not, and the percent of reads supporting the variant type')
subparser_summary.add_argument('--row_filter', choices=['y', 'n'], default='y', help='Choose whether rows where all values are "no" or "NA" are removed [%(default)s]', metavar='y|n')
subparser_summary.add_argument('--var_cols', help='Comma separated list of variant columns to include. Choose from: groups, grouped, ungrouped, novel [none by default]', metavar='col1,col2,...', default='')
subparser_summary.add_argument('--min_id', type=float, help='Minimum percent identity cutoff to count as assembled [%(default)s]', default=90, metavar='FLOAT')
diff --git a/setup.py b/setup.py
index c2bbbb1..77ba935 100644
--- a/setup.py
+++ b/setup.py
@@ -51,7 +51,7 @@ fermilite_mod = Extension(
setup(
ext_modules=[minimap_mod, fermilite_mod],
name='ariba',
- version='2.0.0',
+ version='2.1.0',
description='ARIBA: Antibiotic Resistance Identification By Assembly',
packages = find_packages(),
package_data={'ariba': ['test_run_data/*']},
--
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