# HG changeset patch
# User greg
# Date 1700667254 0
# Node ID e958c5f7c9d15fa897ea12259b6a9e54d45578c1

Uploaded

diff -r 000000000000 -r e958c5f7c9d1 .shed.yml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/.shed.yml	Wed Nov 22 15:34:14 2023 +0000
@@ -0,0 +1,9 @@
+name: cfsan_snp_pipeline_merge_vcfs
+owner: greg
+description: Merge the consensus vcf files from all samples into a single multi-vcf file.
+long_description: Merge the consensus vcf files from all samples into a single multi-vcf file
+categories: 
+- Metagenomics
+remote_repository_url: https://github.com/gregvonkuster/galaxy_tools/tree/master/snp_pipeline/cfsan_snp_pipeline_merge_vcfs
+homepage_url: https://github.com/gregvonkuster/galaxy_tools
+type: unrestricted
diff -r 000000000000 -r e958c5f7c9d1 cfsan_snp_pipeline_merge_vcfs.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cfsan_snp_pipeline_merge_vcfs.xml	Wed Nov 22 15:34:14 2023 +0000
@@ -0,0 +1,56 @@
+<tool id="cfsan_snp_pipeline_merge_vcfs" name="CFSAN SNP Pipeline: merge vcfs" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>from multiple samples</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+python '$__tool_directory__/snp_wind.py' ./
+#if str($input_type_cond.input_type) == 'single':
+    -n '$input_vcf.element_identifier'
+    -f '$input_vcf'
+#else:
+    #for $input_vcf in $input_vcf_collection
+        -n '$input_vcf.element_identifier'
+        -f '$input_vcf'
+    #end for
+#end if
+-p 'consensus.vcf' > ./file
+&& cfsan_snp_pipeline merge_vcfs ./file
+    ]]></command>
+    <inputs>
+        <expand macro="input_type_cond"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="vcf"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_type" value="collection"/>
+            <param name="input_vcf_collection">
+                <collection type="list">
+                    <element name="sample1" value="samples/sample1/consensus.vcf" ftype="vcf"/>
+                    <element name="sample2" value="samples/sample2/consensus.vcf" ftype="vcf"/>
+                    <element name="sample3" value="samples/sample3/consensus.vcf" ftype="vcf"/>
+                    <element name="sample4" value="samples/sample4/consensus.vcf" ftype="vcf"/>
+                </collection>
+            </param>
+            <output name="output" ftype="vcf">
+                <assert_contents>
+                    <has_size value="0" delta="100"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+Merges the consensus vcf files from all samples into a single multi-vcf file.
+
+**More information**
+
+CFSAN SNP Pipeline `merge sites documentation <https://snp-pipeline.readthedocs.io/en/latest/cmd_ref.html#merge-sites>`_
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
+
diff -r 000000000000 -r e958c5f7c9d1 macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Wed Nov 22 15:34:14 2023 +0000
@@ -0,0 +1,33 @@
+<macros>
+    <token name="@TOOL_VERSION@">2.2.1</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">21.01</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="1.18">bcftools</requirement>
+            <requirement type="package" version="3.11.5">python</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">snp-pipeline</requirement>
+            <requirement type="package" version="1.11">tabix</requirement>
+        </requirements>
+    </xml>
+    <xml name="input_type_cond">
+        <conditional name="input_type_cond">
+            <param name="input_type" type="select" label="Choose the category for the files to be analyzed">
+                <option value="single" selected="true">Single files</option>
+                <option value="collection">Collection of files</option>
+            </param>
+            <when value="single">
+                <param name="input_vcf" type="data" format="vcf" label="VCF file"/>
+            </when>
+            <when value="collection">
+                <param name="input_vcf_collection" type="data_collection" format="vcf" collection_type="list" label="Collection of VCF files"/>
+            </when>
+        </conditional>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.7717/peerj-cs.20</citation>
+        </citations>
+    </xml>
+</macros>
+
diff -r 000000000000 -r e958c5f7c9d1 snp_wind.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/snp_wind.py	Wed Nov 22 15:34:14 2023 +0000
@@ -0,0 +1,42 @@
+#!/usr/bin/env python
+
+import argparse
+import os
+from os.path import join as j
+from itertools import zip_longest
+
+
+def setup(base_dir, names=[], fwds=[], revs=[], extension='vcf', pattern="{name}.{orient}.{ext}"):
+    if fwds and revs and names and len(fwds) != len(revs) != len(names):
+        raise ValueError('number of forward reads must equal number of reverse reads and names')
+    elif len(fwds) != len(names) or not fwds or not names:
+        raise ValueError('number of forward reads must equal number of names')
+    with open(j(base_dir, 'snp-unwind.sh'), 'w') as unwind:
+        for i, (name, fwd, rev) in enumerate(zip_longest(names, fwds, revs)):
+            dir = j(base_dir, str(i))
+            sample_dir = j(dir, name)
+            os.makedirs(sample_dir)
+            target_f = j(sample_dir, pattern.format(name=name, orient=1, ext=extension))
+            if rev:
+                target_r = j(sample_dir, pattern.format(name=name, orient=2, ext=extension))
+            os.symlink(fwd, target_f)
+            if rev:
+                os.symlink(rev, target_r)
+            print(sample_dir)
+            if rev:
+                unwind.write('unlink {}\n'.format(target_r))
+            unwind.write('unlink {}\n'.format(target_f))
+            unwind.write('rmdir {}\n'.format(sample_dir))
+        unwind.write('rmdir {}\n'.format(dir))
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(description="set up vcf symlink directories for snp-pipeline")
+    parser.add_argument('base_dir')
+    parser.add_argument('-n', dest='names', type=str, action='append', default=[])
+    parser.add_argument('-f', dest='fwds', type=str, action='append', default=[])
+    parser.add_argument('-r', dest='revs', type=str, action='append', default=[])
+    parser.add_argument('-e', dest='extension', default='vcf')
+    parser.add_argument('-p', dest='pattern', default='{name}.{orient}.{ext}')
+    params = parser.parse_args()
+    setup(**vars(params))
diff -r 000000000000 -r e958c5f7c9d1 test-data/output.vcf
diff -r 000000000000 -r e958c5f7c9d1 test-data/output2.vcf
diff -r 000000000000 -r e958c5f7c9d1 test-data/samples/sample1/consensus.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/samples/sample1/consensus.vcf	Wed Nov 22 15:34:14 2023 +0000
@@ -0,0 +1,186 @@
+##fileformat=VCFv4.1
+##fileDate=20180103
+##source=CFSAN SNP-Pipeline 1.0.1
+##reference=lambda_virus.fasta
+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=SDP,Number=1,Type=Integer,Description="Raw read depth">
+##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)">
+##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Depth of variant-supporting bases (reads2)">
+##FORMAT=<ID=RDF,Number=1,Type=Integer,Description="Depth of reference-supporting bases on forward strand (reads1plus)">
+##FORMAT=<ID=RDR,Number=1,Type=Integer,Description="Depth of reference-supporting bases on reverse strand (reads1minus)">
+##FORMAT=<ID=ADF,Number=1,Type=Integer,Description="Depth of variant-supporting bases on forward strand (reads2plus)">
+##FORMAT=<ID=ADR,Number=1,Type=Integer,Description="Depth of variant-supporting bases on reverse strand (reads2minus)">
+##FORMAT=<ID=FT,Number=1,Type=String,Description="Genotype filters using the same codes as the FILTER data element">
+##FILTER=<ID=PASS,Description="All filters passed">
+##FILTER=<ID=RawDpth,Description="No read depth">
+##FILTER=<ID=VarFreq60,Description="Variant base frequency below 0.60">
+##FILTER=<ID=StrDpth0,Description="Less than 0 variant-supporing reads on at least one strand">
+##FILTER=<ID=StrBias0,Description="Fraction of variant supporting reads below 0.00 on one strand">
+##FILTER=<ID=Region,Description="Position is in dense region of snps or near the end of the contig.">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sample1
+gi|9626243|ref|NC_001416.1|	403	.	G	A	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:27:0:27:0:0:13:14:PASS
+gi|9626243|ref|NC_001416.1|	550	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:22:21:1:13:8:0:1:PASS
+gi|9626243|ref|NC_001416.1|	586	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:18:18:0:12:6:0:0:PASS
+gi|9626243|ref|NC_001416.1|	753	.	G	A	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:25:0:24:0:0:16:8:PASS
+gi|9626243|ref|NC_001416.1|	1019	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:25:25:0:10:15:0:0:PASS
+gi|9626243|ref|NC_001416.1|	1079	.	T	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:26:0:25:0:0:9:16:PASS
+gi|9626243|ref|NC_001416.1|	1540	.	A	G	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:24:0:24:0:0:13:11:PASS
+gi|9626243|ref|NC_001416.1|	1620	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:31:31:0:14:17:0:0:PASS
+gi|9626243|ref|NC_001416.1|	1650	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:31:31:0:14:17:0:0:PASS
+gi|9626243|ref|NC_001416.1|	1788	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:24:24:0:10:14:0:0:PASS
+gi|9626243|ref|NC_001416.1|	1804	.	G	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:23:0:23:0:0:11:12:PASS
+gi|9626243|ref|NC_001416.1|	2123	.	G	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:24:0:24:0:0:11:13:PASS
+gi|9626243|ref|NC_001416.1|	2439	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:23:23:0:13:10:0:0:PASS
+gi|9626243|ref|NC_001416.1|	2452	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:19:18:1:9:9:0:1:PASS
+gi|9626243|ref|NC_001416.1|	2599	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:28:28:0:16:12:0:0:PASS
+gi|9626243|ref|NC_001416.1|	3063	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:26:26:0:16:10:0:0:PASS
+gi|9626243|ref|NC_001416.1|	3351	.	C	G	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:24:0:24:0:0:10:14:PASS
+gi|9626243|ref|NC_001416.1|	3648	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:24:24:0:13:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	3656	.	T	G	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:25:0:25:0:0:13:12:PASS
+gi|9626243|ref|NC_001416.1|	3678	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:17:17:0:7:10:0:0:PASS
+gi|9626243|ref|NC_001416.1|	4977	.	G	A	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:25:0:25:0:0:12:13:PASS
+gi|9626243|ref|NC_001416.1|	5142	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:24:21:3:11:10:3:0:PASS
+gi|9626243|ref|NC_001416.1|	5336	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:23:23:0:12:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	5462	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:25:25:0:14:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	5482	.	G	A	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:18:0:18:0:0:9:9:PASS
+gi|9626243|ref|NC_001416.1|	5516	.	T	A	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:16:0:16:0:0:9:7:PASS
+gi|9626243|ref|NC_001416.1|	5800	.	G	A	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:19:0:19:0:0:5:14:PASS
+gi|9626243|ref|NC_001416.1|	5818	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:25:25:0:10:15:0:0:PASS
+gi|9626243|ref|NC_001416.1|	5994	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:15:15:0:6:9:0:0:PASS
+gi|9626243|ref|NC_001416.1|	6296	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:19:19:0:11:8:0:0:PASS
+gi|9626243|ref|NC_001416.1|	6535	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:26:26:0:15:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	6824	.	A	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:19:0:19:0:0:11:8:PASS
+gi|9626243|ref|NC_001416.1|	7424	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:20:19:1:8:11:0:1:PASS
+gi|9626243|ref|NC_001416.1|	7668	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:27:26:1:17:9:0:1:PASS
+gi|9626243|ref|NC_001416.1|	7897	.	G	A	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:26:0:26:0:0:13:13:PASS
+gi|9626243|ref|NC_001416.1|	8420	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:31:31:0:19:12:0:0:PASS
+gi|9626243|ref|NC_001416.1|	8938	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:22:22:0:13:9:0:0:PASS
+gi|9626243|ref|NC_001416.1|	9175	.	A	G	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:22:0:22:0:0:8:14:PASS
+gi|9626243|ref|NC_001416.1|	9234	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:23:22:1:12:10:0:1:PASS
+gi|9626243|ref|NC_001416.1|	9919	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:32:32:0:16:16:0:0:PASS
+gi|9626243|ref|NC_001416.1|	10127	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:26:25:1:13:12:0:1:PASS
+gi|9626243|ref|NC_001416.1|	10264	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:30:30:0:20:10:0:0:PASS
+gi|9626243|ref|NC_001416.1|	10421	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:16:16:0:7:9:0:0:PASS
+gi|9626243|ref|NC_001416.1|	10568	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:23:22:1:14:8:0:1:PASS
+gi|9626243|ref|NC_001416.1|	11066	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:24:23:1:12:11:0:1:PASS
+gi|9626243|ref|NC_001416.1|	11128	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:13:13:0:7:6:0:0:PASS
+gi|9626243|ref|NC_001416.1|	11782	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:22:22:0:15:7:0:0:PASS
+gi|9626243|ref|NC_001416.1|	12070	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:18:16:2:7:9:2:0:PASS
+gi|9626243|ref|NC_001416.1|	12717	.	G	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:29:0:28:0:0:13:15:PASS
+gi|9626243|ref|NC_001416.1|	12795	.	C	T	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:27:0:27:0:0:17:10:PASS
+gi|9626243|ref|NC_001416.1|	12876	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:29:29:0:17:12:0:0:PASS
+gi|9626243|ref|NC_001416.1|	12959	.	T	G	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:22:0:22:0:0:14:8:PASS
+gi|9626243|ref|NC_001416.1|	12970	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:19:19:0:9:10:0:0:PASS
+gi|9626243|ref|NC_001416.1|	13107	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:18:17:1:7:10:0:1:PASS
+gi|9626243|ref|NC_001416.1|	13264	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:16:15:1:7:8:1:0:PASS
+gi|9626243|ref|NC_001416.1|	13542	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:25:25:0:13:12:0:0:PASS
+gi|9626243|ref|NC_001416.1|	13647	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:21:20:1:8:12:0:1:PASS
+gi|9626243|ref|NC_001416.1|	13952	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:26:26:0:9:17:0:0:PASS
+gi|9626243|ref|NC_001416.1|	13971	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:18:17:1:8:9:0:1:PASS
+gi|9626243|ref|NC_001416.1|	15384	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:25:24:1:17:7:1:0:PASS
+gi|9626243|ref|NC_001416.1|	15715	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:19:19:0:8:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	15967	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:10:10:0:10:0:0:0:PASS
+gi|9626243|ref|NC_001416.1|	16070	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:12:12:0:9:3:0:0:PASS
+gi|9626243|ref|NC_001416.1|	16654	.	C	G	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:24:0:24:0:0:15:9:PASS
+gi|9626243|ref|NC_001416.1|	16715	.	T	G	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:19:0:19:0:0:9:10:PASS
+gi|9626243|ref|NC_001416.1|	17142	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:17:17:0:10:7:0:0:PASS
+gi|9626243|ref|NC_001416.1|	17311	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:24:24:0:15:9:0:0:PASS
+gi|9626243|ref|NC_001416.1|	17854	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:21:21:0:10:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	18151	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:18:18:0:9:9:0:0:PASS
+gi|9626243|ref|NC_001416.1|	18188	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:24:24:0:11:13:0:0:PASS
+gi|9626243|ref|NC_001416.1|	18210	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:19:19:0:12:7:0:0:PASS
+gi|9626243|ref|NC_001416.1|	18420	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:24:24:0:11:13:0:0:PASS
+gi|9626243|ref|NC_001416.1|	18598	.	C	G	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:25:0:25:0:0:14:11:PASS
+gi|9626243|ref|NC_001416.1|	18652	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:24:24:0:12:12:0:0:PASS
+gi|9626243|ref|NC_001416.1|	18989	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:32:32:0:12:20:0:0:PASS
+gi|9626243|ref|NC_001416.1|	19208	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:22:22:0:10:12:0:0:PASS
+gi|9626243|ref|NC_001416.1|	19448	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:17:17:0:7:10:0:0:PASS
+gi|9626243|ref|NC_001416.1|	19469	.	G	T	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:21:0:21:0:0:11:10:PASS
+gi|9626243|ref|NC_001416.1|	20079	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:26:26:0:14:12:0:0:PASS
+gi|9626243|ref|NC_001416.1|	20099	.	C	T	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:28:0:28:0:0:14:14:PASS
+gi|9626243|ref|NC_001416.1|	20289	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:32:31:1:15:16:1:0:PASS
+gi|9626243|ref|NC_001416.1|	20367	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:29:29:0:9:20:0:0:PASS
+gi|9626243|ref|NC_001416.1|	21110	.	T	G	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:18:0:18:0:0:6:12:PASS
+gi|9626243|ref|NC_001416.1|	21320	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:26:26:0:12:14:0:0:PASS
+gi|9626243|ref|NC_001416.1|	21653	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:25:24:1:10:14:1:0:PASS
+gi|9626243|ref|NC_001416.1|	22220	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:21:21:0:10:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	22357	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:18:18:0:10:8:0:0:PASS
+gi|9626243|ref|NC_001416.1|	22747	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:21:21:0:11:10:0:0:PASS
+gi|9626243|ref|NC_001416.1|	23362	.	T	A	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:14:0:14:0:0:5:9:PASS
+gi|9626243|ref|NC_001416.1|	23457	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:28:28:0:10:18:0:0:PASS
+gi|9626243|ref|NC_001416.1|	24043	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:26:25:1:11:14:1:0:PASS
+gi|9626243|ref|NC_001416.1|	24319	.	G	T	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:19:0:19:0:0:7:12:PASS
+gi|9626243|ref|NC_001416.1|	24766	.	G	A	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:19:0:19:0:0:8:11:PASS
+gi|9626243|ref|NC_001416.1|	24930	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:21:20:1:10:10:1:0:PASS
+gi|9626243|ref|NC_001416.1|	25005	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:21:20:1:11:9:1:0:PASS
+gi|9626243|ref|NC_001416.1|	25158	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:22:21:1:10:11:1:0:PASS
+gi|9626243|ref|NC_001416.1|	25645	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:16:16:0:7:9:0:0:PASS
+gi|9626243|ref|NC_001416.1|	26173	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:19:18:1:8:10:1:0:PASS
+gi|9626243|ref|NC_001416.1|	26728	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:26:26:0:15:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	26972	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:26:26:0:20:6:0:0:PASS
+gi|9626243|ref|NC_001416.1|	27412	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:25:25:0:8:17:0:0:PASS
+gi|9626243|ref|NC_001416.1|	27539	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:29:29:0:16:13:0:0:PASS
+gi|9626243|ref|NC_001416.1|	27661	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:23:23:0:14:9:0:0:PASS
+gi|9626243|ref|NC_001416.1|	27722	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:25:25:0:9:16:0:0:PASS
+gi|9626243|ref|NC_001416.1|	27790	.	A	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:20:0:19:0:0:8:11:PASS
+gi|9626243|ref|NC_001416.1|	27825	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:24:24:0:13:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	27834	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:16:15:1:4:11:0:1:PASS
+gi|9626243|ref|NC_001416.1|	28045	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:26:24:2:15:9:0:2:PASS
+gi|9626243|ref|NC_001416.1|	28362	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:25:25:0:8:17:0:0:PASS
+gi|9626243|ref|NC_001416.1|	29265	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:24:24:0:13:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	29411	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:28:28:0:18:10:0:0:PASS
+gi|9626243|ref|NC_001416.1|	29435	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:33:33:0:16:17:0:0:PASS
+gi|9626243|ref|NC_001416.1|	29891	.	G	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:21:0:21:0:0:9:12:PASS
+gi|9626243|ref|NC_001416.1|	30125	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:20:20:0:11:9:0:0:PASS
+gi|9626243|ref|NC_001416.1|	30757	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:24:23:1:8:15:1:0:PASS
+gi|9626243|ref|NC_001416.1|	30890	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:28:28:0:12:16:0:0:PASS
+gi|9626243|ref|NC_001416.1|	31328	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:15:14:1:7:7:0:1:PASS
+gi|9626243|ref|NC_001416.1|	31363	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:23:23:0:12:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	31551	.	A	G	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:16:0:16:0:0:8:8:PASS
+gi|9626243|ref|NC_001416.1|	32086	.	T	A	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:17:1:16:1:0:7:9:PASS
+gi|9626243|ref|NC_001416.1|	32660	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:24:24:0:14:10:0:0:PASS
+gi|9626243|ref|NC_001416.1|	33000	.	C	T	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:18:0:18:0:0:8:10:PASS
+gi|9626243|ref|NC_001416.1|	33591	.	T	G	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:30:0:30:0:0:16:14:PASS
+gi|9626243|ref|NC_001416.1|	33612	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:29:29:0:14:15:0:0:PASS
+gi|9626243|ref|NC_001416.1|	33865	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:25:25:0:12:13:0:0:PASS
+gi|9626243|ref|NC_001416.1|	34137	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:27:27:0:13:14:0:0:PASS
+gi|9626243|ref|NC_001416.1|	34370	.	A	G	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:23:0:22:0:0:10:12:PASS
+gi|9626243|ref|NC_001416.1|	34812	.	A	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:16:0:15:0:0:11:4:PASS
+gi|9626243|ref|NC_001416.1|	34920	.	T	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:16:0:16:0:0:9:7:PASS
+gi|9626243|ref|NC_001416.1|	35148	.	C	A	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:16:0:16:0:0:10:6:PASS
+gi|9626243|ref|NC_001416.1|	35802	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:19:19:0:5:14:0:0:PASS
+gi|9626243|ref|NC_001416.1|	35907	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:16:16:0:1:15:0:0:PASS
+gi|9626243|ref|NC_001416.1|	36010	.	C	T	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:9:0:9:0:0:0:9:PASS
+gi|9626243|ref|NC_001416.1|	36169	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:6:6:0:4:2:0:0:PASS
+gi|9626243|ref|NC_001416.1|	36642	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:15:15:0:2:13:0:0:PASS
+gi|9626243|ref|NC_001416.1|	37208	.	G	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:19:0:19:0:0:8:11:PASS
+gi|9626243|ref|NC_001416.1|	37387	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:22:22:0:12:10:0:0:PASS
+gi|9626243|ref|NC_001416.1|	37519	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:22:20:2:8:12:2:0:PASS
+gi|9626243|ref|NC_001416.1|	37898	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:18:18:0:10:8:0:0:PASS
+gi|9626243|ref|NC_001416.1|	38073	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:22:22:0:11:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	38165	.	T	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:29:0:29:0:0:19:10:PASS
+gi|9626243|ref|NC_001416.1|	38575	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:14:13:1:7:6:1:0:PASS
+gi|9626243|ref|NC_001416.1|	39003	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:9:8:1:8:0:1:0:PASS
+gi|9626243|ref|NC_001416.1|	39206	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:22:22:0:12:10:0:0:PASS
+gi|9626243|ref|NC_001416.1|	39484	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:23:23:0:13:10:0:0:PASS
+gi|9626243|ref|NC_001416.1|	39485	.	A	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:20:0:20:0:0:10:10:PASS
+gi|9626243|ref|NC_001416.1|	40457	.	T	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:28:1:27:1:0:11:16:PASS
+gi|9626243|ref|NC_001416.1|	40835	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:18:18:0:11:7:0:0:PASS
+gi|9626243|ref|NC_001416.1|	40984	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:22:22:0:12:10:0:0:PASS
+gi|9626243|ref|NC_001416.1|	41064	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:26:26:0:14:12:0:0:PASS
+gi|9626243|ref|NC_001416.1|	41448	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:34:34:0:14:20:0:0:PASS
+gi|9626243|ref|NC_001416.1|	41954	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:23:23:0:13:10:0:0:PASS
+gi|9626243|ref|NC_001416.1|	42439	.	A	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:28:0:28:0:0:20:8:PASS
+gi|9626243|ref|NC_001416.1|	43306	.	T	G	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:33:0:32:0:0:12:20:PASS
+gi|9626243|ref|NC_001416.1|	43470	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:24:23:1:12:11:0:1:PASS
+gi|9626243|ref|NC_001416.1|	44134	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:28:28:0:14:14:0:0:PASS
+gi|9626243|ref|NC_001416.1|	44201	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:28:28:0:12:16:0:0:PASS
+gi|9626243|ref|NC_001416.1|	44413	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:29:29:0:15:14:0:0:PASS
+gi|9626243|ref|NC_001416.1|	45364	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:31:31:0:18:13:0:0:PASS
+gi|9626243|ref|NC_001416.1|	45409	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:30:30:0:19:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	46237	.	G	A	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:27:0:27:0:0:12:15:PASS
+gi|9626243|ref|NC_001416.1|	46283	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:24:24:0:11:13:0:0:PASS
+gi|9626243|ref|NC_001416.1|	46842	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:18:17:1:4:13:0:1:PASS
+gi|9626243|ref|NC_001416.1|	47425	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:23:23:0:12:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	47893	.	G	A	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:28:0:28:0:0:12:16:PASS
diff -r 000000000000 -r e958c5f7c9d1 test-data/samples/sample2/consensus.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/samples/sample2/consensus.vcf	Wed Nov 22 15:34:14 2023 +0000
@@ -0,0 +1,186 @@
+##fileformat=VCFv4.1
+##fileDate=20180103
+##source=CFSAN SNP-Pipeline 1.0.1
+##reference=lambda_virus.fasta
+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=SDP,Number=1,Type=Integer,Description="Raw read depth">
+##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)">
+##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Depth of variant-supporting bases (reads2)">
+##FORMAT=<ID=RDF,Number=1,Type=Integer,Description="Depth of reference-supporting bases on forward strand (reads1plus)">
+##FORMAT=<ID=RDR,Number=1,Type=Integer,Description="Depth of reference-supporting bases on reverse strand (reads1minus)">
+##FORMAT=<ID=ADF,Number=1,Type=Integer,Description="Depth of variant-supporting bases on forward strand (reads2plus)">
+##FORMAT=<ID=ADR,Number=1,Type=Integer,Description="Depth of variant-supporting bases on reverse strand (reads2minus)">
+##FORMAT=<ID=FT,Number=1,Type=String,Description="Genotype filters using the same codes as the FILTER data element">
+##FILTER=<ID=PASS,Description="All filters passed">
+##FILTER=<ID=RawDpth,Description="No read depth">
+##FILTER=<ID=VarFreq60,Description="Variant base frequency below 0.60">
+##FILTER=<ID=StrDpth0,Description="Less than 0 variant-supporing reads on at least one strand">
+##FILTER=<ID=StrBias0,Description="Fraction of variant supporting reads below 0.00 on one strand">
+##FILTER=<ID=Region,Description="Position is in dense region of snps or near the end of the contig.">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sample2
+gi|9626243|ref|NC_001416.1|	403	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:24:24:0:11:13:0:0:PASS
+gi|9626243|ref|NC_001416.1|	550	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:26:26:0:14:12:0:0:PASS
+gi|9626243|ref|NC_001416.1|	586	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:23:23:0:12:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	753	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:27:27:0:10:17:0:0:PASS
+gi|9626243|ref|NC_001416.1|	1019	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:18:18:0:7:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	1079	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:20:20:0:10:10:0:0:PASS
+gi|9626243|ref|NC_001416.1|	1540	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:22:22:0:3:19:0:0:PASS
+gi|9626243|ref|NC_001416.1|	1620	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:11:10:1:0:10:0:1:PASS
+gi|9626243|ref|NC_001416.1|	1650	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:9:9:0:0:9:0:0:PASS
+gi|9626243|ref|NC_001416.1|	1788	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:8:8:0:8:0:0:0:PASS
+gi|9626243|ref|NC_001416.1|	1804	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:11:11:0:10:1:0:0:PASS
+gi|9626243|ref|NC_001416.1|	2123	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:20:20:0:10:10:0:0:PASS
+gi|9626243|ref|NC_001416.1|	2439	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:16:16:0:10:6:0:0:PASS
+gi|9626243|ref|NC_001416.1|	2452	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:22:21:1:11:10:1:0:PASS
+gi|9626243|ref|NC_001416.1|	2599	.	C	A	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:25:0:25:0:0:8:17:PASS
+gi|9626243|ref|NC_001416.1|	3063	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:26:25:1:16:9:0:1:PASS
+gi|9626243|ref|NC_001416.1|	3351	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:31:30:1:12:18:0:1:PASS
+gi|9626243|ref|NC_001416.1|	3648	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:23:23:0:10:13:0:0:PASS
+gi|9626243|ref|NC_001416.1|	3656	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:20:20:0:8:12:0:0:PASS
+gi|9626243|ref|NC_001416.1|	3678	.	C	T	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:19:1:18:1:0:10:8:PASS
+gi|9626243|ref|NC_001416.1|	4977	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:30:29:1:12:17:1:0:PASS
+gi|9626243|ref|NC_001416.1|	5142	.	C	G	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:18:0:18:0:0:4:14:PASS
+gi|9626243|ref|NC_001416.1|	5336	.	G	T	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:8:0:8:0:0:1:7:PASS
+gi|9626243|ref|NC_001416.1|	5462	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:9:9:0:9:0:0:0:PASS
+gi|9626243|ref|NC_001416.1|	5482	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:12:10:2:10:0:2:0:PASS
+gi|9626243|ref|NC_001416.1|	5516	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:11:10:1:10:0:1:0:PASS
+gi|9626243|ref|NC_001416.1|	5800	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:23:23:0:16:7:0:0:PASS
+gi|9626243|ref|NC_001416.1|	5818	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:26:26:0:15:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	5994	.	A	T	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:21:0:21:0:0:10:11:PASS
+gi|9626243|ref|NC_001416.1|	6296	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:24:24:0:10:14:0:0:PASS
+gi|9626243|ref|NC_001416.1|	6535	.	C	A	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:22:0:21:0:0:8:13:PASS
+gi|9626243|ref|NC_001416.1|	6824	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:24:23:1:8:15:1:0:PASS
+gi|9626243|ref|NC_001416.1|	7424	.	G	T	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:25:0:24:0:0:15:9:PASS
+gi|9626243|ref|NC_001416.1|	7668	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:26:26:0:14:12:0:0:PASS
+gi|9626243|ref|NC_001416.1|	7897	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:26:26:0:9:17:0:0:PASS
+gi|9626243|ref|NC_001416.1|	8420	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:26:26:0:11:15:0:0:PASS
+gi|9626243|ref|NC_001416.1|	8938	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:25:25:0:12:13:0:0:PASS
+gi|9626243|ref|NC_001416.1|	9175	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:13:12:1:3:9:0:1:PASS
+gi|9626243|ref|NC_001416.1|	9234	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:21:21:0:10:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	9919	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:19:19:0:8:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	10127	.	G	A	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:32:0:32:0:0:17:15:PASS
+gi|9626243|ref|NC_001416.1|	10264	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:21:21:0:10:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	10421	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:30:30:0:22:8:0:0:PASS
+gi|9626243|ref|NC_001416.1|	10568	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:24:24:0:11:13:0:0:PASS
+gi|9626243|ref|NC_001416.1|	11066	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:26:26:0:11:15:0:0:PASS
+gi|9626243|ref|NC_001416.1|	11128	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:28:28:0:11:17:0:0:PASS
+gi|9626243|ref|NC_001416.1|	11782	.	A	G	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:17:0:17:0:0:7:10:PASS
+gi|9626243|ref|NC_001416.1|	12070	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:20:20:0:9:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	12717	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:22:22:0:7:15:0:0:PASS
+gi|9626243|ref|NC_001416.1|	12795	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:23:23:0:11:12:0:0:PASS
+gi|9626243|ref|NC_001416.1|	12876	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:25:25:0:14:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	12959	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:19:19:0:8:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	12970	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:20:20:0:9:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	13107	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:21:20:1:7:13:1:0:PASS
+gi|9626243|ref|NC_001416.1|	13264	.	C	T	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:23:0:23:0:0:15:8:PASS
+gi|9626243|ref|NC_001416.1|	13542	.	C	G	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:26:0:25:0:0:16:9:PASS
+gi|9626243|ref|NC_001416.1|	13647	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:27:27:0:15:12:0:0:PASS
+gi|9626243|ref|NC_001416.1|	13952	.	G	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:33:0:33:0:0:14:19:PASS
+gi|9626243|ref|NC_001416.1|	13971	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:28:28:0:13:15:0:0:PASS
+gi|9626243|ref|NC_001416.1|	15384	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:30:30:0:14:16:0:0:PASS
+gi|9626243|ref|NC_001416.1|	15715	.	G	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:24:0:24:0:0:17:7:PASS
+gi|9626243|ref|NC_001416.1|	15967	.	A	T	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:28:0:26:0:0:14:12:PASS
+gi|9626243|ref|NC_001416.1|	16070	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:27:27:0:19:8:0:0:PASS
+gi|9626243|ref|NC_001416.1|	16654	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:20:20:0:8:12:0:0:PASS
+gi|9626243|ref|NC_001416.1|	16715	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:27:27:0:14:13:0:0:PASS
+gi|9626243|ref|NC_001416.1|	17142	.	G	A	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:27:0:27:0:0:14:13:PASS
+gi|9626243|ref|NC_001416.1|	17311	.	G	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:35:0:35:0:0:15:20:PASS
+gi|9626243|ref|NC_001416.1|	17854	.	G	T	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:20:0:20:0:0:6:14:PASS
+gi|9626243|ref|NC_001416.1|	18151	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:27:27:0:16:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	18188	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:31:31:0:14:17:0:0:PASS
+gi|9626243|ref|NC_001416.1|	18210	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:30:28:2:13:15:0:2:PASS
+gi|9626243|ref|NC_001416.1|	18420	.	G	T	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:18:0:18:0:0:10:8:PASS
+gi|9626243|ref|NC_001416.1|	18598	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:28:27:1:14:13:0:1:PASS
+gi|9626243|ref|NC_001416.1|	18652	.	G	T	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:25:0:25:0:0:15:10:PASS
+gi|9626243|ref|NC_001416.1|	18989	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:26:26:0:15:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	19208	.	A	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:17:0:17:0:0:9:8:PASS
+gi|9626243|ref|NC_001416.1|	19448	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:32:32:0:14:18:0:0:PASS
+gi|9626243|ref|NC_001416.1|	19469	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:30:30:0:12:18:0:0:PASS
+gi|9626243|ref|NC_001416.1|	20079	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:23:23:0:14:9:0:0:PASS
+gi|9626243|ref|NC_001416.1|	20099	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:28:28:0:16:12:0:0:PASS
+gi|9626243|ref|NC_001416.1|	20289	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:34:34:0:19:15:0:0:PASS
+gi|9626243|ref|NC_001416.1|	20367	.	G	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:32:0:32:0:0:20:12:PASS
+gi|9626243|ref|NC_001416.1|	21110	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:31:31:0:20:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	21320	.	T	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:25:0:25:0:0:12:13:PASS
+gi|9626243|ref|NC_001416.1|	21653	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:23:22:1:8:14:1:0:PASS
+gi|9626243|ref|NC_001416.1|	22220	.	A	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:28:0:28:0:0:17:11:PASS
+gi|9626243|ref|NC_001416.1|	22357	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:17:17:0:6:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	22747	.	G	A	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:19:0:19:0:0:7:12:PASS
+gi|9626243|ref|NC_001416.1|	23362	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:21:20:1:9:11:1:0:PASS
+gi|9626243|ref|NC_001416.1|	23457	.	A	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:20:0:19:0:0:12:7:PASS
+gi|9626243|ref|NC_001416.1|	24043	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:23:23:0:12:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	24319	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:21:20:1:9:11:1:0:PASS
+gi|9626243|ref|NC_001416.1|	24766	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:19:19:0:7:12:0:0:PASS
+gi|9626243|ref|NC_001416.1|	24930	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:15:15:0:8:7:0:0:PASS
+gi|9626243|ref|NC_001416.1|	25005	.	A	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:12:0:12:0:0:6:6:PASS
+gi|9626243|ref|NC_001416.1|	25158	.	A	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:22:0:22:0:0:11:11:PASS
+gi|9626243|ref|NC_001416.1|	25645	.	C	G	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:26:0:26:0:0:11:15:PASS
+gi|9626243|ref|NC_001416.1|	26173	.	G	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:21:0:21:0:0:10:11:PASS
+gi|9626243|ref|NC_001416.1|	26728	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:28:28:0:12:16:0:0:PASS
+gi|9626243|ref|NC_001416.1|	26972	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:26:25:1:11:14:1:0:PASS
+gi|9626243|ref|NC_001416.1|	27412	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:24:24:0:13:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	27539	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:31:31:0:13:18:0:0:PASS
+gi|9626243|ref|NC_001416.1|	27661	.	T	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:25:0:24:0:0:14:10:PASS
+gi|9626243|ref|NC_001416.1|	27722	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:30:29:1:12:17:1:0:PASS
+gi|9626243|ref|NC_001416.1|	27790	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:27:26:1:13:13:1:0:PASS
+gi|9626243|ref|NC_001416.1|	27825	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:23:23:0:14:9:0:0:PASS
+gi|9626243|ref|NC_001416.1|	27834	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:32:32:0:18:14:0:0:PASS
+gi|9626243|ref|NC_001416.1|	28045	.	G	T	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:25:0:25:0:0:13:12:PASS
+gi|9626243|ref|NC_001416.1|	28362	.	T	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:22:0:22:0:0:12:10:PASS
+gi|9626243|ref|NC_001416.1|	29265	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:21:21:0:13:8:0:0:PASS
+gi|9626243|ref|NC_001416.1|	29411	.	T	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:31:0:31:0:0:15:16:PASS
+gi|9626243|ref|NC_001416.1|	29435	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:29:27:2:12:15:1:1:PASS
+gi|9626243|ref|NC_001416.1|	29891	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:19:19:0:10:9:0:0:PASS
+gi|9626243|ref|NC_001416.1|	30125	.	A	G	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:21:0:21:0:0:11:10:PASS
+gi|9626243|ref|NC_001416.1|	30757	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:22:22:0:9:13:0:0:PASS
+gi|9626243|ref|NC_001416.1|	30890	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:23:23:0:11:12:0:0:PASS
+gi|9626243|ref|NC_001416.1|	31328	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:21:21:0:11:10:0:0:PASS
+gi|9626243|ref|NC_001416.1|	31363	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:22:22:0:10:12:0:0:PASS
+gi|9626243|ref|NC_001416.1|	31551	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:21:21:0:10:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	32086	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:26:25:1:10:15:0:1:PASS
+gi|9626243|ref|NC_001416.1|	32660	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:21:20:1:12:8:1:0:PASS
+gi|9626243|ref|NC_001416.1|	33000	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:15:14:1:10:4:1:0:PASS
+gi|9626243|ref|NC_001416.1|	33591	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:26:25:1:11:14:1:0:PASS
+gi|9626243|ref|NC_001416.1|	33612	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:25:24:1:8:16:1:0:PASS
+gi|9626243|ref|NC_001416.1|	33865	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:24:24:0:11:13:0:0:PASS
+gi|9626243|ref|NC_001416.1|	34137	.	T	G	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:34:0:33:0:0:18:15:PASS
+gi|9626243|ref|NC_001416.1|	34370	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:31:31:0:12:19:0:0:PASS
+gi|9626243|ref|NC_001416.1|	34812	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:18:18:0:7:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	34920	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:23:23:0:12:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	35148	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:28:28:0:13:15:0:0:PASS
+gi|9626243|ref|NC_001416.1|	35802	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:23:23:0:15:8:0:0:PASS
+gi|9626243|ref|NC_001416.1|	35907	.	G	T	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:32:0:30:0:0:19:11:PASS
+gi|9626243|ref|NC_001416.1|	36010	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:28:28:0:12:16:0:0:PASS
+gi|9626243|ref|NC_001416.1|	36169	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:29:28:1:15:13:0:1:PASS
+gi|9626243|ref|NC_001416.1|	36642	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:26:26:0:14:12:0:0:PASS
+gi|9626243|ref|NC_001416.1|	37208	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:26:26:0:19:7:0:0:PASS
+gi|9626243|ref|NC_001416.1|	37387	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:29:29:0:13:16:0:0:PASS
+gi|9626243|ref|NC_001416.1|	37519	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:19:19:0:10:9:0:0:PASS
+gi|9626243|ref|NC_001416.1|	37898	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:29:28:1:14:14:1:0:PASS
+gi|9626243|ref|NC_001416.1|	38073	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:27:26:1:15:11:0:1:PASS
+gi|9626243|ref|NC_001416.1|	38165	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:19:18:1:14:4:0:1:PASS
+gi|9626243|ref|NC_001416.1|	38575	.	A	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:21:0:21:0:0:10:11:PASS
+gi|9626243|ref|NC_001416.1|	39003	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:16:16:0:6:10:0:0:PASS
+gi|9626243|ref|NC_001416.1|	39206	.	T	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:20:0:19:0:0:7:12:PASS
+gi|9626243|ref|NC_001416.1|	39484	.	C	A	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:20:0:20:0:0:12:8:PASS
+gi|9626243|ref|NC_001416.1|	39485	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:21:21:0:14:7:0:0:PASS
+gi|9626243|ref|NC_001416.1|	40457	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:32:31:1:15:16:1:0:PASS
+gi|9626243|ref|NC_001416.1|	40835	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:33:33:0:17:16:0:0:PASS
+gi|9626243|ref|NC_001416.1|	40984	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:19:19:0:7:12:0:0:PASS
+gi|9626243|ref|NC_001416.1|	41064	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:31:31:0:17:14:0:0:PASS
+gi|9626243|ref|NC_001416.1|	41448	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:26:26:0:12:14:0:0:PASS
+gi|9626243|ref|NC_001416.1|	41954	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:32:32:0:16:16:0:0:PASS
+gi|9626243|ref|NC_001416.1|	42439	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:23:23:0:13:10:0:0:PASS
+gi|9626243|ref|NC_001416.1|	43306	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:29:29:0:13:16:0:0:PASS
+gi|9626243|ref|NC_001416.1|	43470	.	G	T	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:25:0:25:0:0:14:11:PASS
+gi|9626243|ref|NC_001416.1|	44134	.	T	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:22:0:21:0:0:12:9:PASS
+gi|9626243|ref|NC_001416.1|	44201	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:30:30:0:13:17:0:0:PASS
+gi|9626243|ref|NC_001416.1|	44413	.	G	T	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:32:0:32:0:0:13:19:PASS
+gi|9626243|ref|NC_001416.1|	45364	.	A	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:27:0:25:0:0:16:9:PASS
+gi|9626243|ref|NC_001416.1|	45409	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:26:26:0:13:13:0:0:PASS
+gi|9626243|ref|NC_001416.1|	46237	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:19:19:0:3:16:0:0:PASS
+gi|9626243|ref|NC_001416.1|	46283	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:12:12:0:1:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	46842	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:29:28:1:12:16:1:0:PASS
+gi|9626243|ref|NC_001416.1|	47425	.	T	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:19:0:18:0:0:11:7:PASS
+gi|9626243|ref|NC_001416.1|	47893	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:11:11:0:5:6:0:0:PASS
diff -r 000000000000 -r e958c5f7c9d1 test-data/samples/sample3/consensus.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/samples/sample3/consensus.vcf	Wed Nov 22 15:34:14 2023 +0000
@@ -0,0 +1,186 @@
+##fileformat=VCFv4.1
+##fileDate=20180103
+##source=CFSAN SNP-Pipeline 1.0.1
+##reference=lambda_virus.fasta
+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=SDP,Number=1,Type=Integer,Description="Raw read depth">
+##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)">
+##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Depth of variant-supporting bases (reads2)">
+##FORMAT=<ID=RDF,Number=1,Type=Integer,Description="Depth of reference-supporting bases on forward strand (reads1plus)">
+##FORMAT=<ID=RDR,Number=1,Type=Integer,Description="Depth of reference-supporting bases on reverse strand (reads1minus)">
+##FORMAT=<ID=ADF,Number=1,Type=Integer,Description="Depth of variant-supporting bases on forward strand (reads2plus)">
+##FORMAT=<ID=ADR,Number=1,Type=Integer,Description="Depth of variant-supporting bases on reverse strand (reads2minus)">
+##FORMAT=<ID=FT,Number=1,Type=String,Description="Genotype filters using the same codes as the FILTER data element">
+##FILTER=<ID=PASS,Description="All filters passed">
+##FILTER=<ID=RawDpth,Description="No read depth">
+##FILTER=<ID=VarFreq60,Description="Variant base frequency below 0.60">
+##FILTER=<ID=StrDpth0,Description="Less than 0 variant-supporing reads on at least one strand">
+##FILTER=<ID=StrBias0,Description="Fraction of variant supporting reads below 0.00 on one strand">
+##FILTER=<ID=Region,Description="Position is in dense region of snps or near the end of the contig.">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sample3
+gi|9626243|ref|NC_001416.1|	403	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:26:26:0:13:13:0:0:PASS
+gi|9626243|ref|NC_001416.1|	550	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:29:29:0:13:16:0:0:PASS
+gi|9626243|ref|NC_001416.1|	586	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:37:37:0:15:22:0:0:PASS
+gi|9626243|ref|NC_001416.1|	753	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:26:24:2:13:11:0:2:PASS
+gi|9626243|ref|NC_001416.1|	1019	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:25:25:0:10:15:0:0:PASS
+gi|9626243|ref|NC_001416.1|	1079	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:31:30:1:16:14:1:0:PASS
+gi|9626243|ref|NC_001416.1|	1540	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:21:21:0:10:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	1620	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:23:23:0:10:13:0:0:PASS
+gi|9626243|ref|NC_001416.1|	1650	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:21:21:0:11:10:0:0:PASS
+gi|9626243|ref|NC_001416.1|	1788	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:13:13:0:3:10:0:0:PASS
+gi|9626243|ref|NC_001416.1|	1804	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:14:14:0:7:7:0:0:PASS
+gi|9626243|ref|NC_001416.1|	2123	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:23:23:0:10:13:0:0:PASS
+gi|9626243|ref|NC_001416.1|	2439	.	C	T	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:16:0:16:0:0:8:8:PASS
+gi|9626243|ref|NC_001416.1|	2452	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:21:20:1:10:10:0:1:PASS
+gi|9626243|ref|NC_001416.1|	2599	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:24:24:0:12:12:0:0:PASS
+gi|9626243|ref|NC_001416.1|	3063	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:25:24:1:11:13:0:1:PASS
+gi|9626243|ref|NC_001416.1|	3351	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:29:29:0:15:14:0:0:PASS
+gi|9626243|ref|NC_001416.1|	3648	.	C	T	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:28:0:27:0:0:15:12:PASS
+gi|9626243|ref|NC_001416.1|	3656	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:24:24:0:12:12:0:0:PASS
+gi|9626243|ref|NC_001416.1|	3678	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:24:24:0:15:9:0:0:PASS
+gi|9626243|ref|NC_001416.1|	4977	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:27:27:0:11:16:0:0:PASS
+gi|9626243|ref|NC_001416.1|	5142	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:21:21:0:12:9:0:0:PASS
+gi|9626243|ref|NC_001416.1|	5336	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:18:17:1:11:6:1:0:PASS
+gi|9626243|ref|NC_001416.1|	5462	.	C	T	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:24:0:22:0:0:17:5:PASS
+gi|9626243|ref|NC_001416.1|	5482	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:22:22:0:14:8:0:0:PASS
+gi|9626243|ref|NC_001416.1|	5516	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:19:19:0:11:8:0:0:PASS
+gi|9626243|ref|NC_001416.1|	5800	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:23:23:0:10:13:0:0:PASS
+gi|9626243|ref|NC_001416.1|	5818	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:22:21:1:10:11:1:0:PASS
+gi|9626243|ref|NC_001416.1|	5994	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:22:22:0:9:13:0:0:PASS
+gi|9626243|ref|NC_001416.1|	6296	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:25:25:0:11:14:0:0:PASS
+gi|9626243|ref|NC_001416.1|	6535	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:19:19:0:7:12:0:0:PASS
+gi|9626243|ref|NC_001416.1|	6824	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:14:13:1:5:8:0:1:PASS
+gi|9626243|ref|NC_001416.1|	7424	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:29:28:1:11:17:0:1:PASS
+gi|9626243|ref|NC_001416.1|	7668	.	A	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:17:0:17:0:0:6:11:PASS
+gi|9626243|ref|NC_001416.1|	7897	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:23:23:0:13:10:0:0:PASS
+gi|9626243|ref|NC_001416.1|	8420	.	T	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:32:0:32:0:0:22:10:PASS
+gi|9626243|ref|NC_001416.1|	8938	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:29:29:0:19:10:0:0:PASS
+gi|9626243|ref|NC_001416.1|	9175	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:25:25:0:15:10:0:0:PASS
+gi|9626243|ref|NC_001416.1|	9234	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:27:27:0:11:16:0:0:PASS
+gi|9626243|ref|NC_001416.1|	9919	.	A	G	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:24:0:24:0:0:14:10:PASS
+gi|9626243|ref|NC_001416.1|	10127	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:25:25:0:14:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	10264	.	G	T	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:24:0:24:0:0:10:14:PASS
+gi|9626243|ref|NC_001416.1|	10421	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:16:14:2:6:8:2:0:PASS
+gi|9626243|ref|NC_001416.1|	10568	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:16:16:0:9:7:0:0:PASS
+gi|9626243|ref|NC_001416.1|	11066	.	G	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:20:0:20:0:0:6:14:PASS
+gi|9626243|ref|NC_001416.1|	11128	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:13:13:0:3:10:0:0:PASS
+gi|9626243|ref|NC_001416.1|	11782	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:14:14:0:4:10:0:0:PASS
+gi|9626243|ref|NC_001416.1|	12070	.	C	T	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:11:0:11:0:0:8:3:PASS
+gi|9626243|ref|NC_001416.1|	12717	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:18:18:0:13:5:0:0:PASS
+gi|9626243|ref|NC_001416.1|	12795	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:16:15:1:7:8:1:0:PASS
+gi|9626243|ref|NC_001416.1|	12876	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:21:20:1:12:8:1:0:PASS
+gi|9626243|ref|NC_001416.1|	12959	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:27:27:0:13:14:0:0:PASS
+gi|9626243|ref|NC_001416.1|	12970	.	A	G	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:26:0:26:0:0:14:12:PASS
+gi|9626243|ref|NC_001416.1|	13107	.	C	A	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:16:0:16:0:0:11:5:PASS
+gi|9626243|ref|NC_001416.1|	13264	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:21:21:0:10:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	13542	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:19:19:0:12:7:0:0:PASS
+gi|9626243|ref|NC_001416.1|	13647	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:25:25:0:20:5:0:0:PASS
+gi|9626243|ref|NC_001416.1|	13952	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:20:19:1:8:11:1:0:PASS
+gi|9626243|ref|NC_001416.1|	13971	.	G	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:27:0:27:0:0:12:15:PASS
+gi|9626243|ref|NC_001416.1|	15384	.	T	G	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:24:0:24:0:0:15:9:PASS
+gi|9626243|ref|NC_001416.1|	15715	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:24:24:0:13:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	15967	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:25:25:0:11:14:0:0:PASS
+gi|9626243|ref|NC_001416.1|	16070	.	C	A	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:22:0:21:0:0:14:7:PASS
+gi|9626243|ref|NC_001416.1|	16654	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:10:10:0:4:6:0:0:PASS
+gi|9626243|ref|NC_001416.1|	16715	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:17:17:0:11:6:0:0:PASS
+gi|9626243|ref|NC_001416.1|	17142	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:24:24:0:9:15:0:0:PASS
+gi|9626243|ref|NC_001416.1|	17311	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:20:20:0:11:9:0:0:PASS
+gi|9626243|ref|NC_001416.1|	17854	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:20:20:0:10:10:0:0:PASS
+gi|9626243|ref|NC_001416.1|	18151	.	A	T	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:22:0:22:0:0:11:11:PASS
+gi|9626243|ref|NC_001416.1|	18188	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:20:19:1:9:10:0:1:PASS
+gi|9626243|ref|NC_001416.1|	18210	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:22:22:0:11:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	18420	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:31:31:0:18:13:0:0:PASS
+gi|9626243|ref|NC_001416.1|	18598	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:17:17:0:11:6:0:0:PASS
+gi|9626243|ref|NC_001416.1|	18652	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:17:17:0:8:9:0:0:PASS
+gi|9626243|ref|NC_001416.1|	18989	.	G	T	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:30:0:30:0:0:13:17:PASS
+gi|9626243|ref|NC_001416.1|	19208	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:31:31:0:16:15:0:0:PASS
+gi|9626243|ref|NC_001416.1|	19448	.	C	A	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:20:1:19:1:0:7:12:PASS
+gi|9626243|ref|NC_001416.1|	19469	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:26:24:2:11:13:1:1:PASS
+gi|9626243|ref|NC_001416.1|	20079	.	C	G	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:36:0:36:0:0:19:17:PASS
+gi|9626243|ref|NC_001416.1|	20099	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:26:26:0:13:13:0:0:PASS
+gi|9626243|ref|NC_001416.1|	20289	.	T	A	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:23:0:23:0:0:7:16:PASS
+gi|9626243|ref|NC_001416.1|	20367	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:26:26:0:12:14:0:0:PASS
+gi|9626243|ref|NC_001416.1|	21110	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:12:12:0:1:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	21320	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:8:8:0:8:0:0:0:PASS
+gi|9626243|ref|NC_001416.1|	21653	.	G	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:22:0:22:0:0:16:6:PASS
+gi|9626243|ref|NC_001416.1|	22220	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:21:20:1:11:9:0:1:PASS
+gi|9626243|ref|NC_001416.1|	22357	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:22:22:0:6:16:0:0:PASS
+gi|9626243|ref|NC_001416.1|	22747	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:15:15:0:6:9:0:0:PASS
+gi|9626243|ref|NC_001416.1|	23362	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:4:4:0:0:4:0:0:PASS
+gi|9626243|ref|NC_001416.1|	23457	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:10:10:0:10:0:0:0:PASS
+gi|9626243|ref|NC_001416.1|	24043	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:21:21:0:13:8:0:0:PASS
+gi|9626243|ref|NC_001416.1|	24319	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:27:26:1:13:13:0:1:PASS
+gi|9626243|ref|NC_001416.1|	24766	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:19:19:0:6:13:0:0:PASS
+gi|9626243|ref|NC_001416.1|	24930	.	A	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:26:0:26:0:0:12:14:PASS
+gi|9626243|ref|NC_001416.1|	25005	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:22:22:0:10:12:0:0:PASS
+gi|9626243|ref|NC_001416.1|	25158	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:15:15:0:10:5:0:0:PASS
+gi|9626243|ref|NC_001416.1|	25645	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:21:21:0:10:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	26173	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:31:28:3:10:18:2:1:PASS
+gi|9626243|ref|NC_001416.1|	26728	.	A	T	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:25:0:25:0:0:13:12:PASS
+gi|9626243|ref|NC_001416.1|	26972	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:30:30:0:14:16:0:0:PASS
+gi|9626243|ref|NC_001416.1|	27412	.	C	G	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:15:0:15:0:0:6:9:PASS
+gi|9626243|ref|NC_001416.1|	27539	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:15:15:0:11:4:0:0:PASS
+gi|9626243|ref|NC_001416.1|	27661	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:15:15:0:7:8:0:0:PASS
+gi|9626243|ref|NC_001416.1|	27722	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:19:18:1:6:12:1:0:PASS
+gi|9626243|ref|NC_001416.1|	27790	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:21:21:0:11:10:0:0:PASS
+gi|9626243|ref|NC_001416.1|	27825	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:23:23:0:14:9:0:0:PASS
+gi|9626243|ref|NC_001416.1|	27834	.	C	A	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:16:0:15:0:0:10:5:PASS
+gi|9626243|ref|NC_001416.1|	28045	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:29:29:0:14:15:0:0:PASS
+gi|9626243|ref|NC_001416.1|	28362	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:23:23:0:8:15:0:0:PASS
+gi|9626243|ref|NC_001416.1|	29265	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:3:2:1:2:0:0:1:PASS
+gi|9626243|ref|NC_001416.1|	29411	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:18:18:0:10:8:0:0:PASS
+gi|9626243|ref|NC_001416.1|	29435	.	T	A	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:18:0:18:0:0:11:7:PASS
+gi|9626243|ref|NC_001416.1|	29891	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:30:29:1:16:13:0:1:PASS
+gi|9626243|ref|NC_001416.1|	30125	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:29:29:0:20:9:0:0:PASS
+gi|9626243|ref|NC_001416.1|	30757	.	T	A	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:24:0:24:0:0:10:14:PASS
+gi|9626243|ref|NC_001416.1|	30890	.	G	A	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:18:0:17:0:0:7:10:PASS
+gi|9626243|ref|NC_001416.1|	31328	.	G	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:21:0:21:0:0:9:12:PASS
+gi|9626243|ref|NC_001416.1|	31363	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:31:31:0:14:17:0:0:PASS
+gi|9626243|ref|NC_001416.1|	31551	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:26:26:0:14:12:0:0:PASS
+gi|9626243|ref|NC_001416.1|	32086	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:17:17:0:10:7:0:0:PASS
+gi|9626243|ref|NC_001416.1|	32660	.	C	A	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:17:0:17:0:0:11:6:PASS
+gi|9626243|ref|NC_001416.1|	33000	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:15:15:0:9:6:0:0:PASS
+gi|9626243|ref|NC_001416.1|	33591	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:27:27:0:14:13:0:0:PASS
+gi|9626243|ref|NC_001416.1|	33612	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:22:22:0:14:8:0:0:PASS
+gi|9626243|ref|NC_001416.1|	33865	.	T	G	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:28:0:28:0:0:15:13:PASS
+gi|9626243|ref|NC_001416.1|	34137	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:22:21:1:8:13:1:0:PASS
+gi|9626243|ref|NC_001416.1|	34370	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:29:29:0:12:17:0:0:PASS
+gi|9626243|ref|NC_001416.1|	34812	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:30:29:1:11:18:1:0:PASS
+gi|9626243|ref|NC_001416.1|	34920	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:24:24:0:12:12:0:0:PASS
+gi|9626243|ref|NC_001416.1|	35148	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:31:30:1:15:15:0:1:PASS
+gi|9626243|ref|NC_001416.1|	35802	.	G	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:28:0:28:0:0:13:15:PASS
+gi|9626243|ref|NC_001416.1|	35907	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:21:21:0:11:10:0:0:PASS
+gi|9626243|ref|NC_001416.1|	36010	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:26:26:0:14:12:0:0:PASS
+gi|9626243|ref|NC_001416.1|	36169	.	G	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:15:0:15:0:0:5:10:PASS
+gi|9626243|ref|NC_001416.1|	36642	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:19:18:1:10:8:1:0:PASS
+gi|9626243|ref|NC_001416.1|	37208	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:23:23:0:13:10:0:0:PASS
+gi|9626243|ref|NC_001416.1|	37387	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:24:24:0:11:13:0:0:PASS
+gi|9626243|ref|NC_001416.1|	37519	.	G	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:13:0:13:0:0:6:7:PASS
+gi|9626243|ref|NC_001416.1|	37898	.	C	G	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:27:0:26:0:0:8:18:PASS
+gi|9626243|ref|NC_001416.1|	38073	.	A	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:25:0:24:0:0:17:7:PASS
+gi|9626243|ref|NC_001416.1|	38165	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:17:16:1:11:5:0:1:PASS
+gi|9626243|ref|NC_001416.1|	38575	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:25:25:0:14:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	39003	.	T	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:17:0:17:0:0:9:8:PASS
+gi|9626243|ref|NC_001416.1|	39206	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:20:20:0:8:12:0:0:PASS
+gi|9626243|ref|NC_001416.1|	39484	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:20:20:0:7:13:0:0:PASS
+gi|9626243|ref|NC_001416.1|	39485	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:16:16:0:4:12:0:0:PASS
+gi|9626243|ref|NC_001416.1|	40457	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:25:24:1:7:17:1:0:PASS
+gi|9626243|ref|NC_001416.1|	40835	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:28:28:0:17:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	40984	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:37:36:1:20:16:0:1:PASS
+gi|9626243|ref|NC_001416.1|	41064	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:30:30:0:15:15:0:0:PASS
+gi|9626243|ref|NC_001416.1|	41448	.	A	G	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:21:0:21:0:0:8:13:PASS
+gi|9626243|ref|NC_001416.1|	41954	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:20:19:1:6:13:1:0:PASS
+gi|9626243|ref|NC_001416.1|	42439	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:20:20:0:11:9:0:0:PASS
+gi|9626243|ref|NC_001416.1|	43306	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:23:23:0:6:17:0:0:PASS
+gi|9626243|ref|NC_001416.1|	43470	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:25:25:0:14:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	44134	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:20:20:0:10:10:0:0:PASS
+gi|9626243|ref|NC_001416.1|	44201	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:25:25:0:16:9:0:0:PASS
+gi|9626243|ref|NC_001416.1|	44413	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:23:23:0:9:14:0:0:PASS
+gi|9626243|ref|NC_001416.1|	45364	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:29:28:1:13:15:1:0:PASS
+gi|9626243|ref|NC_001416.1|	45409	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:27:27:0:16:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	46237	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:17:16:1:8:8:0:1:PASS
+gi|9626243|ref|NC_001416.1|	46283	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:25:25:0:11:14:0:0:PASS
+gi|9626243|ref|NC_001416.1|	46842	.	G	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:28:0:27:0:0:17:10:PASS
+gi|9626243|ref|NC_001416.1|	47425	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:12:11:1:11:0:1:0:PASS
+gi|9626243|ref|NC_001416.1|	47893	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:27:27:0:12:15:0:0:PASS
diff -r 000000000000 -r e958c5f7c9d1 test-data/samples/sample4/consensus.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/samples/sample4/consensus.vcf	Wed Nov 22 15:34:14 2023 +0000
@@ -0,0 +1,186 @@
+##fileformat=VCFv4.1
+##fileDate=20180103
+##source=CFSAN SNP-Pipeline 1.0.1
+##reference=lambda_virus.fasta
+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=SDP,Number=1,Type=Integer,Description="Raw read depth">
+##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)">
+##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Depth of variant-supporting bases (reads2)">
+##FORMAT=<ID=RDF,Number=1,Type=Integer,Description="Depth of reference-supporting bases on forward strand (reads1plus)">
+##FORMAT=<ID=RDR,Number=1,Type=Integer,Description="Depth of reference-supporting bases on reverse strand (reads1minus)">
+##FORMAT=<ID=ADF,Number=1,Type=Integer,Description="Depth of variant-supporting bases on forward strand (reads2plus)">
+##FORMAT=<ID=ADR,Number=1,Type=Integer,Description="Depth of variant-supporting bases on reverse strand (reads2minus)">
+##FORMAT=<ID=FT,Number=1,Type=String,Description="Genotype filters using the same codes as the FILTER data element">
+##FILTER=<ID=PASS,Description="All filters passed">
+##FILTER=<ID=RawDpth,Description="No read depth">
+##FILTER=<ID=VarFreq60,Description="Variant base frequency below 0.60">
+##FILTER=<ID=StrDpth0,Description="Less than 0 variant-supporing reads on at least one strand">
+##FILTER=<ID=StrBias0,Description="Fraction of variant supporting reads below 0.00 on one strand">
+##FILTER=<ID=Region,Description="Position is in dense region of snps or near the end of the contig.">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sample4
+gi|9626243|ref|NC_001416.1|	403	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:15:15:0:11:4:0:0:PASS
+gi|9626243|ref|NC_001416.1|	550	.	G	A	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:26:0:26:0:0:14:12:PASS
+gi|9626243|ref|NC_001416.1|	586	.	C	G	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:27:0:25:0:0:17:8:PASS
+gi|9626243|ref|NC_001416.1|	753	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:23:23:0:12:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	1019	.	C	T	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:22:0:22:0:0:8:14:PASS
+gi|9626243|ref|NC_001416.1|	1079	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:27:27:0:11:16:0:0:PASS
+gi|9626243|ref|NC_001416.1|	1540	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:28:28:0:14:14:0:0:PASS
+gi|9626243|ref|NC_001416.1|	1620	.	G	A	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:19:0:19:0:0:7:12:PASS
+gi|9626243|ref|NC_001416.1|	1650	.	G	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:26:0:26:0:0:10:16:PASS
+gi|9626243|ref|NC_001416.1|	1788	.	A	T	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:16:0:16:0:0:9:7:PASS
+gi|9626243|ref|NC_001416.1|	1804	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:18:18:0:7:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	2123	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:28:28:0:13:15:0:0:PASS
+gi|9626243|ref|NC_001416.1|	2439	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:27:27:0:10:17:0:0:PASS
+gi|9626243|ref|NC_001416.1|	2452	.	A	T	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:23:1:22:1:0:13:9:PASS
+gi|9626243|ref|NC_001416.1|	2599	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:19:19:0:8:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	3063	.	G	A	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:22:0:21:0:0:10:11:PASS
+gi|9626243|ref|NC_001416.1|	3351	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:24:24:0:10:14:0:0:PASS
+gi|9626243|ref|NC_001416.1|	3648	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:22:22:0:10:12:0:0:PASS
+gi|9626243|ref|NC_001416.1|	3656	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:28:28:0:18:10:0:0:PASS
+gi|9626243|ref|NC_001416.1|	3678	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:22:22:0:11:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	4977	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:27:26:1:14:12:0:1:PASS
+gi|9626243|ref|NC_001416.1|	5142	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:25:25:0:9:16:0:0:PASS
+gi|9626243|ref|NC_001416.1|	5336	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:33:33:0:11:22:0:0:PASS
+gi|9626243|ref|NC_001416.1|	5462	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:32:32:0:10:22:0:0:PASS
+gi|9626243|ref|NC_001416.1|	5482	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:26:25:1:13:12:0:1:PASS
+gi|9626243|ref|NC_001416.1|	5516	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:25:23:2:13:10:0:2:PASS
+gi|9626243|ref|NC_001416.1|	5800	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:18:18:0:10:8:0:0:PASS
+gi|9626243|ref|NC_001416.1|	5818	.	G	T	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:23:0:22:0:0:11:11:PASS
+gi|9626243|ref|NC_001416.1|	5994	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:25:25:0:15:10:0:0:PASS
+gi|9626243|ref|NC_001416.1|	6296	.	T	A	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:26:0:25:0:0:13:12:PASS
+gi|9626243|ref|NC_001416.1|	6535	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:27:27:0:13:14:0:0:PASS
+gi|9626243|ref|NC_001416.1|	6824	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:23:23:0:12:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	7424	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:6:6:0:0:6:0:0:PASS
+gi|9626243|ref|NC_001416.1|	7668	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:14:14:0:10:4:0:0:PASS
+gi|9626243|ref|NC_001416.1|	7897	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:21:21:0:11:10:0:0:PASS
+gi|9626243|ref|NC_001416.1|	8420	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:24:24:0:12:12:0:0:PASS
+gi|9626243|ref|NC_001416.1|	8938	.	T	A	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:29:0:29:0:0:17:12:PASS
+gi|9626243|ref|NC_001416.1|	9175	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:31:31:0:13:18:0:0:PASS
+gi|9626243|ref|NC_001416.1|	9234	.	C	T	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:21:0:21:0:0:10:11:PASS
+gi|9626243|ref|NC_001416.1|	9919	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:24:24:0:11:13:0:0:PASS
+gi|9626243|ref|NC_001416.1|	10127	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:24:24:0:12:12:0:0:PASS
+gi|9626243|ref|NC_001416.1|	10264	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:18:18:0:14:4:0:0:PASS
+gi|9626243|ref|NC_001416.1|	10421	.	G	T	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:18:0:18:0:0:8:10:PASS
+gi|9626243|ref|NC_001416.1|	10568	.	C	T	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:21:0:21:0:0:10:11:PASS
+gi|9626243|ref|NC_001416.1|	11066	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:27:26:1:9:17:0:1:PASS
+gi|9626243|ref|NC_001416.1|	11128	.	T	A	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:25:0:25:0:0:10:15:PASS
+gi|9626243|ref|NC_001416.1|	11782	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:23:23:0:11:12:0:0:PASS
+gi|9626243|ref|NC_001416.1|	12070	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:18:18:0:12:6:0:0:PASS
+gi|9626243|ref|NC_001416.1|	12717	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:20:19:1:7:12:1:0:PASS
+gi|9626243|ref|NC_001416.1|	12795	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:24:24:0:15:9:0:0:PASS
+gi|9626243|ref|NC_001416.1|	12876	.	G	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:19:0:19:0:0:7:12:PASS
+gi|9626243|ref|NC_001416.1|	12959	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:23:21:2:10:11:2:0:PASS
+gi|9626243|ref|NC_001416.1|	12970	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:23:23:0:13:10:0:0:PASS
+gi|9626243|ref|NC_001416.1|	13107	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:22:21:1:8:13:0:1:PASS
+gi|9626243|ref|NC_001416.1|	13264	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:23:23:0:12:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	13542	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:23:23:0:13:10:0:0:PASS
+gi|9626243|ref|NC_001416.1|	13647	.	C	T	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:17:0:17:0:0:11:6:PASS
+gi|9626243|ref|NC_001416.1|	13952	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:33:33:0:12:21:0:0:PASS
+gi|9626243|ref|NC_001416.1|	13971	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:30:29:1:11:18:0:1:PASS
+gi|9626243|ref|NC_001416.1|	15384	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:24:24:0:14:10:0:0:PASS
+gi|9626243|ref|NC_001416.1|	15715	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:23:23:0:8:15:0:0:PASS
+gi|9626243|ref|NC_001416.1|	15967	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:29:28:1:14:14:1:0:PASS
+gi|9626243|ref|NC_001416.1|	16070	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:25:24:1:11:13:0:1:PASS
+gi|9626243|ref|NC_001416.1|	16654	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:25:25:0:10:15:0:0:PASS
+gi|9626243|ref|NC_001416.1|	16715	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:20:20:0:6:14:0:0:PASS
+gi|9626243|ref|NC_001416.1|	17142	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:15:15:0:6:9:0:0:PASS
+gi|9626243|ref|NC_001416.1|	17311	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:10:10:0:1:9:0:0:PASS
+gi|9626243|ref|NC_001416.1|	17854	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:36:34:2:18:16:0:2:PASS
+gi|9626243|ref|NC_001416.1|	18151	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:25:25:0:14:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	18188	.	T	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:31:0:31:0:0:17:14:PASS
+gi|9626243|ref|NC_001416.1|	18210	.	C	G	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:29:0:29:0:0:15:14:PASS
+gi|9626243|ref|NC_001416.1|	18420	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:17:17:0:6:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	18598	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:20:20:0:12:8:0:0:PASS
+gi|9626243|ref|NC_001416.1|	18652	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:21:21:0:12:9:0:0:PASS
+gi|9626243|ref|NC_001416.1|	18989	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:21:21:0:7:14:0:0:PASS
+gi|9626243|ref|NC_001416.1|	19208	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:31:30:1:15:15:0:1:PASS
+gi|9626243|ref|NC_001416.1|	19448	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:33:33:0:21:12:0:0:PASS
+gi|9626243|ref|NC_001416.1|	19469	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:31:31:0:17:14:0:0:PASS
+gi|9626243|ref|NC_001416.1|	20079	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:32:32:0:17:15:0:0:PASS
+gi|9626243|ref|NC_001416.1|	20099	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:22:22:0:10:12:0:0:PASS
+gi|9626243|ref|NC_001416.1|	20289	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:29:28:1:13:15:1:0:PASS
+gi|9626243|ref|NC_001416.1|	20367	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:26:26:0:10:16:0:0:PASS
+gi|9626243|ref|NC_001416.1|	21110	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:16:16:0:9:7:0:0:PASS
+gi|9626243|ref|NC_001416.1|	21320	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:25:25:0:9:16:0:0:PASS
+gi|9626243|ref|NC_001416.1|	21653	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:19:19:0:10:9:0:0:PASS
+gi|9626243|ref|NC_001416.1|	22220	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:23:22:1:8:14:0:1:PASS
+gi|9626243|ref|NC_001416.1|	22357	.	G	A	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:21:0:21:0:0:11:10:PASS
+gi|9626243|ref|NC_001416.1|	22747	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:21:21:0:8:13:0:0:PASS
+gi|9626243|ref|NC_001416.1|	23362	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:24:24:0:11:13:0:0:PASS
+gi|9626243|ref|NC_001416.1|	23457	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:26:25:1:12:13:1:0:PASS
+gi|9626243|ref|NC_001416.1|	24043	.	C	A	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:15:0:15:0:0:7:8:PASS
+gi|9626243|ref|NC_001416.1|	24319	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:21:21:0:11:10:0:0:PASS
+gi|9626243|ref|NC_001416.1|	24766	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:14:14:0:5:9:0:0:PASS
+gi|9626243|ref|NC_001416.1|	24930	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:10:9:1:4:5:1:0:PASS
+gi|9626243|ref|NC_001416.1|	25005	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:16:16:0:10:6:0:0:PASS
+gi|9626243|ref|NC_001416.1|	25158	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:21:20:1:12:8:0:1:PASS
+gi|9626243|ref|NC_001416.1|	25645	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:26:26:0:13:13:0:0:PASS
+gi|9626243|ref|NC_001416.1|	26173	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:25:25:0:11:14:0:0:PASS
+gi|9626243|ref|NC_001416.1|	26728	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:22:22:0:9:13:0:0:PASS
+gi|9626243|ref|NC_001416.1|	26972	.	A	T	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:22:1:21:1:0:11:10:PASS
+gi|9626243|ref|NC_001416.1|	27412	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:15:15:0:7:8:0:0:PASS
+gi|9626243|ref|NC_001416.1|	27539	.	A	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:11:0:11:0:0:5:6:PASS
+gi|9626243|ref|NC_001416.1|	27661	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:18:18:0:10:8:0:0:PASS
+gi|9626243|ref|NC_001416.1|	27722	.	C	A	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:26:0:26:0:0:16:10:PASS
+gi|9626243|ref|NC_001416.1|	27790	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:19:19:0:14:5:0:0:PASS
+gi|9626243|ref|NC_001416.1|	27825	.	A	G	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:22:0:22:0:0:14:8:PASS
+gi|9626243|ref|NC_001416.1|	27834	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:21:20:1:11:9:1:0:PASS
+gi|9626243|ref|NC_001416.1|	28045	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:18:18:0:9:9:0:0:PASS
+gi|9626243|ref|NC_001416.1|	28362	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:13:13:0:13:0:0:0:PASS
+gi|9626243|ref|NC_001416.1|	29265	.	T	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:28:0:27:0:0:9:18:PASS
+gi|9626243|ref|NC_001416.1|	29411	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:36:35:1:17:18:1:0:PASS
+gi|9626243|ref|NC_001416.1|	29435	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:32:31:1:15:16:1:0:PASS
+gi|9626243|ref|NC_001416.1|	29891	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:29:28:1:15:13:1:0:PASS
+gi|9626243|ref|NC_001416.1|	30125	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:31:29:2:11:18:1:1:PASS
+gi|9626243|ref|NC_001416.1|	30757	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:28:28:0:13:15:0:0:PASS
+gi|9626243|ref|NC_001416.1|	30890	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:24:24:0:11:13:0:0:PASS
+gi|9626243|ref|NC_001416.1|	31328	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:9:9:0:9:0:0:0:PASS
+gi|9626243|ref|NC_001416.1|	31363	.	C	G	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:9:0:9:0:0:8:1:PASS
+gi|9626243|ref|NC_001416.1|	31551	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:21:21:0:14:7:0:0:PASS
+gi|9626243|ref|NC_001416.1|	32086	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:19:19:0:10:9:0:0:PASS
+gi|9626243|ref|NC_001416.1|	32660	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:24:23:1:12:11:1:0:PASS
+gi|9626243|ref|NC_001416.1|	33000	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:27:26:1:12:14:0:1:PASS
+gi|9626243|ref|NC_001416.1|	33591	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:19:19:0:9:10:0:0:PASS
+gi|9626243|ref|NC_001416.1|	33612	.	C	A	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:19:0:18:0:0:7:11:PASS
+gi|9626243|ref|NC_001416.1|	33865	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:21:21:0:12:9:0:0:PASS
+gi|9626243|ref|NC_001416.1|	34137	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:24:24:0:13:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	34370	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:32:31:1:15:16:1:0:PASS
+gi|9626243|ref|NC_001416.1|	34812	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:31:31:0:12:19:0:0:PASS
+gi|9626243|ref|NC_001416.1|	34920	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:22:22:0:6:16:0:0:PASS
+gi|9626243|ref|NC_001416.1|	35148	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:17:17:0:11:6:0:0:PASS
+gi|9626243|ref|NC_001416.1|	35802	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:21:21:0:7:14:0:0:PASS
+gi|9626243|ref|NC_001416.1|	35907	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:19:18:1:12:6:0:1:PASS
+gi|9626243|ref|NC_001416.1|	36010	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:23:23:0:11:12:0:0:PASS
+gi|9626243|ref|NC_001416.1|	36169	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:28:28:0:10:18:0:0:PASS
+gi|9626243|ref|NC_001416.1|	36642	.	T	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:17:0:17:0:0:2:15:PASS
+gi|9626243|ref|NC_001416.1|	37208	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:25:25:0:14:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	37387	.	A	T	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:15:0:15:0:0:7:8:PASS
+gi|9626243|ref|NC_001416.1|	37519	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:19:18:1:12:6:1:0:PASS
+gi|9626243|ref|NC_001416.1|	37898	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:16:15:1:11:4:0:1:PASS
+gi|9626243|ref|NC_001416.1|	38073	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:14:14:0:9:5:0:0:PASS
+gi|9626243|ref|NC_001416.1|	38165	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:18:18:0:7:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	38575	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:24:23:1:16:7:0:1:PASS
+gi|9626243|ref|NC_001416.1|	39003	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:25:25:0:14:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	39206	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:25:25:0:11:14:0:0:PASS
+gi|9626243|ref|NC_001416.1|	39484	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:21:21:0:10:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	39485	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:19:19:0:7:12:0:0:PASS
+gi|9626243|ref|NC_001416.1|	40457	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:30:30:0:15:15:0:0:PASS
+gi|9626243|ref|NC_001416.1|	40835	.	T	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:25:0:25:0:0:16:9:PASS
+gi|9626243|ref|NC_001416.1|	40984	.	A	G	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:22:0:21:0:0:12:9:PASS
+gi|9626243|ref|NC_001416.1|	41064	.	T	G	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:22:0:21:0:0:10:11:PASS
+gi|9626243|ref|NC_001416.1|	41448	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:19:18:1:9:9:1:0:PASS
+gi|9626243|ref|NC_001416.1|	41954	.	T	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:23:0:23:0:0:11:12:PASS
+gi|9626243|ref|NC_001416.1|	42439	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:25:25:0:11:14:0:0:PASS
+gi|9626243|ref|NC_001416.1|	43306	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:28:28:0:10:18:0:0:PASS
+gi|9626243|ref|NC_001416.1|	43470	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:27:26:1:17:9:0:1:PASS
+gi|9626243|ref|NC_001416.1|	44134	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:27:26:1:13:13:0:1:PASS
+gi|9626243|ref|NC_001416.1|	44201	.	G	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:25:0:24:0:0:15:9:PASS
+gi|9626243|ref|NC_001416.1|	44413	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:15:15:0:1:14:0:0:PASS
+gi|9626243|ref|NC_001416.1|	45364	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:27:26:1:11:15:1:0:PASS
+gi|9626243|ref|NC_001416.1|	45409	.	C	G	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:21:0:21:0:0:8:13:PASS
+gi|9626243|ref|NC_001416.1|	46237	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:28:26:2:10:16:0:2:PASS
+gi|9626243|ref|NC_001416.1|	46283	.	C	G	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:22:0:22:0:0:11:11:PASS
+gi|9626243|ref|NC_001416.1|	46842	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:25:25:0:10:15:0:0:PASS
+gi|9626243|ref|NC_001416.1|	47425	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:23:23:0:12:11:0:0:PASS
+gi|9626243|ref|NC_001416.1|	47893	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:22:22:0:11:11:0:0:PASS