Mercurial > repos > iuc > virheat

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Wed May 15 13:37:49 2024 +0000
@@ -0,0 +1,48 @@
+<?xml version="1.0"?>
+<macros>
+    <token name="@TOOL_VERSION@">0.6</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">21.01</token>
+    <xml name="biotools">
+        <xrefs>
+            <xref type="bio.tools">virheat</xref>
+        </xrefs>
+    </xml>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">virheat</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+    <xml name="version">
+        <version_command>virheat --version</version_command>
+    </xml>
+    <token name="@HELP_HEADER@"><![CDATA[
+What it does
+============
+
+This tool generates multi-sample variant-frequency plots from SnpEff-annotated
+viral variant lists.  The tool provides a condensed look at variant frequencies after mapping  raw reads to a viral/bacterial reference genome and compares multiple vcf files at the same time.
+
+The tool expects either the length of a reference genome or the gff3 file if the sequence annotation is needed.
+
+Additionally, to analyze whether mutations are sufficiently covered and to display non-covered cells in grey, first create per-base coverage TSV files for each BAM file with Qualimap and provide them in the same folder as the VCF files. Give them the same name as your VCF files.
+
+The tool expects input variant lists in VCF format. VCF datasets as produced by standard variant callers with
+
+   - variant allele frequencies encoded in an ``AF`` INFO field
+   - variant functional genomic effects annotated using SnpEff's EFF format
+
+]]></token>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">@unpublished{Fuchs2020,
+                author = {Fuchs, Jonas},
+                title = {},
+                year = {2020},
+                note = {Multi-sample annotated viral variant-frequency plots based on the R pheatmap package.},
+                address = {Institute for Virology, University of Freiburg}
+            }</citation>
+        </citations>
+    </xml>
+</macros>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SARS-CoV-2.gff3	Wed May 15 13:37:49 2024 +0000
@@ -0,0 +1,65 @@
+##gff-version 3
+#!gff-spec-version 1.21
+#!processor NCBI annotwriter
+##sequence-region NC_045512.2 1 29903
+##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=2697049
+NC_045512.2	RefSeq	region	1	29903	.	+	.	ID=NC_045512.2:1..29903;Dbxref=taxon:2697049;collection-date=Dec-2019;country=China;gb-acronym=SARS-CoV-2;gbkey=Src;genome=genomic;isolate=Wuhan-Hu-1;mol_type=genomic RNA;nat-host=Homo sapiens;old-name=Wuhan seafood market pneumonia virus
+NC_045512.2	RefSeq	five_prime_UTR	1	265	.	+	.	ID=id-NC_045512.2:1..265;gbkey=5'UTR
+NC_045512.2	RefSeq	gene	266	21555	.	+	.	ID=gene-GU280_gp01;Dbxref=GeneID:43740578;Name=ORF1ab;gbkey=Gene;gene=ORF1ab;gene_biotype=protein_coding;locus_tag=GU280_gp01
+NC_045512.2	RefSeq	CDS	266	13468	.	+	0	ID=cds-YP_009724389.1;Parent=gene-GU280_gp01;Dbxref=GenBank:YP_009724389.1,GeneID:43740578;Name=YP_009724389.1;Note=pp1ab%3B translated by -1 ribosomal frameshift;exception=ribosomal slippage;gbkey=CDS;gene=ORF1ab;locus_tag=GU280_gp01;product=ORF1ab polyprotein;protein_id=YP_009724389.1
+NC_045512.2	RefSeq	CDS	13468	21555	.	+	0	ID=cds-YP_009724389.1;Parent=gene-GU280_gp01;Dbxref=GenBank:YP_009724389.1,GeneID:43740578;Name=YP_009724389.1;Note=pp1ab%3B translated by -1 ribosomal frameshift;exception=ribosomal slippage;gbkey=CDS;gene=ORF1ab;locus_tag=GU280_gp01;product=ORF1ab polyprotein;protein_id=YP_009724389.1
+NC_045512.2	RefSeq	mature_protein_region_of_CDS	266	805	.	+	.	ID=id-YP_009724389.1:1..180;Note=nsp1%3B produced by both pp1a and pp1ab;Parent=cds-YP_009724389.1;gbkey=Prot;product=leader protein;protein_id=YP_009725297.1
+NC_045512.2	RefSeq	mature_protein_region_of_CDS	806	2719	.	+	.	ID=id-YP_009724389.1:181..818;Note=produced by both pp1a and pp1ab;Parent=cds-YP_009724389.1;gbkey=Prot;product=nsp2;protein_id=YP_009725298.1
+NC_045512.2	RefSeq	mature_protein_region_of_CDS	2720	8554	.	+	.	ID=id-YP_009724389.1:819..2763;Note=former nsp1%3B conserved domains are: N-terminal acidic (Ac)%2C predicted phosphoesterase%2C papain-like proteinase%2C Y-domain%2C transmembrane domain 1 (TM1)%2C adenosine diphosphate-ribose 1''-phosphatase (ADRP)%3B produced by both pp1a and pp1ab;Parent=cds-YP_009724389.1;gbkey=Prot;product=nsp3;protein_id=YP_009725299.1
+NC_045512.2	RefSeq	mature_protein_region_of_CDS	8555	10054	.	+	.	ID=id-YP_009724389.1:2764..3263;Note=nsp4B_TM%3B contains transmembrane domain 2 (TM2)%3B produced by both pp1a and pp1ab;Parent=cds-YP_009724389.1;gbkey=Prot;product=nsp4;protein_id=YP_009725300.1
+NC_045512.2	RefSeq	mature_protein_region_of_CDS	10055	10972	.	+	.	ID=id-YP_009724389.1:3264..3569;Note=nsp5A_3CLpro and nsp5B_3CLpro%3B main proteinase (Mpro)%3B mediates cleavages downstream of nsp4. 3D structure of the SARSr-CoV homolog has been determined (Yang et al.%2C 2003)%3B produced by both pp1a and pp1ab;Parent=cds-YP_009724389.1;gbkey=Prot;product=3C-like proteinase;protein_id=YP_009725301.1
+NC_045512.2	RefSeq	mature_protein_region_of_CDS	10973	11842	.	+	.	ID=id-YP_009724389.1:3570..3859;Note=nsp6_TM%3B putative transmembrane domain%3B produced by both pp1a and pp1ab;Parent=cds-YP_009724389.1;gbkey=Prot;product=nsp6;protein_id=YP_009725302.1
+NC_045512.2	RefSeq	mature_protein_region_of_CDS	11843	12091	.	+	.	ID=id-YP_009724389.1:3860..3942;Note=produced by both pp1a and pp1ab;Parent=cds-YP_009724389.1;gbkey=Prot;product=nsp7;protein_id=YP_009725303.1
+NC_045512.2	RefSeq	mature_protein_region_of_CDS	12092	12685	.	+	.	ID=id-YP_009724389.1:3943..4140;Note=produced by both pp1a and pp1ab;Parent=cds-YP_009724389.1;gbkey=Prot;product=nsp8;protein_id=YP_009725304.1
+NC_045512.2	RefSeq	mature_protein_region_of_CDS	12686	13024	.	+	.	ID=id-YP_009724389.1:4141..4253;Note=ssRNA-binding protein%3B produced by both pp1a and pp1ab;Parent=cds-YP_009724389.1;gbkey=Prot;product=nsp9;protein_id=YP_009725305.1
+NC_045512.2	RefSeq	mature_protein_region_of_CDS	13025	13441	.	+	.	ID=id-YP_009724389.1:4254..4392;Note=nsp10_CysHis%3B formerly known as growth-factor-like protein (GFL)%3B produced by both pp1a and pp1ab;Parent=cds-YP_009724389.1;gbkey=Prot;product=nsp10;protein_id=YP_009725306.1
+NC_045512.2	RefSeq	mature_protein_region_of_CDS	13442	13468	.	+	.	ID=id-YP_009724389.1:4393..5324;Note=nsp12%3B NiRAN and RdRp%3B produced by pp1ab only;Parent=cds-YP_009724389.1;gbkey=Prot;product=RNA-dependent RNA polymerase;protein_id=YP_009725307.1
+NC_045512.2	RefSeq	mature_protein_region_of_CDS	13468	16236	.	+	.	ID=id-YP_009724389.1:4393..5324;Note=nsp12%3B NiRAN and RdRp%3B produced by pp1ab only;Parent=cds-YP_009724389.1;gbkey=Prot;product=RNA-dependent RNA polymerase;protein_id=YP_009725307.1
+NC_045512.2	RefSeq	mature_protein_region_of_CDS	16237	18039	.	+	.	ID=id-YP_009724389.1:5325..5925;Note=nsp13_ZBD%2C nsp13_TB%2C and nsp_HEL1core%3B zinc-binding domain (ZD)%2C NTPase/helicase domain (HEL)%2C RNA 5'-triphosphatase%3B produced by pp1ab only;Parent=cds-YP_009724389.1;gbkey=Prot;product=helicase;protein_id=YP_009725308.1
+NC_045512.2	RefSeq	mature_protein_region_of_CDS	18040	19620	.	+	.	ID=id-YP_009724389.1:5926..6452;Note=nsp14A2_ExoN and nsp14B_NMT%3B produced by pp1ab only;Parent=cds-YP_009724389.1;gbkey=Prot;product=3'-to-5' exonuclease;protein_id=YP_009725309.1
+NC_045512.2	RefSeq	mature_protein_region_of_CDS	19621	20658	.	+	.	ID=id-YP_009724389.1:6453..6798;Note=nsp15-A1 and nsp15B-NendoU%3B produced by pp1ab only;Parent=cds-YP_009724389.1;gbkey=Prot;product=endoRNAse;protein_id=YP_009725310.1
+NC_045512.2	RefSeq	mature_protein_region_of_CDS	20659	21552	.	+	.	ID=id-YP_009724389.1:6799..7096;Note=nsp16_OMT%3B 2'-o-MT%3B produced by pp1ab only;Parent=cds-YP_009724389.1;gbkey=Prot;product=2'-O-ribose methyltransferase;protein_id=YP_009725311.1
+NC_045512.2	RefSeq	CDS	266	13483	.	+	0	ID=cds-YP_009725295.1;Parent=gene-GU280_gp01;Dbxref=GenBank:YP_009725295.1,GeneID:43740578;Name=YP_009725295.1;Note=pp1a;gbkey=CDS;gene=ORF1ab;locus_tag=GU280_gp01;product=ORF1a polyprotein;protein_id=YP_009725295.1
+NC_045512.2	RefSeq	mature_protein_region_of_CDS	266	805	.	+	.	ID=id-YP_009725295.1:1..180;Note=nsp1%3B produced by both pp1a and pp1ab;Parent=cds-YP_009725295.1;gbkey=Prot;product=leader protein;protein_id=YP_009742608.1
+NC_045512.2	RefSeq	mature_protein_region_of_CDS	806	2719	.	+	.	ID=id-YP_009725295.1:181..818;Note=produced by both pp1a and pp1ab;Parent=cds-YP_009725295.1;gbkey=Prot;product=nsp2;protein_id=YP_009742609.1
+NC_045512.2	RefSeq	mature_protein_region_of_CDS	2720	8554	.	+	.	ID=id-YP_009725295.1:819..2763;Note=former nsp1%3B conserved domains are: N-terminal acidic (Ac)%2C predicted phosphoesterase%2C papain-like proteinase%2C Y-domain%2C transmembrane domain 1 (TM1)%2C adenosine diphosphate-ribose 1''-phosphatase (ADRP)%3B produced by both pp1a and pp1ab;Parent=cds-YP_009725295.1;gbkey=Prot;product=nsp3;protein_id=YP_009742610.1
+NC_045512.2	RefSeq	mature_protein_region_of_CDS	8555	10054	.	+	.	ID=id-YP_009725295.1:2764..3263;Note=nsp4B_TM%3B contains transmembrane domain 2 (TM2)%3B produced by both pp1a and pp1ab;Parent=cds-YP_009725295.1;gbkey=Prot;product=nsp4;protein_id=YP_009742611.1
+NC_045512.2	RefSeq	mature_protein_region_of_CDS	10055	10972	.	+	.	ID=id-YP_009725295.1:3264..3569;Note=nsp5A_3CLpro and nsp5B_3CLpro%3B main proteinase (Mpro)%3B mediates cleavages downstream of nsp4. 3D structure of the SARSr-CoV homolog has been determined (Yang et al.%2C 2003)%3B produced by both pp1a and pp1ab;Parent=cds-YP_009725295.1;gbkey=Prot;product=3C-like proteinase;protein_id=YP_009742612.1
+NC_045512.2	RefSeq	mature_protein_region_of_CDS	10973	11842	.	+	.	ID=id-YP_009725295.1:3570..3859;Note=nsp6_TM%3B putative transmembrane domain%3B produced by both pp1a and pp1ab;Parent=cds-YP_009725295.1;gbkey=Prot;product=nsp6;protein_id=YP_009742613.1
+NC_045512.2	RefSeq	mature_protein_region_of_CDS	11843	12091	.	+	.	ID=id-YP_009725295.1:3860..3942;Note=produced by both pp1a and pp1ab;Parent=cds-YP_009725295.1;gbkey=Prot;product=nsp7;protein_id=YP_009742614.1
+NC_045512.2	RefSeq	mature_protein_region_of_CDS	12092	12685	.	+	.	ID=id-YP_009725295.1:3943..4140;Note=produced by both pp1a and pp1ab;Parent=cds-YP_009725295.1;gbkey=Prot;product=nsp8;protein_id=YP_009742615.1
+NC_045512.2	RefSeq	mature_protein_region_of_CDS	12686	13024	.	+	.	ID=id-YP_009725295.1:4141..4253;Note=ssRNA-binding protein%3B produced by both pp1a and pp1ab;Parent=cds-YP_009725295.1;gbkey=Prot;product=nsp9;protein_id=YP_009742616.1
+NC_045512.2	RefSeq	mature_protein_region_of_CDS	13025	13441	.	+	.	ID=id-YP_009725295.1:4254..4392;Note=nsp10_CysHis%3B formerly known as growth-factor-like protein (GFL)%3B produced by both pp1a and pp1ab;Parent=cds-YP_009725295.1;gbkey=Prot;product=nsp10;protein_id=YP_009742617.1
+NC_045512.2	RefSeq	mature_protein_region_of_CDS	13442	13480	.	+	.	ID=id-YP_009725295.1:4393..4405;Note=produced by pp1a only;Parent=cds-YP_009725295.1;gbkey=Prot;product=nsp11;protein_id=YP_009725312.1
+NC_045512.2	RefSeq	stem_loop	13476	13503	.	+	.	ID=id-GU280_gp01;Dbxref=GeneID:43740578;function=Coronavirus frameshifting stimulation element stem-loop 1;gbkey=stem_loop;gene=ORF1ab;inference=COORDINATES: profile:Rfam-release-14.1:RF00507%2CInfernal:1.1.2;locus_tag=GU280_gp01
+NC_045512.2	RefSeq	stem_loop	13488	13542	.	+	.	ID=id-GU280_gp01-2;Dbxref=GeneID:43740578;function=Coronavirus frameshifting stimulation element stem-loop 2;gbkey=stem_loop;gene=ORF1ab;inference=COORDINATES: profile:Rfam-release-14.1:RF00507%2CInfernal:1.1.2;locus_tag=GU280_gp01
+NC_045512.2	RefSeq	gene	21563	25384	.	+	.	ID=gene-GU280_gp02;Dbxref=GeneID:43740568;Name=S;gbkey=Gene;gene=S;gene_biotype=protein_coding;gene_synonym=spike glycoprotein;locus_tag=GU280_gp02
+NC_045512.2	RefSeq	CDS	21563	25384	.	+	0	ID=cds-YP_009724390.1;Parent=gene-GU280_gp02;Dbxref=GenBank:YP_009724390.1,GeneID:43740568;Name=YP_009724390.1;Note=structural protein%3B spike protein;gbkey=CDS;gene=S;locus_tag=GU280_gp02;product=surface glycoprotein;protein_id=YP_009724390.1
+NC_045512.2	RefSeq	gene	25393	26220	.	+	.	ID=gene-GU280_gp03;Dbxref=GeneID:43740569;Name=ORF3a;gbkey=Gene;gene=ORF3a;gene_biotype=protein_coding;locus_tag=GU280_gp03
+NC_045512.2	RefSeq	CDS	25393	26220	.	+	0	ID=cds-YP_009724391.1;Parent=gene-GU280_gp03;Dbxref=GenBank:YP_009724391.1,GeneID:43740569;Name=YP_009724391.1;gbkey=CDS;gene=ORF3a;locus_tag=GU280_gp03;product=ORF3a protein;protein_id=YP_009724391.1
+NC_045512.2	RefSeq	gene	26245	26472	.	+	.	ID=gene-GU280_gp04;Dbxref=GeneID:43740570;Name=E;gbkey=Gene;gene=E;gene_biotype=protein_coding;locus_tag=GU280_gp04
+NC_045512.2	RefSeq	CDS	26245	26472	.	+	0	ID=cds-YP_009724392.1;Parent=gene-GU280_gp04;Dbxref=GenBank:YP_009724392.1,GeneID:43740570;Name=YP_009724392.1;Note=ORF4%3B structural protein%3B E protein;gbkey=CDS;gene=E;locus_tag=GU280_gp04;product=envelope protein;protein_id=YP_009724392.1
+NC_045512.2	RefSeq	gene	26523	27191	.	+	.	ID=gene-GU280_gp05;Dbxref=GeneID:43740571;Name=M;gbkey=Gene;gene=M;gene_biotype=protein_coding;locus_tag=GU280_gp05
+NC_045512.2	RefSeq	CDS	26523	27191	.	+	0	ID=cds-YP_009724393.1;Parent=gene-GU280_gp05;Dbxref=GenBank:YP_009724393.1,GeneID:43740571;Name=YP_009724393.1;Note=ORF5%3B structural protein;gbkey=CDS;gene=M;locus_tag=GU280_gp05;product=membrane glycoprotein;protein_id=YP_009724393.1
+NC_045512.2	RefSeq	gene	27202	27387	.	+	.	ID=gene-GU280_gp06;Dbxref=GeneID:43740572;Name=ORF6;gbkey=Gene;gene=ORF6;gene_biotype=protein_coding;locus_tag=GU280_gp06
+NC_045512.2	RefSeq	CDS	27202	27387	.	+	0	ID=cds-YP_009724394.1;Parent=gene-GU280_gp06;Dbxref=GenBank:YP_009724394.1,GeneID:43740572;Name=YP_009724394.1;gbkey=CDS;gene=ORF6;locus_tag=GU280_gp06;product=ORF6 protein;protein_id=YP_009724394.1
+NC_045512.2	RefSeq	gene	27394	27759	.	+	.	ID=gene-GU280_gp07;Dbxref=GeneID:43740573;Name=ORF7a;gbkey=Gene;gene=ORF7a;gene_biotype=protein_coding;locus_tag=GU280_gp07
+NC_045512.2	RefSeq	CDS	27394	27759	.	+	0	ID=cds-YP_009724395.1;Parent=gene-GU280_gp07;Dbxref=GenBank:YP_009724395.1,GeneID:43740573;Name=YP_009724395.1;gbkey=CDS;gene=ORF7a;locus_tag=GU280_gp07;product=ORF7a protein;protein_id=YP_009724395.1
+NC_045512.2	RefSeq	gene	27756	27887	.	+	.	ID=gene-GU280_gp08;Dbxref=GeneID:43740574;Name=ORF7b;gbkey=Gene;gene=ORF7b;gene_biotype=protein_coding;locus_tag=GU280_gp08
+NC_045512.2	RefSeq	CDS	27756	27887	.	+	0	ID=cds-YP_009725318.1;Parent=gene-GU280_gp08;Dbxref=GenBank:YP_009725318.1,GeneID:43740574;Name=YP_009725318.1;gbkey=CDS;gene=ORF7b;locus_tag=GU280_gp08;product=ORF7b;protein_id=YP_009725318.1
+NC_045512.2	RefSeq	gene	27894	28259	.	+	.	ID=gene-GU280_gp09;Dbxref=GeneID:43740577;Name=ORF8;gbkey=Gene;gene=ORF8;gene_biotype=protein_coding;locus_tag=GU280_gp09
+NC_045512.2	RefSeq	CDS	27894	28259	.	+	0	ID=cds-YP_009724396.1;Parent=gene-GU280_gp09;Dbxref=GenBank:YP_009724396.1,GeneID:43740577;Name=YP_009724396.1;gbkey=CDS;gene=ORF8;locus_tag=GU280_gp09;product=ORF8 protein;protein_id=YP_009724396.1
+NC_045512.2	RefSeq	gene	28274	29533	.	+	.	ID=gene-GU280_gp10;Dbxref=GeneID:43740575;Name=N;gbkey=Gene;gene=N;gene_biotype=protein_coding;locus_tag=GU280_gp10
+NC_045512.2	RefSeq	CDS	28274	29533	.	+	0	ID=cds-YP_009724397.2;Parent=gene-GU280_gp10;Dbxref=GenBank:YP_009724397.2,GeneID:43740575;Name=YP_009724397.2;Note=ORF9%3B structural protein;gbkey=CDS;gene=N;locus_tag=GU280_gp10;product=nucleocapsid phosphoprotein;protein_id=YP_009724397.2
+NC_045512.2	RefSeq	gene	29558	29674	.	+	.	ID=gene-GU280_gp11;Dbxref=GeneID:43740576;Name=ORF10;gbkey=Gene;gene=ORF10;gene_biotype=protein_coding;locus_tag=GU280_gp11
+NC_045512.2	RefSeq	CDS	29558	29674	.	+	0	ID=cds-YP_009725255.1;Parent=gene-GU280_gp11;Dbxref=GenBank:YP_009725255.1,GeneID:43740576;Name=YP_009725255.1;gbkey=CDS;gene=ORF10;locus_tag=GU280_gp11;product=ORF10 protein;protein_id=YP_009725255.1
+NC_045512.2	RefSeq	stem_loop	29609	29644	.	+	.	ID=id-GU280_gp11;Dbxref=GeneID:43740576;function=Coronavirus 3' UTR pseudoknot stem-loop 1;gbkey=stem_loop;gene=ORF10;inference=COORDINATES: profile::Rfam-release-14.1:RF00165%2CInfernal:1.1.2;locus_tag=GU280_gp11
+NC_045512.2	RefSeq	stem_loop	29629	29657	.	+	.	ID=id-GU280_gp11-2;Dbxref=GeneID:43740576;function=Coronavirus 3' UTR pseudoknot stem-loop 2;gbkey=stem_loop;gene=ORF10;inference=COORDINATES: profile::Rfam-release-14.1:RF00165%2CInfernal:1.1.2;locus_tag=GU280_gp11
+NC_045512.2	RefSeq	three_prime_UTR	29675	29903	.	+	.	ID=id-NC_045512.2:29675..29903;gbkey=3'UTR
+NC_045512.2	RefSeq	stem_loop	29728	29768	.	+	.	ID=id-NC_045512.2:29728..29768;Note=basepair exception: alignment to the Rfam model implies coordinates 29740:29758 form a noncanonical C:T basepair%2C but the homologous positions form a highly conserved C:G basepair in other viruses%2C including SARS (NC_004718.3);function=Coronavirus 3' stem-loop II-like motif (s2m);gbkey=stem_loop;inference=COORDINATES: profile:Rfam-release-14.1:RF00164%2CInfernal:1.1.2
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/day_0.vcf	Wed May 15 13:37:49 2024 +0000
@@ -0,0 +1,115 @@
+##fileformat=VCFv4.0
+##fileDate=20221107
+##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 20 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.001 --bonf dynamic --no-default-filter --no-default-filter -r NC_045512:1-7475 -o /data/jwd/main/051/983/51983887/tmp/lofreq2_call_parallel5jc80x1b/0.vcf.gz reads.bam
+##reference=reference.fa
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth">
+##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
+##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias at this position">
+##INFO=<ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">
+##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position">
+##FILTER=<ID=min_snvqual_68,Description="Minimum SNV Quality (Phred) 68">
+##FILTER=<ID=min_indelqual_52,Description="Minimum Indel Quality (Phred) 52">
+##FILTER=<ID=min_snvqual_75,Description="Minimum SNV Quality (Phred) 75">
+##FILTER=<ID=min_indelqual_59,Description="Minimum Indel Quality (Phred) 59">
+##FILTER=<ID=min_af_0.100000,Description="Minimum allele frequency 0.100000">
+##FILTER=<ID=min_dp_20,Description="Minimum Coverage 20">
+##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000">
+##SnpEffVersion="4.3t (build 2017-11-24 10:18), by Pablo Cingolani"
+##SnpEffCmd="SnpEff  -i vcf -o vcf -formatEff -classic -no-downstream -no-intergenic -no-intron -no-upstream -stats /data/jwd/main/051/984/51984232/outputs/galaxy_dataset_f67ea69f-27ab-4c3a-8123-aa00ce3bcfc5.dat -csvStats /data/jwd/main/051/984/51984232/outputs/galaxy_dataset_b24403cd-d8d0-4f8b-8135-dd54e4d95bb6.dat SARS-CoV-2 /data/dnb06/galaxy_db/files/9/e/2/dataset_9e2f8143-a5e2-4252-a581-f7ebfdbad1a0.dat "
+##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_Change| Amino_Acid_length | Gene_Name | Transcript_BioType | Gene_Coding | Transcript_ID | Exon_Rank  | Genotype [ | ERRORS | WARNINGS ] )' ">
+##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
+##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+NC_045512	509	.	GGTCATGTTA	G	49314.0	PASS	AF=0.985068;DP=2143;DP4=115,135,1144,967;HRUN=2;SB=18;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggtcatgttatg/gtg|GHVM82V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	670	.	T	G	49314.0	PASS	AF=0.946303;DP=2272;DP4=0,1,1147,1122;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agT/agG|S135R|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	900	.	C	T	49314.0	PASS	AF=0.956388;DP=4563;DP4=2,1,2338,2219;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S212L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	1980	.	G	T	8807.0	PASS	AF=0.932806;DP=253;DP4=0,0,120,132;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gTa|G572V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	2790	.	C	T	38289.0	PASS	AF=0.939585;DP=1109;DP4=1,0,544,559;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T842I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	3037	.	C	T	49314.0	PASS	AF=0.942435;DP=2571;DP4=1,0,1309,1252;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	4184	.	G	A	49314.0	PASS	AF=0.957771;DP=1705;DP4=1,3,980,720;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G1307S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
+NC_045512	4321	.	C	T	25301.0	PASS	AF=0.559110;DP=1438;DP4=560,9,445,420;SB=1004;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A1352|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	9344	.	C	T	42764.0	PASS	AF=0.962932;DP=1187;DP4=0,0,585,600;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L3027F|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	9424	.	A	G	39669.0	PASS	AF=0.939264;DP=1169;DP4=0,1,571,594;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V3053|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	9534	.	C	T	49314.0	PASS	AF=0.953536;DP=1937;DP4=0,0,954,979;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T3090I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	9866	.	C	T	46582.0	PASS	AF=0.947727;DP=1320;DP4=1,0,728,589;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L3201F|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	10007	.	G	T	8795.0	PASS	AF=0.163850;DP=2130;DP4=835,931,175,188;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Ttt|V3248F|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	10029	.	C	T	49314.0	PASS	AF=0.921837;DP=2047;DP4=1,1,980,1059;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T3255I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	10198	.	C	T	49314.0	PASS	AF=0.966712;DP=1472;DP4=0,0,732,739;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D3311|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	10447	.	G	A	20327.0	PASS	AF=0.937824;DP=579;DP4=0,1,279,294;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R3394|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
+NC_045512	10449	.	C	A	20378.0	PASS	AF=0.937075;DP=588;DP4=0,1,290,294;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cAc|P3395H|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
+NC_045512	11287	.	GTCTGGTTTT	G	11976.0	PASS	AF=0.992188;DP=384;DP4=25,32,186,195;HRUN=1;SB=2;INDEL;EFF=CODON_DELETION(MODERATE||tctggtttt/|SGF3675|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	11986	.	CT	C	9884.0	PASS	AF=0.180684;DP=1843;DP4=734,794,158,175;HRUN=3;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/|F3908|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|1|1.00)
+NC_045512	12010	.	T	C	9640.0	PASS	AF=0.197383;DP=1834;DP4=690,757,180,200;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctT/ctC|L3915|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|C)
+NC_045512	12880	.	C	T	28248.0	PASS	AF=0.952261;DP=796;DP4=0,0,395,400;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I4205|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	14408	.	C	T	49314.0	PASS	AF=0.948265;DP=3054;DP4=1,0,1504,1544;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P4720L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	15451	.	G	A	49314.0	PASS	AF=0.668282;DP=2683;DP4=422,343,1040,871;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G5068S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|A)
+NC_045512	15714	.	C	T	49314.0	PASS	AF=0.952639;DP=2027;DP4=0,2,1001,1018;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L5155|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	17410	.	C	T	21064.0	PASS	AF=0.953177;DP=598;DP4=0,0,305,292;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R5721C|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	18099	.	T	C	2222.0	PASS	AF=0.195699;DP=465;DP4=178,186,49,52;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P5950|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|C)
+NC_045512	18109	.	C	T	2238.0	PASS	AF=0.202899;DP=414;DP4=157,163,42,49;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P5954S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	18163	.	A	G	12159.0	PASS	AF=0.915761;DP=368;DP4=1,0,189,177;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I5972V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G)
+NC_045512	19567	.	G	A	3996.0	PASS	AF=0.122390;DP=1389;DP4=399,801,80,108;SB=18;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V6440I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|A)
+NC_045512	19573	.	A	G	4596.0	PASS	AF=0.133286;DP=1418;DP4=444,765,73,136;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aaa/Gaa|K6442E|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G)
+NC_045512	19955	.	C	T	49314.0	PASS	AF=0.935817;DP=2228;DP4=2,1,1095,1125;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T6569I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	20055	.	A	G	14927.0	PASS	AF=0.849794;DP=486;DP4=33,1,222,229;SB=82;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E6602|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G)
+NC_045512	20719	.	C	T	12143.0	PASS	AF=0.906077;DP=362;DP4=0,0,194,166;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L6824|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	21618	.	C	T	49314.0	PASS	AF=0.958417;DP=1491;DP4=0,2,708,779;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T19I|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	21632	.	TTACCCCCTG	T	45139.0	PASS	AF=0.979167;DP=1344;DP4=62,51,610,706;HRUN=2;SB=10;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ttaccccctgca/tca|LPPA24S|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	21987	.	G	A	49314.0	PASS	AF=0.916475;DP=1736;DP4=1,0,947,785;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G142D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22200	.	T	G	43891.0	PASS	AF=0.923369;DP=1318;DP4=2,0,598,712;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gGg|V213G|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	22578	.	G	A	49314.0	PASS	AF=0.916014;DP=2298;DP4=1,2,1129,1159;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G339D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22629	.	A	C	49314.0	PASS	AF=0.941638;DP=2039;DP4=1,2,1001,1029;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aCg|K356T|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22664	.	C	A	49314.0	PASS	AF=0.931017;DP=1986;DP4=3,2,952,1020;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cta/Ata|L368I|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22674	.	C	T	49314.0	PASS	AF=0.923038;DP=1962;DP4=0,0,934,1020;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S371F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22679	.	T	C	49314.0	PASS	AF=0.924305;DP=1942;DP4=5,2,932,999;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Cca|S373P|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22686	.	C	T	49314.0	PASS	AF=0.944383;DP=1816;DP4=1,3,872,930;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S375F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22688	.	A	G	49314.0	PASS	AF=0.930825;DP=1807;DP4=1,3,878,920;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T376A|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	22716	.	C	T	49314.0	PASS	AF=0.943596;DP=1702;DP4=0,1,861,835;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T385I|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22775	.	G	A	35776.0	PASS	AF=0.497243;DP=5440;DP4=1181,1454,1224,1580;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D405N|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22786	.	A	C	49314.0	PASS	AF=0.899777;DP=3143;DP4=4,10,1370,1749;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agA/agC|R408S|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22792	.	C	T	49314.0	PASS	AF=0.951280;DP=3202;DP4=1,3,1397,1798;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I410|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22813	.	G	T	49314.0	PASS	AF=0.955807;DP=3530;DP4=0,0,1594,1929;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaG/aaT|K417N|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22882	.	T	G	49314.0	PASS	AF=0.914912;DP=2374;DP4=2,5,1226,1137;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N440K|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	22992	.	G	A	49314.0	PASS	AF=0.949436;DP=2393;DP4=1,3,1142,1241;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S477N|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22995	.	C	A	49314.0	PASS	AF=0.953994;DP=2391;DP4=1,0,1143,1237;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aAa|T478K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	23013	.	A	C	49314.0	PASS	AF=0.925880;DP=2415;DP4=6,8,1143,1254;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gCa|E484A|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	23040	.	A	G	49314.0	PASS	AF=0.934878;DP=2288;DP4=1,1,1075,1204;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q493R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23055	.	A	G	49314.0	PASS	AF=0.923908;DP=2129;DP4=0,1,996,1130;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q498R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23063	.	A	T	49314.0	PASS	AF=0.949386;DP=2035;DP4=1,0,957,1073;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Tat|N501Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	23075	.	T	C	49314.0	PASS	AF=0.929851;DP=2010;DP4=1,2,968,1036;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y505H|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	23403	.	A	G	13496.0	PASS	AF=0.911111;DP=405;DP4=0,0,194,209;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D614G|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23525	.	C	T	13061.0	PASS	AF=0.961749;DP=366;DP4=0,0,179,186;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H655Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	23599	.	T	G	25427.0	PASS	AF=0.933060;DP=732;DP4=1,0,357,374;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N679K|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23604	.	C	A	25309.0	PASS	AF=0.950207;DP=723;DP4=1,0,355,367;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cAt|P681H|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	23854	.	C	A	13475.0	PASS	AF=0.936061;DP=391;DP4=0,3,201,187;SB=9;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaC/aaA|N764K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	23896	.	C	A	14321.0	PASS	AF=0.924706;DP=425;DP4=1,0,218,204;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acA|T778|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	23948	.	G	T	15027.0	PASS	AF=0.945368;DP=421;DP4=0,0,211,208;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Tat|D796Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	24414	.	T	C	6543.0	PASS	AF=0.109148;DP=2547;DP4=1157,1077,145,151;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V951A|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	24424	.	A	T	49314.0	PASS	AF=0.941726;DP=2677;DP4=2,6,1383,1284;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caA/caT|Q954H|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	24469	.	T	A	49314.0	PASS	AF=0.938789;DP=3104;DP4=4,5,1574,1511;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaA|N969K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	24966	.	A	G	39163.0	PASS	AF=0.592112;DP=2079;DP4=355,383,644,670;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aGc|N1135S|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	25000	.	C	T	49314.0	PASS	AF=0.929600;DP=1875;DP4=2,2,933,929;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D1146|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	25584	.	C	T	49314.0	PASS	AF=0.791209;DP=1911;DP4=116,111,898,783;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T64|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
+NC_045512	26060	.	C	T	49009.0	PASS	AF=0.932336;DP=1404;DP4=0,0,688,704;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T223I|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
+NC_045512	26270	.	C	T	16453.0	PASS	AF=0.950216;DP=462;DP4=0,0,237,225;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T9I|75|E|protein_coding|CODING|GU280_gp04|1|T)
+NC_045512	26577	.	C	G	49314.0	PASS	AF=0.936701;DP=1564;DP4=0,0,777,780;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q19E|222|M|protein_coding|CODING|GU280_gp05|1|G)
+NC_045512	26709	.	G	A	49314.0	PASS	AF=0.935736;DP=2303;DP4=1,4,1144,1147;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A63T|222|M|protein_coding|CODING|GU280_gp05|1|A)
+NC_045512	26801	.	C	T	49314.0	PASS	AF=0.938601;DP=2101;DP4=0,0,996,1101;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L93|222|M|protein_coding|CODING|GU280_gp05|1|T)
+NC_045512	26858	.	C	T	49314.0	PASS	AF=0.957931;DP=1759;DP4=1,1,822,931;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F112|222|M|protein_coding|CODING|GU280_gp05|1|T)
+NC_045512	27259	.	A	C	44987.0	PASS	AF=0.935045;DP=1324;DP4=0,1,622,699;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Agg/Cgg|R20|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
+NC_045512	27382	.	G	C	18297.0	PASS	AF=0.947059;DP=510;DP4=0,0,261,247;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Cat|D61H|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
+NC_045512	27383	.	A	T	18139.0	PASS	AF=0.940711;DP=506;DP4=0,0,260,245;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gTt|D61V|61|ORF6|protein_coding|CODING|GU280_gp06|1|T)
+NC_045512	27384	.	T	C	18232.0	PASS	AF=0.932563;DP=519;DP4=1,1,266,249;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D61|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
+NC_045512	27481	.	C	T	21723.0	PASS	AF=0.939873;DP=632;DP4=0,0,317,313;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L30F|121|ORF7a|protein_coding|CODING|GU280_gp07|1|T)
+NC_045512	27549	.	C	T	49314.0	PASS	AF=0.955696;DP=1738;DP4=0,0,889,845;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N52|121|ORF7a|protein_coding|CODING|GU280_gp07|1|T)
+NC_045512	27807	.	C	T	38239.0	PASS	AF=0.954248;DP=1071;DP4=0,1,536,532;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L18|43|ORF7b|protein_coding|CODING|GU280_gp08|1|T)
+NC_045512	28271	.	A	T	49314.0	PASS	AF=0.938308;DP=2010;DP4=3,7,1017,983;SB=6
+NC_045512	28311	.	C	T	49314.0	PASS	AF=0.876293;DP=2126;DP4=6,3,1078,1031;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cTc|P13L|419|N|protein_coding|CODING|GU280_gp10|1|T)
+NC_045512	28361	.	GGAGAACGCA	G	45389.0	PASS	AF=0.770975;DP=1764;DP4=274,137,617,743;HRUN=2;SB=135;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggagaacgcagt/ggt|GERS30G|419|N|protein_coding|CODING|GU280_gp10|1|G|INFO_REALIGN_3_PRIME)
+NC_045512	28881	.	G	A	49314.0	PASS	AF=0.944488;DP=2540;DP4=1,0,1235,1301;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aAg|R203K|419|N|protein_coding|CODING|GU280_gp10|1|A)
+NC_045512	28882	.	G	A	49314.0	PASS	AF=0.927811;DP=2535;DP4=1,3,1230,1289;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R203|419|N|protein_coding|CODING|GU280_gp10|1|A)
+NC_045512	28883	.	G	C	49314.0	PASS	AF=0.943889;DP=2602;DP4=0,0,1268,1330;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gga/Cga|G204R|419|N|protein_coding|CODING|GU280_gp10|1|C)
+NC_045512	29510	.	A	C	49314.0	PASS	AF=0.942593;DP=5400;DP4=3,3,2537,2850;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agt/Cgt|S413R|419|N|protein_coding|CODING|GU280_gp10|1|C)
+NC_045512	29733	.	CGAGGCCACGCGGAGTACGATCGAGTG	C	49314.0	PASS	AF=0.986599;DP=2164;DP4=460,413,897,1238;HRUN=1;SB=69;INDEL
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/day_100.vcf	Wed May 15 13:37:49 2024 +0000
@@ -0,0 +1,123 @@
+##fileformat=VCFv4.0
+##fileDate=20221107
+##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 20 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.001 --bonf dynamic --no-default-filter --no-default-filter -r NC_045512:1-7475 -o /data/jwd/main/051/983/51983886/tmp/lofreq2_call_parallel739h_0kf/0.vcf.gz reads.bam
+##reference=reference.fa
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth">
+##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
+##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias at this position">
+##INFO=<ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">
+##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position">
+##FILTER=<ID=min_snvqual_67,Description="Minimum SNV Quality (Phred) 67">
+##FILTER=<ID=min_indelqual_51,Description="Minimum Indel Quality (Phred) 51">
+##FILTER=<ID=min_snvqual_75,Description="Minimum SNV Quality (Phred) 75">
+##FILTER=<ID=min_indelqual_59,Description="Minimum Indel Quality (Phred) 59">
+##FILTER=<ID=min_af_0.100000,Description="Minimum allele frequency 0.100000">
+##FILTER=<ID=min_dp_20,Description="Minimum Coverage 20">
+##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000">
+##SnpEffVersion="4.3t (build 2017-11-24 10:18), by Pablo Cingolani"
+##SnpEffCmd="SnpEff  -i vcf -o vcf -formatEff -classic -no-downstream -no-intergenic -no-intron -no-upstream -stats /data/jwd01/main/051/984/51984231/outputs/galaxy_dataset_2a6dc736-1c58-4b90-a56b-3c41b5b241ad.dat -csvStats /data/jwd01/main/051/984/51984231/outputs/galaxy_dataset_a3db7d9d-012b-4774-8ac9-298af3edbf29.dat SARS-CoV-2 /data/dnb07/galaxy_db/files/f/4/0/dataset_f402fbb5-67b8-463c-a425-3fd5d921cfdb.dat "
+##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_Change| Amino_Acid_length | Gene_Name | Transcript_BioType | Gene_Coding | Transcript_ID | Exon_Rank  | Genotype [ | ERRORS | WARNINGS ] )' ">
+##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
+##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+NC_045512	509	.	GGTCATGTTA	G	49314.0	PASS	AF=0.991453;DP=1638;DP4=78,102,891,733;HRUN=2;SB=24;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggtcatgttatg/gtg|GHVM82V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	670	.	T	G	49314.0	PASS	AF=0.936671;DP=1658;DP4=0,1,818,837;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agT/agG|S135R|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	900	.	C	T	49314.0	PASS	AF=0.963995;DP=2944;DP4=0,0,1497,1442;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S212L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	1980	.	G	T	11162.0	PASS	AF=0.920000;DP=325;DP4=2,1,151,170;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gTa|G572V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	2790	.	C	T	32452.0	PASS	AF=0.949134;DP=924;DP4=0,0,467,454;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T842I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	3037	.	C	T	49314.0	PASS	AF=0.947160;DP=1514;DP4=0,0,751,753;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	4184	.	G	A	30094.0	PASS	AF=0.946387;DP=858;DP4=1,1,504,349;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G1307S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
+NC_045512	4276	.	C	T	36928.0	PASS	AF=0.956772;DP=1041;DP4=1,0,699,339;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y1337|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	4321	.	C	T	25367.0	PASS	AF=0.732809;DP=1018;DP4=207,8,412,388;SB=398;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A1352|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	5302	.	A	G	22744.0	PASS	AF=0.476312;DP=1562;DP4=406,385,386,382;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A1679|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	5628	.	C	T	33093.0	PASS	AF=0.967161;DP=944;DP4=2,1,464,477;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T1788M|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	6354	.	C	T	18176.0	PASS	AF=0.551521;DP=1019;DP4=415,0,341,260;SB=723;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S2030L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	9344	.	C	T	38314.0	PASS	AF=0.961718;DP=1071;DP4=0,0,532,537;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L3027F|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	9424	.	A	G	32921.0	PASS	AF=0.938797;DP=964;DP4=0,1,477,483;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V3053|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	9534	.	C	T	49314.0	PASS	AF=0.951883;DP=1912;DP4=0,0,952,953;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T3090I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	9866	.	C	T	41117.0	PASS	AF=0.943364;DP=1183;DP4=0,0,632,546;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L3201F|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	10029	.	C	T	49314.0	PASS	AF=0.917537;DP=1819;DP4=1,1,874,935;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T3255I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	10198	.	C	T	42686.0	PASS	AF=0.946414;DP=1213;DP4=0,0,616,594;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D3311|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	10447	.	G	A	34188.0	PASS	AF=0.929293;DP=990;DP4=0,0,489,499;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R3394|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
+NC_045512	10449	.	C	A	33538.0	PASS	AF=0.913968;DP=988;DP4=1,1,489,494;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cAc|P3395H|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
+NC_045512	11287	.	GTCTGGTTTT	G	14876.0	PASS	AF=0.981289;DP=481;DP4=32,39,234,238;HRUN=1;SB=2;INDEL;EFF=CODON_DELETION(MODERATE||tctggtttt/|SGF3675|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	12036	.	C	T	41955.0	PASS	AF=0.926772;DP=1270;DP4=1,1,633,631;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A3924V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	12624	.	C	A	13590.0	PASS	AF=0.375369;DP=1356;DP4=381,440,250,283;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cAt|P4120H|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
+NC_045512	12854	.	C	T	28796.0	PASS	AF=0.926506;DP=830;DP4=1,1,403,422;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P4197S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	12880	.	C	T	29279.0	PASS	AF=0.946860;DP=828;DP4=0,0,397,428;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I4205|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	14408	.	C	T	49314.0	PASS	AF=0.951433;DP=2512;DP4=1,1,1232,1273;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P4720L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	15451	.	G	A	49314.0	PASS	AF=0.917309;DP=1947;DP4=20,20,1022,883;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G5068S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|A)
+NC_045512	15714	.	C	T	49314.0	PASS	AF=0.947186;DP=1439;DP4=0,0,709,724;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L5155|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	16915	.	C	T	2734.0	PASS	AF=0.133886;DP=844;DP4=342,376,58,66;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L5556|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	17410	.	C	T	19215.0	PASS	AF=0.938406;DP=552;DP4=0,0,269,280;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R5721C|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	18163	.	A	G	15895.0	PASS	AF=0.924843;DP=479;DP4=1,1,239,238;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I5972V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G)
+NC_045512	19955	.	C	T	49314.0	PASS	AF=0.943801;DP=2847;DP4=1,0,1468,1375;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T6569I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	20055	.	A	G	26271.0	PASS	AF=0.905000;DP=800;DP4=25,2,382,389;SB=53;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E6602|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G)
+NC_045512	20719	.	C	T	11109.0	PASS	AF=0.928349;DP=321;DP4=0,0,165,154;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L6824|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	21618	.	C	T	49314.0	PASS	AF=0.958054;DP=2384;DP4=0,0,1161,1218;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T19I|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	21632	.	TTACCCCCTG	T	49314.0	PASS	AF=0.979592;DP=2156;DP4=73,71,1008,1104;HRUN=2;SB=3;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ttaccccctgca/tca|LPPA24S|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	21851	.	A	C	4638.0	PASS	AF=0.285217;DP=575;DP4=201,194,91,88;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aag/Cag|K97Q|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	21987	.	G	A	49314.0	PASS	AF=0.912939;DP=2079;DP4=1,2,1084,985;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G142D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22200	.	T	G	37598.0	PASS	AF=0.928826;DP=1124;DP4=4,0,516,602;SB=13;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gGg|V213G|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	22578	.	G	A	49314.0	PASS	AF=0.929839;DP=2366;DP4=5,5,1155,1192;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G339D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22599	.	G	C	49314.0	PASS	AF=0.954260;DP=2230;DP4=0,0,1094,1131;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGa/aCa|R346T|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22629	.	A	C	49314.0	PASS	AF=0.949074;DP=2160;DP4=0,1,1062,1095;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aCg|K356T|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22664	.	C	A	49314.0	PASS	AF=0.940941;DP=1998;DP4=2,1,962,1029;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cta/Ata|L368I|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22674	.	C	T	49314.0	PASS	AF=0.931911;DP=1968;DP4=0,0,919,1041;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S371F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22679	.	T	C	49314.0	PASS	AF=0.927711;DP=1909;DP4=1,1,907,995;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Cca|S373P|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22686	.	C	T	49314.0	PASS	AF=0.940745;DP=1772;DP4=1,2,855,907;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S375F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22688	.	A	G	49314.0	PASS	AF=0.917285;DP=1753;DP4=1,0,854,892;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T376A|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	22716	.	C	T	49314.0	PASS	AF=0.939832;DP=1662;DP4=1,0,839,819;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T385I|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22775	.	G	A	49314.0	PASS	AF=0.546070;DP=5166;DP4=1022,1217,1310,1612;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D405N|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22786	.	A	C	49314.0	PASS	AF=0.902530;DP=3201;DP4=4,15,1426,1748;SB=14;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agA/agC|R408S|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22792	.	C	T	49314.0	PASS	AF=0.953403;DP=3262;DP4=0,0,1467,1793;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I410|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22813	.	G	T	49314.0	PASS	AF=0.957267;DP=3557;DP4=0,3,1634,1915;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaG/aaT|K417N|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22882	.	T	G	49314.0	PASS	AF=0.927554;DP=2457;DP4=3,5,1261,1185;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N440K|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	22992	.	G	A	49314.0	PASS	AF=0.961011;DP=2334;DP4=0,0,1125,1199;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S477N|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22995	.	C	A	49314.0	PASS	AF=0.951303;DP=2341;DP4=0,3,1136,1201;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aAa|T478K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	23013	.	A	C	49314.0	PASS	AF=0.919054;DP=2409;DP4=11,12,1145,1237;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gCa|E484A|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	23040	.	A	G	49314.0	PASS	AF=0.934744;DP=2268;DP4=2,2,1075,1185;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q493R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23055	.	A	G	49314.0	PASS	AF=0.923112;DP=2185;DP4=1,4,1048,1127;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q498R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23063	.	A	T	49314.0	PASS	AF=0.970673;DP=2080;DP4=0,0,1009,1070;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Tat|N501Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	23075	.	T	C	49314.0	PASS	AF=0.924171;DP=2110;DP4=1,1,1034,1072;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y505H|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	23403	.	A	G	17452.0	PASS	AF=0.944554;DP=505;DP4=0,0,249,254;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D614G|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23525	.	C	T	15743.0	PASS	AF=0.921569;DP=459;DP4=0,0,219,239;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H655Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	23599	.	T	G	49314.0	PASS	AF=0.936208;DP=1693;DP4=1,2,868,820;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N679K|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23604	.	C	A	49314.0	PASS	AF=0.948901;DP=1683;DP4=1,1,864,817;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cAt|P681H|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	23781	.	T	C	48027.0	PASS	AF=0.939855;DP=1380;DP4=1,3,684,689;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M740T|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	23854	.	C	A	38813.0	PASS	AF=0.944593;DP=1119;DP4=0,2,553,558;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaC/aaA|N764K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	23948	.	G	T	49314.0	PASS	AF=0.951482;DP=1484;DP4=0,0,752,729;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Tat|D796Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	24424	.	A	T	49314.0	PASS	AF=0.939243;DP=3012;DP4=3,8,1569,1427;SB=8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caA/caT|Q954H|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	24469	.	T	A	49314.0	PASS	AF=0.933240;DP=3580;DP4=4,1,1833,1737;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaA|N969K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	24821	.	G	T	49314.0	PASS	AF=0.443133;DP=5337;DP4=1396,1351,1294,1272;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Tca|A1087S|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	24966	.	A	G	49314.0	PASS	AF=0.915657;DP=2229;DP4=1,4,1078,1118;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aGc|N1135S|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	25000	.	C	T	49314.0	PASS	AF=0.941489;DP=2068;DP4=1,2,1046,1013;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D1146|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	25584	.	C	T	49314.0	PASS	AF=0.889061;DP=2578;DP4=4,4,1376,1190;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T64|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
+NC_045512	26060	.	C	T	49314.0	PASS	AF=0.944794;DP=2862;DP4=1,1,1439,1419;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T223I|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
+NC_045512	26195	.	C	T	42512.0	PASS	AF=0.922109;DP=1271;DP4=1,0,616,646;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T268M|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
+NC_045512	26270	.	C	T	48617.0	PASS	AF=0.956458;DP=1355;DP4=1,0,691,661;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T9I|75|E|protein_coding|CODING|GU280_gp04|1|T)
+NC_045512	26408	.	C	T	49314.0	PASS	AF=0.940901;DP=2775;DP4=1,0,1395,1339;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tTt|S55F|75|E|protein_coding|CODING|GU280_gp04|1|T)
+NC_045512	26577	.	C	G	49314.0	PASS	AF=0.927210;DP=1731;DP4=1,2,842,853;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q19E|222|M|protein_coding|CODING|GU280_gp05|1|G)
+NC_045512	26709	.	G	A	49314.0	PASS	AF=0.940457;DP=3107;DP4=1,2,1566,1529;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A63T|222|M|protein_coding|CODING|GU280_gp05|1|A)
+NC_045512	26801	.	C	T	49314.0	PASS	AF=0.944444;DP=3312;DP4=1,0,1635,1671;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L93|222|M|protein_coding|CODING|GU280_gp05|1|T)
+NC_045512	26858	.	C	T	49314.0	PASS	AF=0.959469;DP=2862;DP4=1,1,1379,1474;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F112|222|M|protein_coding|CODING|GU280_gp05|1|T)
+NC_045512	27259	.	A	C	49314.0	PASS	AF=0.921806;DP=3632;DP4=13,19,1694,1891;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|Agg/Cgg|R20|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
+NC_045512	27382	.	G	C	41385.0	PASS	AF=0.929780;DP=1182;DP4=0,0,575,603;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Cat|D61H|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
+NC_045512	27383	.	A	T	41295.0	PASS	AF=0.931624;DP=1170;DP4=2,2,566,595;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gTt|D61V|61|ORF6|protein_coding|CODING|GU280_gp06|1|T)
+NC_045512	27384	.	T	C	41493.0	PASS	AF=0.926520;DP=1184;DP4=1,0,575,600;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D61|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
+NC_045512	27481	.	C	A	49154.0	PASS	AF=0.936924;DP=1411;DP4=1,1,720,687;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Att|L30I|121|ORF7a|protein_coding|CODING|GU280_gp07|1|A)
+NC_045512	27549	.	C	T	49314.0	PASS	AF=0.955828;DP=3509;DP4=0,0,1775,1729;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N52|121|ORF7a|protein_coding|CODING|GU280_gp07|1|T)
+NC_045512	27807	.	C	T	49314.0	PASS	AF=0.949483;DP=1742;DP4=1,2,854,880;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L18|43|ORF7b|protein_coding|CODING|GU280_gp08|1|T)
+NC_045512	28271	.	A	T	49314.0	PASS	AF=0.938697;DP=3915;DP4=1,14,1939,1948;SB=30
+NC_045512	28307	.	G	A	49314.0	PASS	AF=0.898558;DP=3953;DP4=1,7,1945,1961;SB=11;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A12T|419|N|protein_coding|CODING|GU280_gp10|1|A)
+NC_045512	28311	.	C	T	49314.0	PASS	AF=0.823724;DP=3937;DP4=14,32,1925,1937;SB=19;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cTc|P13L|419|N|protein_coding|CODING|GU280_gp10|1|T)
+NC_045512	28361	.	GGAGAACGCA	G	49314.0	PASS	AF=0.793943;DP=3203;DP4=417,273,1123,1420;HRUN=2;SB=134;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggagaacgcagt/ggt|GERS30G|419|N|protein_coding|CODING|GU280_gp10|1|G|INFO_REALIGN_3_PRIME)
+NC_045512	28483	.	A	G	49314.0	PASS	AF=0.844926;DP=1754;DP4=0,2,808,788;SB=6;EFF=SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q70|419|N|protein_coding|CODING|GU280_gp10|1|G)
+NC_045512	28657	.	C	T	49314.0	PASS	AF=0.923977;DP=3933;DP4=1,2,2032,1877;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D128|419|N|protein_coding|CODING|GU280_gp10|1|T)
+NC_045512	28881	.	G	A	49314.0	PASS	AF=0.941981;DP=1827;DP4=0,1,899,925;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aAg|R203K|419|N|protein_coding|CODING|GU280_gp10|1|A)
+NC_045512	28882	.	G	A	49314.0	PASS	AF=0.932343;DP=1818;DP4=1,3,887,918;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R203|419|N|protein_coding|CODING|GU280_gp10|1|A)
+NC_045512	28883	.	G	C	49314.0	PASS	AF=0.947425;DP=1864;DP4=1,0,913,948;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gga/Cga|G204R|419|N|protein_coding|CODING|GU280_gp10|1|C)
+NC_045512	29510	.	A	C	49314.0	PASS	AF=0.942881;DP=4867;DP4=0,4,2265,2597;SB=8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agt/Cgt|S413R|419|N|protein_coding|CODING|GU280_gp10|1|C)
+NC_045512	29733	.	CGAGGCCACGCGGAGTACGATCGAGTG	C	49314.0	PASS	AF=0.988372;DP=1634;DP4=307,325,681,934;HRUN=1;SB=22;INDEL
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/day_103.vcf	Wed May 15 13:37:49 2024 +0000
@@ -0,0 +1,124 @@
+##fileformat=VCFv4.0
+##fileDate=20220906
+##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 20 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.001 --bonf dynamic --no-default-filter --no-default-filter -r NC_045512:1-7475 -o /data/jwd/main/050/269/50269469/tmp/lofreq2_call_parallelcuwr5kal/0.vcf.gz reads.bam
+##reference=reference.fa
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth">
+##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
+##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias at this position">
+##INFO=<ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">
+##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position">
+##FILTER=<ID=min_snvqual_65,Description="Minimum SNV Quality (Phred) 65">
+##FILTER=<ID=min_indelqual_48,Description="Minimum Indel Quality (Phred) 48">
+##FILTER=<ID=min_snvqual_74,Description="Minimum SNV Quality (Phred) 74">
+##FILTER=<ID=min_indelqual_57,Description="Minimum Indel Quality (Phred) 57">
+##FILTER=<ID=min_af_0.100000,Description="Minimum allele frequency 0.100000">
+##FILTER=<ID=min_dp_20,Description="Minimum Coverage 20">
+##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000">
+##SnpEffVersion="4.3t (build 2017-11-24 10:18), by Pablo Cingolani"
+##SnpEffCmd="SnpEff  -i vcf -o vcf -formatEff -classic -no-downstream -no-intergenic -no-intron -no-upstream -stats /data/jwd01/main/050/269/50269704/outputs/galaxy_dataset_1406dfab-b1f3-45c3-a9b6-bac554061078.dat -csvStats /data/jwd01/main/050/269/50269704/outputs/galaxy_dataset_48d91a15-1687-4370-a8bf-80a1ae5e324e.dat SARS-CoV-2 /data/dnb06/galaxy_db/files/1/e/8/dataset_1e8a611f-9522-456d-aa71-f8aa0c52bd75.dat "
+##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_Change| Amino_Acid_length | Gene_Name | Transcript_BioType | Gene_Coding | Transcript_ID | Exon_Rank  | Genotype [ | ERRORS | WARNINGS ] )' ">
+##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
+##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+NC_045512	509	.	GGTCATGTTA	G	49314.0	PASS	AF=0.950231;DP=1728;DP4=106,95,958,684;HRUN=2;SB=8;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggtcatgttatg/gtg|GHVM82V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	670	.	T	G	39786.0	PASS	AF=0.922306;DP=1197;DP4=0,0,576,617;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agT/agG|S135R|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	751	.	C	T	3293.0	PASS	AF=0.111922;DP=1233;DP4=536,543,78,75;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N162|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	900	.	C	T	49314.0	PASS	AF=0.938511;DP=1854;DP4=1,0,961,891;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S212L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	1238	.	C	T	9465.0	PASS	AF=0.327919;DP=985;DP4=294,335,170,184;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H325Y|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	1980	.	G	T	5469.0	PASS	AF=0.886905;DP=168;DP4=1,1,82,82;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gTa|G572V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	2790	.	C	T	8824.0	PASS	AF=0.937008;DP=254;DP4=1,1,119,131;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T842I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	3037	.	C	T	25966.0	PASS	AF=0.934927;DP=753;DP4=4,3,376,367;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	4184	.	G	A	6923.0	PASS	AF=0.877934;DP=213;DP4=0,0,115,98;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G1307S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
+NC_045512	4276	.	C	T	4760.0	PASS	AF=0.948529;DP=136;DP4=0,0,108,28;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y1337|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	4321	.	C	T	1017.0	PASS	AF=0.387097;DP=93;DP4=53,1,24,15;SB=54;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A1352|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	6354	.	C	T	5868.0	PASS	AF=0.848958;DP=192;DP4=11,0,110,70;SB=21;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S2030L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	9344	.	C	T	29191.0	PASS	AF=0.957265;DP=819;DP4=0,0,417,399;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L3027F|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	9424	.	A	G	25822.0	PASS	AF=0.949062;DP=746;DP4=0,0,372,373;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V3053|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	9495	.	T	C	25358.0	PASS	AF=0.858709;DP=821;DP4=4,59,411,347;SB=142;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTa/gCa|V3077A|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|C)
+NC_045512	9534	.	C	T	38418.0	PASS	AF=0.938588;DP=1091;DP4=0,0,382,707;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T3090I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	9866	.	C	T	18168.0	PASS	AF=0.938697;DP=522;DP4=1,0,335,184;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L3201F|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	10029	.	C	T	27199.0	PASS	AF=0.863046;DP=847;DP4=0,4,525,315;SB=16;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T3255I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	10198	.	C	T	26940.0	PASS	AF=0.910224;DP=802;DP4=3,2,415,381;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D3311|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	10447	.	G	A	16847.0	PASS	AF=0.869732;DP=522;DP4=2,0,252,265;SB=6;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R3394|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
+NC_045512	10449	.	C	A	17359.0	PASS	AF=0.891841;DP=527;DP4=0,2,257,264;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cAc|P3395H|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
+NC_045512	11287	.	GTCTGGTTTT	G	9083.0	PASS	AF=0.976898;DP=303;DP4=19,16,144,152;HRUN=1;SB=2;INDEL;EFF=CODON_DELETION(MODERATE||tctggtttt/|SGF3675|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	12015	.	T	G	1187.0	PASS	AF=0.117096;DP=427;DP4=160,210,23,34;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gGt|V3917G|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	12036	.	C	T	11567.0	PASS	AF=0.903955;DP=354;DP4=0,0,158,196;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A3924V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	12342	.	C	T	16756.0	PASS	AF=0.680999;DP=721;DP4=175,24,312,206;SB=130;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T4026I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	12854	.	C	T	13148.0	PASS	AF=0.882793;DP=401;DP4=0,0,217,183;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P4197S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	12880	.	C	T	14431.0	PASS	AF=0.955112;DP=401;DP4=0,0,212,189;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I4205|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	14408	.	C	T	38296.0	PASS	AF=0.938588;DP=1091;DP4=1,1,547,540;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P4720L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	14724	.	C	T	45290.0	PASS	AF=0.927526;DP=1366;DP4=4,2,634,714;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F4825|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	15451	.	G	A	31057.0	PASS	AF=0.811966;DP=1053;DP4=2,0,634,407;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G5068S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|A)
+NC_045512	15714	.	C	T	38183.0	PASS	AF=0.933817;DP=1103;DP4=10,12,517,558;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L5155|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	17410	.	C	T	4056.0	PASS	AF=0.925000;DP=120;DP4=0,0,57,62;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R5721C|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	18163	.	A	G	7395.0	PASS	AF=0.860169;DP=236;DP4=0,0,123,113;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I5972V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G)
+NC_045512	19955	.	C	T	42798.0	PASS	AF=0.914877;DP=1257;DP4=2,1,658,594;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T6569I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	20055	.	A	G	12436.0	PASS	AF=0.904000;DP=375;DP4=19,0,135,221;SB=76;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E6602|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G)
+NC_045512	20719	.	C	T	11814.0	PASS	AF=0.891061;DP=358;DP4=2,0,237,117;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L6824|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	21618	.	C	T	39403.0	PASS	AF=0.913234;DP=1141;DP4=0,1,553,574;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T19I|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	21632	.	TTACCCCCTG	T	37561.0	PASS	AF=0.993778;DP=1125;DP4=8,18,541,577;HRUN=2;SB=9;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ttaccccctgca/tca|LPPA24S|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	21987	.	G	A	15152.0	PASS	AF=0.850932;DP=483;DP4=1,0,234,247;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G142D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22200	.	T	G	5164.0	PASS	AF=0.947368;DP=152;DP4=0,0,67,85;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gGg|V213G|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	22578	.	G	A	37640.0	PASS	AF=0.877238;DP=1173;DP4=2,1,560,602;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G339D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22599	.	G	C	39078.0	PASS	AF=0.952338;DP=1112;DP4=1,0,537,572;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGa/aCa|R346T|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22629	.	A	C	35645.0	PASS	AF=0.919508;DP=1056;DP4=0,0,517,539;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aCg|K356T|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22664	.	C	A	34060.0	PASS	AF=0.896585;DP=1025;DP4=5,0,439,566;SB=17;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cta/Ata|L368I|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22674	.	C	T	28971.0	PASS	AF=0.812753;DP=988;DP4=0,4,411,568;SB=8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S371F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22679	.	T	C	31759.0	PASS	AF=0.929487;DP=936;DP4=0,0,390,543;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Cca|S373P|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22686	.	C	T	26369.0	PASS	AF=0.863477;DP=857;DP4=0,4,360,487;SB=8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S375F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22688	.	A	G	27392.0	PASS	AF=0.903148;DP=826;DP4=0,1,357,468;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T376A|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	22716	.	C	T	23123.0	PASS	AF=0.952087;DP=647;DP4=0,1,303,342;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T385I|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22775	.	G	A	41610.0	PASS	AF=0.817662;DP=1574;DP4=83,112,686,691;SB=11;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D405N|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22786	.	A	C	49314.0	PASS	AF=0.888278;DP=1638;DP4=1,3,841,788;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agA/agC|R408S|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22792	.	C	T	49314.0	PASS	AF=0.910736;DP=1658;DP4=1,0,856,799;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I410|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22813	.	G	T	49314.0	PASS	AF=0.906464;DP=1903;DP4=7,1,1033,861;SB=11;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaG/aaT|K417N|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22882	.	T	G	49314.0	PASS	AF=0.892879;DP=1643;DP4=5,3,943,686;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N440K|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	22992	.	G	A	49314.0	PASS	AF=0.934586;DP=1544;DP4=0,1,654,884;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S477N|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22995	.	C	A	49314.0	PASS	AF=0.948320;DP=1548;DP4=0,1,659,884;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aAa|T478K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	23013	.	A	C	49314.0	PASS	AF=0.890767;DP=1538;DP4=11,9,637,874;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gCa|E484A|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	23040	.	A	G	46108.0	PASS	AF=0.904110;DP=1387;DP4=1,2,597,785;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q493R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23055	.	A	G	40054.0	PASS	AF=0.895414;DP=1243;DP4=2,1,556,682;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q498R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23063	.	A	T	42199.0	PASS	AF=0.936364;DP=1210;DP4=0,1,558,649;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Tat|N501Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	23075	.	T	C	38081.0	PASS	AF=0.903501;DP=1171;DP4=1,0,570,598;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y505H|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	23278	.	T	C	13812.0	PASS	AF=0.380259;DP=1236;DP4=287,451,192,302;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T572|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	23403	.	A	G	16603.0	PASS	AF=0.913894;DP=511;DP4=1,1,220,287;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D614G|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23525	.	C	T	11697.0	PASS	AF=0.902299;DP=348;DP4=0,0,168,179;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H655Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	23599	.	T	G	36022.0	PASS	AF=0.914953;DP=1070;DP4=4,4,556,505;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N679K|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23604	.	C	A	35013.0	PASS	AF=0.891791;DP=1072;DP4=1,0,551,512;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cAt|P681H|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	23854	.	C	A	20324.0	PASS	AF=0.863706;DP=653;DP4=7,9,323,314;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaC/aaA|N764K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	23948	.	G	T	26988.0	PASS	AF=0.869928;DP=838;DP4=7,11,424,394;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Tat|D796Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	24424	.	A	T	49314.0	PASS	AF=0.896979;DP=2019;DP4=1,10,1115,887;SB=24;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caA/caT|Q954H|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	24469	.	T	A	49314.0	PASS	AF=0.919902;DP=2447;DP4=3,0,1307,1129;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaA|N969K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	24966	.	A	G	41768.0	PASS	AF=0.907801;DP=1269;DP4=2,2,550,708;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aGc|N1135S|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	25000	.	C	T	37059.0	PASS	AF=0.908842;DP=1097;DP4=1,1,527,565;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D1146|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	25584	.	C	T	48242.0	PASS	AF=0.852652;DP=1527;DP4=2,7,893,621;SB=14;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T64|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
+NC_045512	26060	.	C	T	30995.0	PASS	AF=0.955326;DP=873;DP4=0,0,411,462;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T223I|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
+NC_045512	26195	.	C	T	6504.0	PASS	AF=0.864734;DP=207;DP4=2,0,98,106;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T268M|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
+NC_045512	26270	.	C	T	7692.0	PASS	AF=0.914798;DP=223;DP4=0,0,114,107;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T9I|75|E|protein_coding|CODING|GU280_gp04|1|T)
+NC_045512	26333	.	C	T	6516.0	PASS	AF=0.921053;DP=190;DP4=0,0,101,89;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T30I|75|E|protein_coding|CODING|GU280_gp04|1|T)
+NC_045512	26542	.	C	T	2537.0	PASS	AF=0.128571;DP=840;DP4=367,338,65,53;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T7I|222|M|protein_coding|CODING|GU280_gp05|1|T)
+NC_045512	26577	.	C	G	34567.0	PASS	AF=0.905314;DP=1035;DP4=0,0,507,523;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q19E|222|M|protein_coding|CODING|GU280_gp05|1|G)
+NC_045512	26625	.	C	T	39521.0	PASS	AF=0.955896;DP=1111;DP4=1,0,525,576;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L35|222|M|protein_coding|CODING|GU280_gp05|1|T)
+NC_045512	26709	.	G	A	49314.0	PASS	AF=0.924801;DP=2008;DP4=11,9,985,995;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A63T|222|M|protein_coding|CODING|GU280_gp05|1|A)
+NC_045512	26754	.	G	A	43115.0	PASS	AF=0.630244;DP=2050;DP4=305,308,724,707;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G78S|222|M|protein_coding|CODING|GU280_gp05|1|A)
+NC_045512	26801	.	C	T	49314.0	PASS	AF=0.894977;DP=1752;DP4=11,10,842,884;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L93|222|M|protein_coding|CODING|GU280_gp05|1|T)
+NC_045512	26858	.	C	T	33747.0	PASS	AF=0.875120;DP=1041;DP4=6,7,459,562;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F112|222|M|protein_coding|CODING|GU280_gp05|1|T)
+NC_045512	27259	.	A	C	49314.0	PASS	AF=0.884010;DP=2095;DP4=8,15,817,1249;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Agg/Cgg|R20|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
+NC_045512	27382	.	G	C	20379.0	PASS	AF=0.919056;DP=593;DP4=0,0,292,297;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Cat|D61H|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
+NC_045512	27383	.	A	T	19296.0	PASS	AF=0.873720;DP=586;DP4=1,0,289,292;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gTt|D61V|61|ORF6|protein_coding|CODING|GU280_gp06|1|T)
+NC_045512	27384	.	T	C	20584.0	PASS	AF=0.917647;DP=595;DP4=0,0,298,297;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D61|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
+NC_045512	27481	.	C	T	24969.0	PASS	AF=0.942577;DP=714;DP4=0,0,348,364;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L30F|121|ORF7a|protein_coding|CODING|GU280_gp07|1|T)
+NC_045512	27549	.	C	T	42569.0	PASS	AF=0.899366;DP=1262;DP4=0,0,625,635;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N52|121|ORF7a|protein_coding|CODING|GU280_gp07|1|T)
+NC_045512	27807	.	C	T	18628.0	PASS	AF=0.947269;DP=531;DP4=1,0,257,269;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L18|43|ORF7b|protein_coding|CODING|GU280_gp08|1|T)
+NC_045512	28271	.	A	T	49314.0	PASS	AF=0.893357;DP=2213;DP4=2,12,1098,1083;SB=21
+NC_045512	28311	.	C	T	49314.0	PASS	AF=0.806593;DP=2518;DP4=14,27,1260,1205;SB=14;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cTc|P13L|419|N|protein_coding|CODING|GU280_gp10|1|T)
+NC_045512	28361	.	GGAGAACGCA	G	46560.0	PASS	AF=0.712057;DP=2115;DP4=428,205,665,841;HRUN=2;SB=226;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggagaacgcagt/ggt|GERS30G|419|N|protein_coding|CODING|GU280_gp10|1|G|INFO_REALIGN_3_PRIME)
+NC_045512	28657	.	C	T	49314.0	PASS	AF=0.863677;DP=3389;DP4=12,16,1835,1497;SB=5;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D128|419|N|protein_coding|CODING|GU280_gp10|1|T)
+NC_045512	28881	.	G	A	49314.0	PASS	AF=0.943852;DP=1407;DP4=0,1,620,782;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aAg|R203K|419|N|protein_coding|CODING|GU280_gp10|1|A)
+NC_045512	28882	.	G	A	45952.0	PASS	AF=0.889522;DP=1403;DP4=1,0,618,772;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R203|419|N|protein_coding|CODING|GU280_gp10|1|A)
+NC_045512	28883	.	G	C	48422.0	PASS	AF=0.927208;DP=1415;DP4=0,0,623,789;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gga/Cga|G204R|419|N|protein_coding|CODING|GU280_gp10|1|C)
+NC_045512	29510	.	A	C	49314.0	PASS	AF=0.916667;DP=4344;DP4=2,2,1880,2446;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agt/Cgt|S413R|419|N|protein_coding|CODING|GU280_gp10|1|C)
+NC_045512	29733	.	CGAGGCCACGCGGAGTACGATCGAGTG	C	49314.0	PASS	AF=0.990955;DP=1990;DP4=174,138,681,1291;HRUN=1;SB=117;INDEL
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/day_111.vcf	Wed May 15 13:37:49 2024 +0000
@@ -0,0 +1,125 @@
+##fileformat=VCFv4.0
+##fileDate=20220927
+##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 20 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.001 --bonf dynamic --no-default-filter --no-default-filter -r NC_045512:1-7475 -o /data/jwd01/main/050/996/50996342/tmp/lofreq2_call_parallelr6xd9css/0.vcf.gz reads.bam
+##reference=reference.fa
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth">
+##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
+##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias at this position">
+##INFO=<ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">
+##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position">
+##FILTER=<ID=min_snvqual_67,Description="Minimum SNV Quality (Phred) 67">
+##FILTER=<ID=min_indelqual_53,Description="Minimum Indel Quality (Phred) 53">
+##FILTER=<ID=min_snvqual_75,Description="Minimum SNV Quality (Phred) 75">
+##FILTER=<ID=min_indelqual_61,Description="Minimum Indel Quality (Phred) 61">
+##FILTER=<ID=min_af_0.100000,Description="Minimum allele frequency 0.100000">
+##FILTER=<ID=min_dp_20,Description="Minimum Coverage 20">
+##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000">
+##SnpEffVersion="4.3t (build 2017-11-24 10:18), by Pablo Cingolani"
+##SnpEffCmd="SnpEff  -i vcf -o vcf -formatEff -classic -no-downstream -no-intergenic -no-intron -no-upstream -stats /data/jwd01/main/050/996/50996577/outputs/galaxy_dataset_c1fe9188-61a8-4620-a5e5-b8767f365e04.dat -csvStats /data/jwd01/main/050/996/50996577/outputs/galaxy_dataset_1a8b9f67-27f7-485f-930a-8cc569fda1e0.dat SARS-CoV-2 /data/dnb07/galaxy_db/files/a/b/0/dataset_ab07b6bf-259d-40b7-b62a-5a146ab70f14.dat "
+##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_Change| Amino_Acid_length | Gene_Name | Transcript_BioType | Gene_Coding | Transcript_ID | Exon_Rank  | Genotype [ | ERRORS | WARNINGS ] )' ">
+##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
+##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+NC_045512	509	.	GGTCATGTTA	G	20818.0	PASS	AF=0.848225;DP=817;DP4=122,112,431,262;HRUN=2;SB=21;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggtcatgttatg/gtg|GHVM82V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	670	.	T	G	21209.0	PASS	AF=0.911628;DP=645;DP4=1,0,304,336;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agT/agG|S135R|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	900	.	C	T	49314.0	PASS	AF=0.943702;DP=2096;DP4=1,1,1114,977;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S212L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	1980	.	G	T	13514.0	PASS	AF=0.879518;DP=415;DP4=3,0,215,194;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gTa|G572V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	2790	.	C	T	20107.0	PASS	AF=0.919328;DP=595;DP4=0,0,295,299;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T842I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	3037	.	C	T	28270.0	PASS	AF=0.950125;DP=802;DP4=0,0,369,431;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	4184	.	G	A	19564.0	PASS	AF=0.953069;DP=554;DP4=1,0,348,205;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G1307S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
+NC_045512	4276	.	C	T	14879.0	PASS	AF=0.812623;DP=507;DP4=2,1,351,147;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y1337|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	4321	.	C	T	10608.0	PASS	AF=0.699552;DP=446;DP4=113,1,162,170;SB=268;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A1352|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	6354	.	C	T	3284.0	PASS	AF=0.258427;DP=445;DP4=318,1,77,49;SB=287;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S2030L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	7085	.	A	G	7084.0	PASS	AF=0.198809;DP=1343;DP4=512,520,152,138;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T2274A|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	9344	.	C	T	30690.0	PASS	AF=0.933782;DP=891;DP4=0,0,461,423;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L3027F|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	9424	.	A	G	31617.0	PASS	AF=0.924488;DP=927;DP4=0,0,493,424;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V3053|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	9495	.	T	C	31844.0	PASS	AF=0.882353;DP=986;DP4=2,28,509,445;SB=67;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTa/gCa|V3077A|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|C)
+NC_045512	9534	.	C	T	36963.0	PASS	AF=0.812550;DP=1243;DP4=0,1,435,790;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T3090I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	9866	.	C	T	28044.0	PASS	AF=0.944376;DP=809;DP4=3,1,478,324;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L3201F|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	10029	.	C	T	22775.0	PASS	AF=0.880450;DP=711;DP4=0,1,413,295;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T3255I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	10198	.	C	T	29355.0	PASS	AF=0.907029;DP=882;DP4=0,2,462,412;SB=6;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D3311|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	10447	.	G	A	9980.0	PASS	AF=0.880259;DP=309;DP4=1,0,142,163;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R3394|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
+NC_045512	10449	.	C	A	9236.0	PASS	AF=0.828947;DP=304;DP4=4,6,140,153;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cAc|P3395H|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
+NC_045512	11287	.	GTCTGGTTTT	G	3861.0	PASS	AF=1.000000;DP=124;DP4=4,3,61,63;HRUN=1;SB=1;INDEL;EFF=CODON_DELETION(MODERATE||tctggtttt/|SGF3675|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	12036	.	C	T	14354.0	PASS	AF=0.936768;DP=427;DP4=1,1,194,228;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A3924V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	12342	.	C	T	13753.0	PASS	AF=0.357642;DP=1289;DP4=575,202,313,196;SB=55;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T4026I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	12854	.	C	T	9938.0	PASS	AF=0.840125;DP=319;DP4=0,5,154,158;SB=12;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P4197S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	12880	.	C	T	11413.0	PASS	AF=0.980707;DP=311;DP4=0,0,143,167;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I4205|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	13859	.	A	G	1972.0	PASS	AF=0.149446;DP=542;DP4=234,212,42,50;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAc/gGc|D4537G|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G)
+NC_045512	14408	.	C	T	49314.0	PASS	AF=0.967153;DP=1644;DP4=3,2,792,845;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P4720L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	14724	.	C	T	18069.0	PASS	AF=0.457478;DP=1364;DP4=361,349,345,305;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F4825|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	15451	.	G	A	49314.0	PASS	AF=0.943262;DP=1551;DP4=0,2,915,631;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G5068S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|A)
+NC_045512	15714	.	C	T	28421.0	PASS	AF=0.968314;DP=789;DP4=0,0,392,395;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L5155|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	17410	.	C	T	15217.0	PASS	AF=0.870293;DP=478;DP4=0,2,219,250;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R5721C|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	18163	.	A	G	21071.0	PASS	AF=0.878788;DP=660;DP4=1,0,321,333;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I5972V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G)
+NC_045512	18486	.	C	T	1673.0	PASS	AF=0.175676;DP=370;DP4=141,154,40,33;SB=5;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L6079|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	19955	.	C	T	49314.0	PASS	AF=0.940071;DP=2553;DP4=2,3,1202,1341;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T6569I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	20055	.	A	G	12803.0	PASS	AF=0.861575;DP=419;DP4=44,1,182,192;SB=112;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E6602|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G)
+NC_045512	20719	.	C	T	21961.0	PASS	AF=0.945687;DP=626;DP4=0,0,351,275;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L6824|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	21441	.	T	C	8700.0	PASS	AF=0.429825;DP=684;DP4=203,161,174,143;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S7064|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|C)
+NC_045512	21618	.	C	T	48579.0	PASS	AF=0.847995;DP=1546;DP4=0,4,717,805;SB=8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T19I|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	21632	.	TTACCCCCTG	T	43279.0	PASS	AF=0.981413;DP=1345;DP4=75,54,591,729;HRUN=2;SB=23;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ttaccccctgca/tca|LPPA24S|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	21773	.	T	C	4329.0	PASS	AF=0.403846;DP=364;DP4=97,105,73,89;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tct/Cct|S71P|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	21987	.	G	A	42165.0	PASS	AF=0.924071;DP=1238;DP4=2,0,692,539;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G142D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22200	.	T	G	25623.0	PASS	AF=0.942971;DP=754;DP4=2,0,337,415;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gGg|V213G|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	22578	.	G	A	24366.0	PASS	AF=0.859649;DP=798;DP4=2,1,398,386;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G339D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22599	.	G	C	23033.0	PASS	AF=0.874483;DP=725;DP4=0,0,372,343;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGa/aCa|R346T|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22629	.	A	C	24122.0	PASS	AF=0.870180;DP=778;DP4=0,5,393,377;SB=15;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aCg|K356T|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22664	.	C	A	24852.0	PASS	AF=0.918367;DP=735;DP4=0,0,354,377;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cta/Ata|L368I|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22674	.	C	T	24962.0	PASS	AF=0.925134;DP=748;DP4=0,0,355,390;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S371F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22679	.	T	C	24338.0	PASS	AF=0.905711;DP=753;DP4=0,0,361,390;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Cca|S373P|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22686	.	C	T	22895.0	PASS	AF=0.935622;DP=699;DP4=2,1,332,361;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S375F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22688	.	A	G	20503.0	PASS	AF=0.845113;DP=665;DP4=1,3,317,337;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T376A|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	22716	.	C	T	24283.0	PASS	AF=0.932203;DP=708;DP4=1,2,340,363;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T385I|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22775	.	G	A	49314.0	PASS	AF=0.641449;DP=4719;DP4=730,779,1673,1531;SB=18;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D405N|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22786	.	A	C	49314.0	PASS	AF=0.909284;DP=2822;DP4=9,19,1461,1330;SB=14;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agA/agC|R408S|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22792	.	C	T	49314.0	PASS	AF=0.948333;DP=2729;DP4=0,2,1429,1292;SB=6;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I410|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22813	.	G	T	49314.0	PASS	AF=0.924780;DP=2845;DP4=2,3,1482,1350;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaG/aaT|K417N|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22882	.	T	G	49314.0	PASS	AF=0.768566;DP=1966;DP4=6,4,1092,856;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N440K|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	22992	.	G	A	49314.0	PASS	AF=0.924841;DP=1570;DP4=2,1,687,869;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S477N|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22995	.	C	A	49314.0	PASS	AF=0.975765;DP=1568;DP4=1,1,705,858;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aAa|T478K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	23013	.	A	C	49314.0	PASS	AF=0.897420;DP=1628;DP4=7,8,719,884;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gCa|E484A|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	23040	.	A	G	49314.0	PASS	AF=0.909502;DP=1547;DP4=2,4,693,844;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q493R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23055	.	A	G	48995.0	PASS	AF=0.905459;DP=1502;DP4=1,3,682,808;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q498R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23063	.	A	T	49314.0	PASS	AF=0.950538;DP=1395;DP4=0,0,658,737;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Tat|N501Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	23075	.	T	C	48140.0	PASS	AF=0.894947;DP=1504;DP4=9,0,731,764;SB=27;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y505H|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	23403	.	A	G	15329.0	PASS	AF=0.954442;DP=439;DP4=0,0,206,230;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D614G|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23525	.	C	T	11580.0	PASS	AF=0.895184;DP=353;DP4=0,0,178,172;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H655Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	23599	.	T	G	49314.0	PASS	AF=0.919446;DP=1589;DP4=4,0,833,746;SB=8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N679K|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23604	.	C	A	49013.0	PASS	AF=0.877457;DP=1526;DP4=2,1,798,717;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cAt|P681H|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	23854	.	C	A	21886.0	PASS	AF=0.898827;DP=682;DP4=2,3,317,360;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaC/aaA|N764K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	23948	.	G	T	26172.0	PASS	AF=0.900000;DP=780;DP4=0,0,377,398;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Tat|D796Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	24424	.	A	T	49314.0	PASS	AF=0.851435;DP=1777;DP4=1,33,902,840;SB=90;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caA/caT|Q954H|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	24469	.	T	A	49314.0	PASS	AF=0.929825;DP=1881;DP4=6,0,948,922;SB=15;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaA|N969K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	24966	.	A	G	29654.0	PASS	AF=0.887689;DP=926;DP4=0,5,426,490;SB=11;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aGc|N1135S|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	25000	.	C	T	30021.0	PASS	AF=0.927918;DP=874;DP4=0,0,416,456;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D1146|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	25584	.	C	T	40468.0	PASS	AF=0.833333;DP=1320;DP4=1,27,756,534;SB=89;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T64|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
+NC_045512	26060	.	C	T	49314.0	PASS	AF=0.966743;DP=1744;DP4=0,0,928,814;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T223I|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
+NC_045512	26195	.	C	T	23747.0	PASS	AF=0.858257;DP=769;DP4=1,0,374,391;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T268M|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
+NC_045512	26270	.	C	T	24266.0	PASS	AF=0.901389;DP=720;DP4=0,1,367,350;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T9I|75|E|protein_coding|CODING|GU280_gp04|1|T)
+NC_045512	26333	.	C	T	22038.0	PASS	AF=0.905465;DP=677;DP4=0,0,355,316;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T30I|75|E|protein_coding|CODING|GU280_gp04|1|T)
+NC_045512	26577	.	C	G	15659.0	PASS	AF=0.896480;DP=483;DP4=0,0,235,241;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q19E|222|M|protein_coding|CODING|GU280_gp05|1|G)
+NC_045512	26625	.	C	T	7705.0	PASS	AF=0.469582;DP=526;DP4=129,140,120,135;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L35|222|M|protein_coding|CODING|GU280_gp05|1|T)
+NC_045512	26709	.	G	A	49314.0	PASS	AF=0.951613;DP=1736;DP4=1,1,973,756;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A63T|222|M|protein_coding|CODING|GU280_gp05|1|A)
+NC_045512	26754	.	G	A	7424.0	PASS	AF=0.164614;DP=1786;DP4=801,659,174,140;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G78S|222|M|protein_coding|CODING|GU280_gp05|1|A)
+NC_045512	26801	.	C	T	49314.0	PASS	AF=0.938865;DP=1603;DP4=1,1,827,761;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L93|222|M|protein_coding|CODING|GU280_gp05|1|T)
+NC_045512	26858	.	C	T	49314.0	PASS	AF=0.953297;DP=1456;DP4=0,0,662,780;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F112|222|M|protein_coding|CODING|GU280_gp05|1|T)
+NC_045512	26985	.	C	T	13083.0	PASS	AF=0.387238;DP=1144;DP4=326,325,247,243;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H155Y|222|M|protein_coding|CODING|GU280_gp05|1|T)
+NC_045512	27259	.	A	C	49314.0	PASS	AF=0.901447;DP=2212;DP4=3,5,872,1321;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Agg/Cgg|R20|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
+NC_045512	27382	.	G	C	8676.0	PASS	AF=0.881679;DP=262;DP4=0,0,129,131;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Cat|D61H|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
+NC_045512	27383	.	A	T	8693.0	PASS	AF=0.888462;DP=260;DP4=0,0,128,130;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gTt|D61V|61|ORF6|protein_coding|CODING|GU280_gp06|1|T)
+NC_045512	27384	.	T	C	9016.0	PASS	AF=0.906367;DP=267;DP4=1,0,133,133;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D61|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
+NC_045512	27481	.	C	T	11248.0	PASS	AF=0.939577;DP=331;DP4=1,0,175,155;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L30F|121|ORF7a|protein_coding|CODING|GU280_gp07|1|T)
+NC_045512	27549	.	C	T	49314.0	PASS	AF=0.902861;DP=1503;DP4=0,1,805,675;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N52|121|ORF7a|protein_coding|CODING|GU280_gp07|1|T)
+NC_045512	27807	.	C	T	25681.0	PASS	AF=0.934404;DP=747;DP4=0,0,381,365;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L18|43|ORF7b|protein_coding|CODING|GU280_gp08|1|T)
+NC_045512	28271	.	A	T	49314.0	PASS	AF=0.942808;DP=2308;DP4=2,17,1245,1043;SB=39
+NC_045512	28311	.	C	T	49314.0	PASS	AF=0.826858;DP=2368;DP4=7,39,1228,1089;SB=66;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cTc|P13L|419|N|protein_coding|CODING|GU280_gp10|1|T)
+NC_045512	28361	.	GGAGAACGCA	G	48102.0	PASS	AF=0.725214;DP=1987;DP4=462,121,520,921;HRUN=2;SB=713;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggagaacgcagt/ggt|GERS30G|419|N|protein_coding|CODING|GU280_gp10|1|G|INFO_REALIGN_3_PRIME)
+NC_045512	28657	.	C	T	49314.0	PASS	AF=0.915625;DP=2240;DP4=0,1,1299,920;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D128|419|N|protein_coding|CODING|GU280_gp10|1|T)
+NC_045512	28881	.	G	A	25064.0	PASS	AF=0.958153;DP=693;DP4=0,0,323,368;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aAg|R203K|419|N|protein_coding|CODING|GU280_gp10|1|A)
+NC_045512	28882	.	G	A	22700.0	PASS	AF=0.885341;DP=689;DP4=1,0,318,366;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R203|419|N|protein_coding|CODING|GU280_gp10|1|A)
+NC_045512	28883	.	G	C	23625.0	PASS	AF=0.920228;DP=702;DP4=2,0,324,371;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gga/Cga|G204R|419|N|protein_coding|CODING|GU280_gp10|1|C)
+NC_045512	29510	.	A	C	49314.0	PASS	AF=0.885417;DP=2304;DP4=5,1,1010,1280;SB=10;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agt/Cgt|S413R|419|N|protein_coding|CODING|GU280_gp10|1|C)
+NC_045512	29733	.	CGAGGCCACGCGGAGTACGATCGAGTG	C	30870.0	PASS	AF=0.989501;DP=762;DP4=116,100,235,519;HRUN=1;SB=84;INDEL
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/day_18.vcf	Wed May 15 13:37:49 2024 +0000
@@ -0,0 +1,113 @@
+##fileformat=VCFv4.0
+##fileDate=20220830
+##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 20 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.001 --bonf dynamic --no-default-filter --no-default-filter -r NC_045512:1-7475 -o /data/jwd/main/050/063/50063644/tmp/lofreq2_call_parallel717nv31u/0.vcf.gz reads.bam
+##reference=reference.fa
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth">
+##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
+##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias at this position">
+##INFO=<ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">
+##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position">
+##FILTER=<ID=min_snvqual_62,Description="Minimum SNV Quality (Phred) 62">
+##FILTER=<ID=min_indelqual_48,Description="Minimum Indel Quality (Phred) 48">
+##FILTER=<ID=min_snvqual_71,Description="Minimum SNV Quality (Phred) 71">
+##FILTER=<ID=min_indelqual_57,Description="Minimum Indel Quality (Phred) 57">
+##FILTER=<ID=min_af_0.100000,Description="Minimum allele frequency 0.100000">
+##FILTER=<ID=min_dp_20,Description="Minimum Coverage 20">
+##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000">
+##SnpEffVersion="4.3t (build 2017-11-24 10:18), by Pablo Cingolani"
+##SnpEffCmd="SnpEff  -i vcf -o vcf -formatEff -classic -no-downstream -no-intergenic -no-intron -no-upstream -stats /data/jwd/main/050/063/50063750/outputs/galaxy_dataset_232ae126-f2f4-472c-bf70-443ea6a4b576.dat -csvStats /data/jwd/main/050/063/50063750/outputs/galaxy_dataset_801f99b1-8ef7-4504-b4e3-a04f423e6349.dat SARS-CoV-2 /data/dnb07/galaxy_db/files/a/3/d/dataset_a3de6b1f-173b-4ce7-85a4-51a14281eafa.dat "
+##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_Change| Amino_Acid_length | Gene_Name | Transcript_BioType | Gene_Coding | Transcript_ID | Exon_Rank  | Genotype [ | ERRORS | WARNINGS ] )' ">
+##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
+##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+NC_045512	509	.	GGTCATGTTA	G	26636.0	PASS	AF=0.998797;DP=831;DP4=20,27,616,214;HRUN=2;SB=49;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggtcatgttatg/gtg|GHVM82V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	670	.	T	G	18624.0	PASS	AF=0.951128;DP=532;DP4=0,0,250,281;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agT/agG|S135R|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	900	.	C	T	49314.0	PASS	AF=0.969347;DP=1990;DP4=1,0,1026,960;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S212L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	1980	.	G	T	4529.0	PASS	AF=0.967742;DP=124;DP4=0,0,67,57;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gTa|G572V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	2790	.	C	T	8006.0	PASS	AF=0.969163;DP=227;DP4=0,0,116,111;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T842I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	3037	.	C	T	28216.0	PASS	AF=0.962963;DP=783;DP4=0,1,361,419;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	4184	.	G	A	9244.0	PASS	AF=0.968627;DP=255;DP4=0,0,174,81;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G1307S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
+NC_045512	4276	.	C	T	7858.0	PASS	AF=0.981132;DP=212;DP4=0,0,173,39;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y1337|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	4321	.	C	T	1600.0	PASS	AF=0.460870;DP=115;DP4=61,0,27,27;SB=108;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A1352|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	6354	.	C	T	4133.0	PASS	AF=0.774834;DP=151;DP4=29,1,80,41;SB=33;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S2030L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	9344	.	C	T	23951.0	PASS	AF=0.977169;DP=657;DP4=1,0,317,339;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L3027F|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	9424	.	A	G	21689.0	PASS	AF=0.959217;DP=613;DP4=0,0,318,294;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V3053|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	9534	.	C	T	49314.0	PASS	AF=0.974796;DP=1349;DP4=0,0,545,804;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T3090I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	9866	.	C	T	23400.0	PASS	AF=0.959815;DP=647;DP4=0,0,481,166;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L3201F|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	10029	.	C	T	23958.0	PASS	AF=0.933430;DP=691;DP4=0,0,283,405;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T3255I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	10198	.	C	T	17239.0	PASS	AF=0.942623;DP=488;DP4=0,0,252,235;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D3311|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	10447	.	G	A	12177.0	PASS	AF=0.942197;DP=346;DP4=0,1,178,167;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R3394|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
+NC_045512	10449	.	C	A	11904.0	PASS	AF=0.924638;DP=345;DP4=0,1,177,166;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cAc|P3395H|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
+NC_045512	11287	.	GTCTGGTTTT	G	3147.0	PASS	AF=1.000000;DP=96;DP4=5,12,39,57;HRUN=1;SB=3;INDEL;EFF=CODON_DELETION(MODERATE||tctggtttt/|SGF3675|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	12036	.	C	T	19886.0	PASS	AF=0.951473;DP=577;DP4=0,1,262,313;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A3924V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	12854	.	C	T	13932.0	PASS	AF=0.968750;DP=384;DP4=1,1,181,201;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P4197S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	12880	.	C	T	13710.0	PASS	AF=0.973545;DP=378;DP4=0,0,171,207;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I4205|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	14408	.	C	T	49314.0	PASS	AF=0.966997;DP=1515;DP4=0,0,790,723;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P4720L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	15451	.	G	A	36998.0	PASS	AF=0.948989;DP=1039;DP4=0,0,768,270;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G5068S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|A)
+NC_045512	15714	.	C	T	23967.0	PASS	AF=0.978626;DP=655;DP4=0,0,327,328;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L5155|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	17259	.	G	T	671.0	PASS	AF=0.217742;DP=124;DP4=51,45,25,3;SB=34;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaT|E5670D|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	17410	.	C	T	3135.0	PASS	AF=0.977273;DP=88;DP4=0,0,39,49;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R5721C|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	18163	.	A	G	6626.0	PASS	AF=0.978261;DP=184;DP4=0,0,87,97;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I5972V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G)
+NC_045512	19955	.	C	T	48074.0	PASS	AF=0.976209;DP=1303;DP4=0,0,917,385;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T6569I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	20055	.	A	G	13443.0	PASS	AF=0.938303;DP=389;DP4=14,1,179,195;SB=34;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E6602|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G)
+NC_045512	20719	.	C	T	15386.0	PASS	AF=0.965035;DP=429;DP4=0,0,235,194;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L6824|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	21618	.	C	T	49314.0	PASS	AF=0.987821;DP=1478;DP4=1,0,719,758;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T19I|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	21632	.	TTACCCCCTG	T	47313.0	PASS	AF=0.994092;DP=1354;DP4=32,30,649,697;HRUN=2;SB=2;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ttaccccctgca/tca|LPPA24S|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	21987	.	G	A	34703.0	PASS	AF=0.945697;DP=976;DP4=2,1,451,520;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G142D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22200	.	T	G	6387.0	PASS	AF=0.967742;DP=186;DP4=0,0,93,93;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gGg|V213G|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	22578	.	G	A	21408.0	PASS	AF=0.965347;DP=606;DP4=0,0,314,291;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G339D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22629	.	A	C	19252.0	PASS	AF=0.964750;DP=539;DP4=1,1,290,247;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aCg|K356T|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22664	.	C	A	19308.0	PASS	AF=0.977570;DP=535;DP4=0,0,277,256;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cta/Ata|L368I|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22674	.	C	T	18944.0	PASS	AF=0.964618;DP=537;DP4=0,0,282,255;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S371F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22679	.	T	C	18999.0	PASS	AF=0.964684;DP=538;DP4=0,0,287,251;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Cca|S373P|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22686	.	C	T	17680.0	PASS	AF=0.964497;DP=507;DP4=1,0,271,235;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S375F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22688	.	A	G	17586.0	PASS	AF=0.950000;DP=500;DP4=1,0,268,228;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T376A|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	22716	.	C	T	19310.0	PASS	AF=0.967985;DP=531;DP4=0,0,297,234;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T385I|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22775	.	G	A	49314.0	PASS	AF=0.881262;DP=2535;DP4=102,110,1368,953;SB=25;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D405N|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22786	.	A	C	49314.0	PASS	AF=0.941202;DP=2347;DP4=0,1,1367,974;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agA/agC|R408S|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22792	.	C	T	49314.0	PASS	AF=0.966311;DP=2345;DP4=1,1,1366,976;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I410|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22813	.	G	T	49314.0	PASS	AF=0.969281;DP=2474;DP4=0,1,1430,1042;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaG/aaT|K417N|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22882	.	T	G	49314.0	PASS	AF=0.958710;DP=1768;DP4=2,1,1209,555;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N440K|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	22992	.	G	A	36772.0	PASS	AF=0.964355;DP=1038;DP4=0,0,475,563;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S477N|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22995	.	C	A	37275.0	PASS	AF=0.970760;DP=1026;DP4=0,0,471,555;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aAa|T478K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	23013	.	A	C	36561.0	PASS	AF=0.965174;DP=1005;DP4=2,0,456,545;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gCa|E484A|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	23040	.	A	G	34886.0	PASS	AF=0.978079;DP=958;DP4=0,1,442,515;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q493R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23055	.	A	G	33387.0	PASS	AF=0.962065;DP=949;DP4=0,1,448,500;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q498R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23063	.	A	T	33872.0	PASS	AF=0.985792;DP=915;DP4=0,0,449,464;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Tat|N501Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	23075	.	T	C	31911.0	PASS	AF=0.961538;DP=910;DP4=0,0,458,452;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y505H|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	23403	.	A	G	12029.0	PASS	AF=0.972973;DP=333;DP4=0,0,161,172;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D614G|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23525	.	C	T	11185.0	PASS	AF=0.973941;DP=307;DP4=0,0,164,143;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H655Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	23599	.	T	G	49314.0	PASS	AF=0.958807;DP=1408;DP4=0,1,739,667;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N679K|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23604	.	C	A	49314.0	PASS	AF=0.968750;DP=1408;DP4=0,0,740,668;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cAt|P681H|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	23854	.	C	A	18583.0	PASS	AF=0.942379;DP=538;DP4=1,2,258,276;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaC/aaA|N764K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	23948	.	G	T	21728.0	PASS	AF=0.959933;DP=599;DP4=0,0,306,293;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Tat|D796Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	24424	.	A	T	49314.0	PASS	AF=0.950000;DP=2320;DP4=1,1,1222,1094;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caA/caT|Q954H|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	24469	.	T	A	49314.0	PASS	AF=0.951425;DP=2491;DP4=1,1,1302,1183;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaA|N969K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	24966	.	A	G	31324.0	PASS	AF=0.953933;DP=890;DP4=0,0,408,477;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aGc|N1135S|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	25000	.	C	T	30573.0	PASS	AF=0.961131;DP=849;DP4=1,0,382,463;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D1146|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	25584	.	C	T	41217.0	PASS	AF=0.963781;DP=1132;DP4=1,3,726,402;SB=8;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T64|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
+NC_045512	26060	.	C	T	41883.0	PASS	AF=0.971706;DP=1131;DP4=0,0,506,622;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T223I|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
+NC_045512	26195	.	C	T	7270.0	PASS	AF=0.980099;DP=201;DP4=0,0,92,109;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T268M|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
+NC_045512	26270	.	C	T	6219.0	PASS	AF=0.970930;DP=172;DP4=0,0,95,77;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T9I|75|E|protein_coding|CODING|GU280_gp04|1|T)
+NC_045512	26577	.	C	G	19291.0	PASS	AF=0.961039;DP=539;DP4=0,0,247,292;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q19E|222|M|protein_coding|CODING|GU280_gp05|1|G)
+NC_045512	26709	.	G	A	49071.0	PASS	AF=0.968148;DP=1350;DP4=1,1,848,498;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A63T|222|M|protein_coding|CODING|GU280_gp05|1|A)
+NC_045512	26801	.	C	T	49314.0	PASS	AF=0.961560;DP=1795;DP4=0,0,913,881;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L93|222|M|protein_coding|CODING|GU280_gp05|1|T)
+NC_045512	26858	.	C	T	49314.0	PASS	AF=0.979244;DP=1349;DP4=0,0,509,839;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F112|222|M|protein_coding|CODING|GU280_gp05|1|T)
+NC_045512	27259	.	A	C	49314.0	PASS	AF=0.973325;DP=1537;DP4=1,1,428,1105;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|Agg/Cgg|R20|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
+NC_045512	27382	.	G	C	7064.0	PASS	AF=0.954082;DP=196;DP4=0,0,95,101;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Cat|D61H|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
+NC_045512	27383	.	A	T	7052.0	PASS	AF=0.958549;DP=193;DP4=0,0,94,99;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gTt|D61V|61|ORF6|protein_coding|CODING|GU280_gp06|1|T)
+NC_045512	27384	.	T	C	7096.0	PASS	AF=0.953846;DP=195;DP4=1,1,94,99;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D61|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
+NC_045512	27481	.	C	T	10114.0	PASS	AF=0.971530;DP=281;DP4=0,0,151,130;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L30F|121|ORF7a|protein_coding|CODING|GU280_gp07|1|T)
+NC_045512	27549	.	C	T	38892.0	PASS	AF=0.978988;DP=1047;DP4=0,0,543,504;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N52|121|ORF7a|protein_coding|CODING|GU280_gp07|1|T)
+NC_045512	27807	.	C	T	10876.0	PASS	AF=0.967427;DP=307;DP4=1,0,152,154;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L18|43|ORF7b|protein_coding|CODING|GU280_gp08|1|T)
+NC_045512	28271	.	A	T	49314.0	PASS	AF=0.971286;DP=2403;DP4=1,1,1260,1141;SB=0
+NC_045512	28311	.	C	T	49314.0	PASS	AF=0.913405;DP=2402;DP4=2,4,1245,1144;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cTc|P13L|419|N|protein_coding|CODING|GU280_gp10|1|T)
+NC_045512	28361	.	GGAGAACGCA	G	49314.0	PASS	AF=0.682846;DP=2122;DP4=617,58,445,1004;HRUN=2;SB=1661;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggagaacgcagt/ggt|GERS30G|419|N|protein_coding|CODING|GU280_gp10|1|G|INFO_REALIGN_3_PRIME)
+NC_045512	28657	.	C	T	49314.0	PASS	AF=0.943368;DP=2013;DP4=1,0,996,1013;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D128|419|N|protein_coding|CODING|GU280_gp10|1|T)
+NC_045512	28881	.	G	A	20426.0	PASS	AF=0.958929;DP=560;DP4=1,0,283,276;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aAg|R203K|419|N|protein_coding|CODING|GU280_gp10|1|A)
+NC_045512	28882	.	G	A	19564.0	PASS	AF=0.928571;DP=560;DP4=0,0,284,274;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R203|419|N|protein_coding|CODING|GU280_gp10|1|A)
+NC_045512	28883	.	G	C	20254.0	PASS	AF=0.952297;DP=566;DP4=0,0,285,280;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gga/Cga|G204R|419|N|protein_coding|CODING|GU280_gp10|1|C)
+NC_045512	29510	.	A	C	49314.0	PASS	AF=0.958883;DP=1970;DP4=0,2,778,1187;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agt/Cgt|S413R|419|N|protein_coding|CODING|GU280_gp10|1|C)
+NC_045512	29733	.	CGAGGCCACGCGGAGTACGATCGAGTG	C	49314.0	PASS	AF=0.995888;DP=1216;DP4=89,86,224,987;HRUN=1;SB=180;INDEL
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/day_2.vcf	Wed May 15 13:37:49 2024 +0000
@@ -0,0 +1,111 @@
+##fileformat=VCFv4.0
+##fileDate=20220906
+##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 20 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.001 --bonf dynamic --no-default-filter --no-default-filter -r NC_045512:1-7475 -o /data/jwd01/main/050/269/50269463/tmp/lofreq2_call_parallelzjjfw9e7/0.vcf.gz reads.bam
+##reference=reference.fa
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth">
+##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
+##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias at this position">
+##INFO=<ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">
+##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position">
+##FILTER=<ID=min_snvqual_66,Description="Minimum SNV Quality (Phred) 66">
+##FILTER=<ID=min_indelqual_50,Description="Minimum Indel Quality (Phred) 50">
+##FILTER=<ID=min_snvqual_74,Description="Minimum SNV Quality (Phred) 74">
+##FILTER=<ID=min_indelqual_58,Description="Minimum Indel Quality (Phred) 58">
+##FILTER=<ID=min_af_0.100000,Description="Minimum allele frequency 0.100000">
+##FILTER=<ID=min_dp_20,Description="Minimum Coverage 20">
+##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000">
+##SnpEffVersion="4.3t (build 2017-11-24 10:18), by Pablo Cingolani"
+##SnpEffCmd="SnpEff  -i vcf -o vcf -formatEff -classic -no-downstream -no-intergenic -no-intron -no-upstream -stats /data/jwd01/main/050/269/50269698/outputs/galaxy_dataset_88addf3f-f2e4-4637-81e0-e43aa1e91417.dat -csvStats /data/jwd01/main/050/269/50269698/outputs/galaxy_dataset_17b38e29-aa4a-4ae7-bdbe-12272452464e.dat SARS-CoV-2 /data/dnb07/galaxy_db/files/9/e/f/dataset_9ef6f377-a1fd-48d3-99c0-cb0477d7ba5f.dat "
+##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_Change| Amino_Acid_length | Gene_Name | Transcript_BioType | Gene_Coding | Transcript_ID | Exon_Rank  | Genotype [ | ERRORS | WARNINGS ] )' ">
+##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
+##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+NC_045512	509	.	GGTCATGTTA	G	49314.0	PASS	AF=0.969960;DP=1731;DP4=78,84,956,723;HRUN=2;SB=14;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggtcatgttatg/gtg|GHVM82V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	670	.	T	G	40246.0	PASS	AF=0.935565;DP=1195;DP4=0,0,610,585;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agT/agG|S135R|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	761	.	A	G	13864.0	PASS	AF=0.362500;DP=1280;DP4=392,394,250,242;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agc/Ggc|S166G|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	900	.	C	T	49314.0	PASS	AF=0.943740;DP=1813;DP4=1,1,892,917;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S212L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	1980	.	G	T	13418.0	PASS	AF=0.893035;DP=402;DP4=1,0,199,199;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gTa|G572V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	2790	.	C	T	15400.0	PASS	AF=0.933333;DP=450;DP4=0,0,227,220;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T842I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	3037	.	C	T	27805.0	PASS	AF=0.945980;DP=796;DP4=2,2,395,394;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	4184	.	G	A	8444.0	PASS	AF=0.915323;DP=248;DP4=0,0,149,98;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G1307S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
+NC_045512	4321	.	C	T	7289.0	PASS	AF=0.692064;DP=315;DP4=80,3,123,108;SB=139;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A1352|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	5365	.	C	T	7054.0	PASS	AF=0.291717;DP=833;DP4=171,380,130,146;SB=50;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y1700|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	6318	.	C	T	6698.0	PASS	AF=0.314865;DP=740;DP4=230,256,116,137;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCa/cTa|P2018L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	9344	.	C	T	26982.0	PASS	AF=0.967742;DP=744;DP4=0,0,370,374;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L3027F|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	9424	.	A	G	24944.0	PASS	AF=0.929444;DP=737;DP4=1,0,378,357;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V3053|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	9534	.	C	T	47610.0	PASS	AF=0.951347;DP=1336;DP4=0,1,643,690;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T3090I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	9866	.	C	T	19843.0	PASS	AF=0.965642;DP=553;DP4=0,0,325,228;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L3201F|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	9930	.	A	G	3433.0	PASS	AF=0.139558;DP=996;DP4=417,414,86,74;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D3222G|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	10029	.	C	T	34725.0	PASS	AF=0.801016;DP=1181;DP4=0,5,554,616;SB=11;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T3255I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	10198	.	C	T	23131.0	PASS	AF=0.922059;DP=680;DP4=1,0,352,325;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D3311|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	10447	.	G	A	21620.0	PASS	AF=0.906396;DP=641;DP4=0,0,325,311;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R3394|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
+NC_045512	10449	.	C	A	21547.0	PASS	AF=0.903276;DP=641;DP4=1,0,331,308;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cAc|P3395H|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
+NC_045512	10733	.	C	T	7258.0	PASS	AF=0.211905;DP=1260;DP4=491,486,145,137;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L3490F|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	11287	.	GTCTGGTTTT	G	10490.0	PASS	AF=0.985423;DP=343;DP4=18,23,167,171;HRUN=1;SB=2;INDEL;EFF=CODON_DELETION(MODERATE||tctggtttt/|SGF3675|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	12854	.	C	T	6207.0	PASS	AF=0.371025;DP=566;DP4=183,149,131,102;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P4197S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	12880	.	C	T	21798.0	PASS	AF=0.968386;DP=601;DP4=0,0,307,294;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I4205|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	14408	.	C	T	49314.0	PASS	AF=0.945901;DP=1793;DP4=1,0,868,924;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P4720L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	15714	.	C	T	26016.0	PASS	AF=0.940860;DP=744;DP4=0,1,355,385;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L5155|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	17410	.	C	T	8707.0	PASS	AF=0.922780;DP=259;DP4=0,0,128,130;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R5721C|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	18163	.	A	G	14458.0	PASS	AF=0.930876;DP=434;DP4=0,0,223,206;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I5972V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G)
+NC_045512	19955	.	C	T	39871.0	PASS	AF=0.930736;DP=1155;DP4=0,0,593,559;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T6569I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	20055	.	A	G	9831.0	PASS	AF=0.896667;DP=300;DP4=18,0,118,162;SB=64;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E6602|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G)
+NC_045512	20719	.	C	T	10172.0	PASS	AF=0.916944;DP=301;DP4=0,0,186,114;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L6824|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	21618	.	C	T	37737.0	PASS	AF=0.908015;DP=1098;DP4=0,1,534,546;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T19I|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	21632	.	TTACCCCCTG	T	36519.0	PASS	AF=0.987215;DP=1095;DP4=19,13,521,560;HRUN=2;SB=5;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ttaccccctgca/tca|LPPA24S|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	21987	.	G	A	32024.0	PASS	AF=0.830606;DP=1039;DP4=6,1,553,478;SB=8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G142D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22200	.	T	G	14214.0	PASS	AF=0.926014;DP=419;DP4=0,0,178,240;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gGg|V213G|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	22578	.	G	A	31903.0	PASS	AF=0.882294;DP=994;DP4=5,2,476,504;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G339D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22629	.	A	C	30661.0	PASS	AF=0.921892;DP=909;DP4=0,2,428,478;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aCg|K356T|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22664	.	C	A	27838.0	PASS	AF=0.879490;DP=863;DP4=13,9,365,474;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cta/Ata|L368I|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22674	.	C	T	24989.0	PASS	AF=0.836145;DP=830;DP4=0,5,345,479;SB=10;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S371F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22679	.	T	C	27296.0	PASS	AF=0.950255;DP=784;DP4=0,0,325,458;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Cca|S373P|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22686	.	C	T	21778.0	PASS	AF=0.854571;DP=722;DP4=1,4,302,413;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S375F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22688	.	A	G	22939.0	PASS	AF=0.897250;DP=691;DP4=1,1,295,391;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T376A|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	22716	.	C	T	19013.0	PASS	AF=0.940520;DP=538;DP4=0,0,245,292;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T385I|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22775	.	G	A	28337.0	PASS	AF=0.840075;DP=1063;DP4=60,70,404,528;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D405N|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22786	.	A	C	36993.0	PASS	AF=0.908537;DP=1148;DP4=0,1,526,618;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agA/agC|R408S|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22792	.	C	T	39448.0	PASS	AF=0.923010;DP=1156;DP4=0,0,540,614;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I410|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22813	.	G	T	46605.0	PASS	AF=0.910819;DP=1368;DP4=2,2,667,694;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaG/aaT|K417N|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22882	.	T	G	33218.0	PASS	AF=0.903749;DP=987;DP4=3,1,556,426;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N440K|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	22992	.	G	A	33338.0	PASS	AF=0.922686;DP=983;DP4=0,0,439,539;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S477N|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22995	.	C	A	35188.0	PASS	AF=0.960366;DP=984;DP4=0,0,438,542;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aAa|T478K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	23013	.	A	C	32197.0	PASS	AF=0.884615;DP=988;DP4=3,4,432,546;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gCa|E484A|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	23040	.	A	G	28927.0	PASS	AF=0.909817;DP=876;DP4=1,5,392,477;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q493R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23055	.	A	G	25805.0	PASS	AF=0.901126;DP=799;DP4=1,0,375,423;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q498R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23063	.	A	T	27086.0	PASS	AF=0.935149;DP=771;DP4=1,0,374,395;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Tat|N501Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	23075	.	T	C	24760.0	PASS	AF=0.923593;DP=746;DP4=1,0,379,366;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y505H|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	23403	.	A	G	17764.0	PASS	AF=0.926357;DP=516;DP4=0,1,227,287;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D614G|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23525	.	C	T	11671.0	PASS	AF=0.900285;DP=351;DP4=0,0,169,181;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H655Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	23599	.	T	G	28616.0	PASS	AF=0.924641;DP=836;DP4=0,0,423,413;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N679K|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23604	.	C	A	27152.0	PASS	AF=0.889290;DP=831;DP4=3,0,418,408;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cAt|P681H|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	23854	.	C	A	13443.0	PASS	AF=0.882494;DP=417;DP4=0,5,206,205;SB=12;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaC/aaA|N764K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	23948	.	G	T	19483.0	PASS	AF=0.918871;DP=567;DP4=0,0,303,261;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Tat|D796Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	24424	.	A	T	47157.0	PASS	AF=0.917638;DP=1372;DP4=0,10,722,639;SB=32;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caA/caT|Q954H|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	24469	.	T	A	49314.0	PASS	AF=0.940594;DP=1616;DP4=3,0,817,790;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaA|N969K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	24966	.	A	G	37438.0	PASS	AF=0.901051;DP=1142;DP4=1,1,515,615;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aGc|N1135S|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	25000	.	C	T	35713.0	PASS	AF=0.932551;DP=1023;DP4=0,1,497,520;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D1146|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	25584	.	C	T	41364.0	PASS	AF=0.868482;DP=1285;DP4=0,2,728,548;SB=7;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T64|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
+NC_045512	26060	.	C	T	37722.0	PASS	AF=0.959125;DP=1052;DP4=0,0,519,532;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T223I|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
+NC_045512	26270	.	C	T	20075.0	PASS	AF=0.910169;DP=590;DP4=2,1,316,270;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T9I|75|E|protein_coding|CODING|GU280_gp04|1|T)
+NC_045512	26577	.	C	G	28295.0	PASS	AF=0.902353;DP=850;DP4=1,0,424,421;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q19E|222|M|protein_coding|CODING|GU280_gp05|1|G)
+NC_045512	26709	.	G	A	49314.0	PASS	AF=0.932495;DP=1511;DP4=1,0,716,789;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A63T|222|M|protein_coding|CODING|GU280_gp05|1|A)
+NC_045512	26801	.	C	T	41640.0	PASS	AF=0.909458;DP=1237;DP4=0,1,570,663;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L93|222|M|protein_coding|CODING|GU280_gp05|1|T)
+NC_045512	26858	.	C	T	22508.0	PASS	AF=0.874269;DP=684;DP4=0,0,316,365;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F112|222|M|protein_coding|CODING|GU280_gp05|1|T)
+NC_045512	27259	.	A	C	45374.0	PASS	AF=0.890858;DP=1411;DP4=5,10,575,816;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|Agg/Cgg|R20|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
+NC_045512	27382	.	G	C	14766.0	PASS	AF=0.901827;DP=438;DP4=1,0,209,227;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Cat|D61H|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
+NC_045512	27383	.	A	T	14828.0	PASS	AF=0.910138;DP=434;DP4=1,0,207,226;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gTt|D61V|61|ORF6|protein_coding|CODING|GU280_gp06|1|T)
+NC_045512	27384	.	T	C	14918.0	PASS	AF=0.898420;DP=443;DP4=1,0,215,226;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D61|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
+NC_045512	27481	.	C	T	20803.0	PASS	AF=0.941569;DP=599;DP4=0,0,291,304;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L30F|121|ORF7a|protein_coding|CODING|GU280_gp07|1|T)
+NC_045512	27549	.	C	T	42020.0	PASS	AF=0.897189;DP=1245;DP4=0,0,632,599;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N52|121|ORF7a|protein_coding|CODING|GU280_gp07|1|T)
+NC_045512	27807	.	C	T	17266.0	PASS	AF=0.953722;DP=497;DP4=0,0,245,250;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L18|43|ORF7b|protein_coding|CODING|GU280_gp08|1|T)
+NC_045512	28271	.	A	T	46064.0	PASS	AF=0.910096;DP=1357;DP4=2,9,655,689;SB=11
+NC_045512	28311	.	C	T	45477.0	PASS	AF=0.818475;DP=1548;DP4=2,13,761,763;SB=21;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cTc|P13L|419|N|protein_coding|CODING|GU280_gp10|1|T)
+NC_045512	28361	.	GGAGAACGCA	G	30403.0	PASS	AF=0.774089;DP=1235;DP4=184,99,429,527;HRUN=2;SB=85;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggagaacgcagt/ggt|GERS30G|419|N|protein_coding|CODING|GU280_gp10|1|G|INFO_REALIGN_3_PRIME)
+NC_045512	28881	.	G	A	40833.0	PASS	AF=0.945026;DP=1146;DP4=0,0,518,623;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aAg|R203K|419|N|protein_coding|CODING|GU280_gp10|1|A)
+NC_045512	28882	.	G	A	38295.0	PASS	AF=0.908772;DP=1140;DP4=0,1,517,609;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R203|419|N|protein_coding|CODING|GU280_gp10|1|A)
+NC_045512	28883	.	G	C	39272.0	PASS	AF=0.923144;DP=1145;DP4=0,0,515,621;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gga/Cga|G204R|419|N|protein_coding|CODING|GU280_gp10|1|C)
+NC_045512	29510	.	A	C	49314.0	PASS	AF=0.924388;DP=2288;DP4=0,1,1031,1246;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agt/Cgt|S413R|419|N|protein_coding|CODING|GU280_gp10|1|C)
+NC_045512	29733	.	CGAGGCCACGCGGAGTACGATCGAGTG	C	49314.0	PASS	AF=0.992537;DP=1340;DP4=133,109,486,844;HRUN=1;SB=69;INDEL
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/day_26.vcf	Wed May 15 13:37:49 2024 +0000
@@ -0,0 +1,113 @@
+##fileformat=VCFv4.0
+##fileDate=20220830
+##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 20 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.001 --bonf dynamic --no-default-filter --no-default-filter -r NC_045512:1-7475 -o /data/jwd/main/050/067/50067387/tmp/lofreq2_call_parallelawyalhqx/0.vcf.gz reads.bam
+##reference=reference.fa
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth">
+##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
+##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias at this position">
+##INFO=<ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">
+##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position">
+##FILTER=<ID=min_snvqual_67,Description="Minimum SNV Quality (Phred) 67">
+##FILTER=<ID=min_indelqual_52,Description="Minimum Indel Quality (Phred) 52">
+##FILTER=<ID=min_snvqual_74,Description="Minimum SNV Quality (Phred) 74">
+##FILTER=<ID=min_indelqual_60,Description="Minimum Indel Quality (Phred) 60">
+##FILTER=<ID=min_af_0.100000,Description="Minimum allele frequency 0.100000">
+##FILTER=<ID=min_dp_20,Description="Minimum Coverage 20">
+##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000">
+##SnpEffVersion="4.3t (build 2017-11-24 10:18), by Pablo Cingolani"
+##SnpEffCmd="SnpEff  -i vcf -o vcf -formatEff -classic -no-downstream -no-intergenic -no-intron -no-upstream -stats /data/jwd01/main/050/067/50067624/outputs/galaxy_dataset_1f02ecc6-19df-4f6d-aa04-cc785461e78a.dat -csvStats /data/jwd01/main/050/067/50067624/outputs/galaxy_dataset_443b1fc7-832e-41e3-8e2a-105d5489e124.dat SARS-CoV-2 /data/dnb06/galaxy_db/files/f/d/0/dataset_fd092746-8c86-4a76-9631-3e6490e97b29.dat "
+##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_Change| Amino_Acid_length | Gene_Name | Transcript_BioType | Gene_Coding | Transcript_ID | Exon_Rank  | Genotype [ | ERRORS | WARNINGS ] )' ">
+##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
+##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+NC_045512	509	.	GGTCATGTTA	G	32496.0	PASS	AF=0.991159;DP=1018;DP4=51,45,579,430;HRUN=2;SB=3;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggtcatgttatg/gtg|GHVM82V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	670	.	T	G	44671.0	PASS	AF=0.966222;DP=1273;DP4=0,0,659,614;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agT/agG|S135R|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	900	.	C	T	49314.0	PASS	AF=0.975994;DP=2666;DP4=7,5,1345,1308;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S212L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	1980	.	G	T	23479.0	PASS	AF=0.978022;DP=637;DP4=0,0,320,317;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gTa|G572V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	2790	.	C	T	35600.0	PASS	AF=0.990722;DP=970;DP4=0,0,478,492;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T842I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	3037	.	C	T	49314.0	PASS	AF=0.982786;DP=1917;DP4=0,0,962,952;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	4184	.	G	A	28231.0	PASS	AF=0.983073;DP=768;DP4=0,1,451,316;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G1307S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
+NC_045512	4276	.	C	T	25805.0	PASS	AF=0.988571;DP=700;DP4=1,1,501,197;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y1337|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	4321	.	C	T	15676.0	PASS	AF=0.761667;DP=600;DP4=136,1,250,213;SB=287;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A1352|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	6354	.	C	T	23153.0	PASS	AF=0.801462;DP=821;DP4=149,0,406,266;SB=285;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S2030L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	9344	.	C	T	44260.0	PASS	AF=0.984950;DP=1196;DP4=0,0,588,608;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L3027F|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	9424	.	A	G	42091.0	PASS	AF=0.973207;DP=1157;DP4=1,1,571,583;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V3053|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	9534	.	C	T	49314.0	PASS	AF=0.989791;DP=2155;DP4=0,0,1054,1101;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T3090I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	9866	.	C	T	49314.0	PASS	AF=0.980783;DP=1405;DP4=1,1,827,575;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L3201F|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	10029	.	C	T	49314.0	PASS	AF=0.953757;DP=1557;DP4=0,2,681,869;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T3255I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	10198	.	C	T	42819.0	PASS	AF=0.975445;DP=1181;DP4=1,1,612,567;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D3311|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	10447	.	G	A	31832.0	PASS	AF=0.961495;DP=883;DP4=2,1,417,461;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R3394|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
+NC_045512	10449	.	C	A	31879.0	PASS	AF=0.973563;DP=870;DP4=0,1,414,453;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cAc|P3395H|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
+NC_045512	11287	.	GTCTGGTTTT	G	21643.0	PASS	AF=0.992515;DP=668;DP4=49,62,321,342;HRUN=1;SB=3;INDEL;EFF=CODON_DELETION(MODERATE||tctggtttt/|SGF3675|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	12036	.	C	T	44979.0	PASS	AF=0.960187;DP=1281;DP4=0,1,615,663;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A3924V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	12854	.	C	T	30930.0	PASS	AF=0.977300;DP=837;DP4=0,0,420,417;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P4197S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	12880	.	C	T	32562.0	PASS	AF=0.990847;DP=874;DP4=0,0,424,450;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I4205|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	14408	.	C	T	49314.0	PASS	AF=0.982794;DP=2441;DP4=0,2,1219,1220;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P4720L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	15451	.	G	A	49314.0	PASS	AF=0.963636;DP=1485;DP4=3,1,854,627;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G5068S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|A)
+NC_045512	15714	.	C	T	42612.0	PASS	AF=0.976844;DP=1166;DP4=0,0,570,596;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L5155|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	17410	.	C	T	22565.0	PASS	AF=0.990148;DP=609;DP4=0,1,290,318;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R5721C|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	18163	.	A	G	25478.0	PASS	AF=0.973315;DP=712;DP4=0,0,358,354;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I5972V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G)
+NC_045512	19955	.	C	T	49314.0	PASS	AF=0.974684;DP=1738;DP4=3,6,1020,705;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T6569I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	20055	.	A	G	24581.0	PASS	AF=0.956772;DP=694;DP4=15,0,326,353;SB=46;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E6602|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G)
+NC_045512	20719	.	C	T	31418.0	PASS	AF=0.973225;DP=859;DP4=0,0,471,388;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L6824|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	21618	.	C	T	49314.0	PASS	AF=0.989832;DP=2262;DP4=0,0,1089,1173;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T19I|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	21632	.	TTACCCCCTG	T	49314.0	PASS	AF=0.972236;DP=1981;DP4=87,108,921,1005;HRUN=2;SB=3;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ttaccccctgca/tca|LPPA24S|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	21987	.	G	A	49314.0	PASS	AF=0.962881;DP=1805;DP4=0,0,956,847;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G142D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22200	.	T	G	29772.0	PASS	AF=0.953970;DP=869;DP4=1,3,404,460;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gGg|V213G|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	22578	.	G	A	49314.0	PASS	AF=0.970785;DP=1643;DP4=3,2,789,847;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G339D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22629	.	A	C	49314.0	PASS	AF=0.961675;DP=1409;DP4=1,0,703,704;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aCg|K356T|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22664	.	C	A	49314.0	PASS	AF=0.968773;DP=1377;DP4=2,1,661,711;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cta/Ata|L368I|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22674	.	C	T	48559.0	PASS	AF=0.967907;DP=1371;DP4=0,0,668,703;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S371F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22679	.	T	C	48650.0	PASS	AF=0.972874;DP=1364;DP4=0,1,671,691;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Cca|S373P|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22686	.	C	T	46120.0	PASS	AF=0.961861;DP=1311;DP4=2,2,650,653;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S375F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22688	.	A	G	46077.0	PASS	AF=0.960829;DP=1302;DP4=4,4,649,643;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T376A|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	22716	.	C	T	49314.0	PASS	AF=0.985936;DP=1351;DP4=0,0,707,643;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T385I|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22775	.	G	A	49314.0	PASS	AF=0.933405;DP=2778;DP4=61,84,1263,1369;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D405N|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22786	.	A	C	49314.0	PASS	AF=0.962482;DP=2772;DP4=4,4,1316,1441;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agA/agC|R408S|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22792	.	C	T	49314.0	PASS	AF=0.976694;DP=2789;DP4=2,2,1338,1447;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I410|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22813	.	G	T	49314.0	PASS	AF=0.982210;DP=2923;DP4=2,0,1403,1518;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaG/aaT|K417N|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22882	.	T	G	49314.0	PASS	AF=0.967190;DP=2103;DP4=3,1,1167,929;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N440K|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	22992	.	G	A	49314.0	PASS	AF=0.973366;DP=1652;DP4=1,0,759,889;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S477N|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22995	.	C	A	49314.0	PASS	AF=0.976277;DP=1644;DP4=0,0,761,882;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aAa|T478K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	23013	.	A	C	49314.0	PASS	AF=0.968427;DP=1647;DP4=4,1,771,868;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gCa|E484A|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	23040	.	A	G	49314.0	PASS	AF=0.971710;DP=1626;DP4=0,0,782,844;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q493R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23055	.	A	G	49314.0	PASS	AF=0.963467;DP=1615;DP4=0,0,777,838;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q498R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23063	.	A	T	49314.0	PASS	AF=0.987766;DP=1553;DP4=0,0,751,798;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Tat|N501Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	23075	.	T	C	49314.0	PASS	AF=0.975032;DP=1562;DP4=0,0,775,786;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y505H|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	23403	.	A	G	23982.0	PASS	AF=0.968563;DP=668;DP4=0,0,309,358;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D614G|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23525	.	C	T	23629.0	PASS	AF=0.969136;DP=648;DP4=0,0,313,334;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H655Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	23599	.	T	G	49314.0	PASS	AF=0.973811;DP=1451;DP4=1,1,742,707;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N679K|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23604	.	C	A	49314.0	PASS	AF=0.984583;DP=1427;DP4=0,0,727,696;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cAt|P681H|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	23854	.	C	A	41371.0	PASS	AF=0.968885;DP=1157;DP4=1,1,585,569;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaC/aaA|N764K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	23948	.	G	T	44271.0	PASS	AF=0.968543;DP=1208;DP4=2,2,606,594;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Tat|D796Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	24424	.	A	T	49314.0	PASS	AF=0.985166;DP=2764;DP4=3,4,1408,1348;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caA/caT|Q954H|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	24469	.	T	A	49314.0	PASS	AF=0.978951;DP=2993;DP4=1,0,1482,1508;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaA|N969K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	24966	.	A	G	49314.0	PASS	AF=0.974902;DP=1793;DP4=1,0,881,904;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aGc|N1135S|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	25000	.	C	T	49314.0	PASS	AF=0.976404;DP=1780;DP4=0,0,873,904;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D1146|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	25584	.	C	T	49314.0	PASS	AF=0.954421;DP=1821;DP4=0,0,1029,792;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T64|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
+NC_045512	26060	.	C	T	49314.0	PASS	AF=0.985141;DP=2019;DP4=0,2,994,1021;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T223I|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
+NC_045512	26195	.	C	T	30983.0	PASS	AF=0.963636;DP=880;DP4=0,0,431,448;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T268M|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
+NC_045512	26270	.	C	T	33971.0	PASS	AF=0.984699;DP=915;DP4=0,1,480,433;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T9I|75|E|protein_coding|CODING|GU280_gp04|1|T)
+NC_045512	26408	.	C	T	49314.0	PASS	AF=0.838681;DP=2275;DP4=145,128,1020,926;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tTt|S55F|75|E|protein_coding|CODING|GU280_gp04|1|T)
+NC_045512	26577	.	C	G	42818.0	PASS	AF=0.974468;DP=1175;DP4=0,0,552,623;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q19E|222|M|protein_coding|CODING|GU280_gp05|1|G)
+NC_045512	26709	.	G	A	49314.0	PASS	AF=0.974217;DP=2172;DP4=2,1,1212,954;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A63T|222|M|protein_coding|CODING|GU280_gp05|1|A)
+NC_045512	26801	.	C	T	49314.0	PASS	AF=0.977684;DP=2599;DP4=0,2,1303,1292;SB=6;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L93|222|M|protein_coding|CODING|GU280_gp05|1|T)
+NC_045512	26858	.	C	T	49314.0	PASS	AF=0.988884;DP=2249;DP4=1,1,991,1256;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F112|222|M|protein_coding|CODING|GU280_gp05|1|T)
+NC_045512	27259	.	A	C	49314.0	PASS	AF=0.965937;DP=2466;DP4=9,13,1006,1437;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Agg/Cgg|R20|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
+NC_045512	27382	.	G	C	32891.0	PASS	AF=0.977401;DP=885;DP4=0,0,440,445;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Cat|D61H|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
+NC_045512	27383	.	A	T	32874.0	PASS	AF=0.982798;DP=872;DP4=0,1,434,434;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gTt|D61V|61|ORF6|protein_coding|CODING|GU280_gp06|1|T)
+NC_045512	27384	.	T	C	32957.0	PASS	AF=0.976217;DP=883;DP4=0,2,440,441;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D61|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
+NC_045512	27481	.	C	T	31950.0	PASS	AF=0.976136;DP=880;DP4=1,1,429,443;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L30F|121|ORF7a|protein_coding|CODING|GU280_gp07|1|T)
+NC_045512	27549	.	C	T	49314.0	PASS	AF=0.985227;DP=1963;DP4=0,1,996,966;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N52|121|ORF7a|protein_coding|CODING|GU280_gp07|1|T)
+NC_045512	27807	.	C	T	39295.0	PASS	AF=0.981256;DP=1067;DP4=0,0,530,535;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L18|43|ORF7b|protein_coding|CODING|GU280_gp08|1|T)
+NC_045512	28271	.	A	T	49314.0	PASS	AF=0.978363;DP=3420;DP4=2,2,1669,1742;SB=0
+NC_045512	28311	.	C	T	49314.0	PASS	AF=0.948180;DP=3242;DP4=1,2,1575,1662;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cTc|P13L|419|N|protein_coding|CODING|GU280_gp10|1|T)
+NC_045512	28361	.	GGAGAACGCA	G	49314.0	PASS	AF=0.793066;DP=2740;DP4=448,129,803,1370;HRUN=2;SB=691;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggagaacgcagt/ggt|GERS30G|419|N|protein_coding|CODING|GU280_gp10|1|G|INFO_REALIGN_3_PRIME)
+NC_045512	28657	.	C	T	49314.0	PASS	AF=0.963598;DP=2390;DP4=1,2,1275,1108;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D128|419|N|protein_coding|CODING|GU280_gp10|1|T)
+NC_045512	28881	.	G	A	38189.0	PASS	AF=0.972763;DP=1028;DP4=0,0,487,540;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aAg|R203K|419|N|protein_coding|CODING|GU280_gp10|1|A)
+NC_045512	28882	.	G	A	37112.0	PASS	AF=0.962927;DP=1025;DP4=1,1,486,536;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R203|419|N|protein_coding|CODING|GU280_gp10|1|A)
+NC_045512	28883	.	G	C	38233.0	PASS	AF=0.978967;DP=1046;DP4=0,0,499,544;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gga/Cga|G204R|419|N|protein_coding|CODING|GU280_gp10|1|C)
+NC_045512	29510	.	A	C	49314.0	PASS	AF=0.967644;DP=3307;DP4=1,2,1444,1851;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agt/Cgt|S413R|419|N|protein_coding|CODING|GU280_gp10|1|C)
+NC_045512	29733	.	CGAGGCCACGCGGAGTACGATCGAGTG	C	43802.0	PASS	AF=0.990859;DP=1094;DP4=198,202,360,724;HRUN=1;SB=78;INDEL
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/day_32.vcf	Wed May 15 13:37:49 2024 +0000
@@ -0,0 +1,116 @@
+##fileformat=VCFv4.0
+##fileDate=20220830
+##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 20 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.001 --bonf dynamic --no-default-filter --no-default-filter -r NC_045512:1-7475 -o /data/jwd01/main/050/067/50067391/tmp/lofreq2_call_parallel84g9etws/0.vcf.gz reads.bam
+##reference=reference.fa
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth">
+##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
+##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias at this position">
+##INFO=<ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">
+##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position">
+##FILTER=<ID=min_snvqual_63,Description="Minimum SNV Quality (Phred) 63">
+##FILTER=<ID=min_indelqual_48,Description="Minimum Indel Quality (Phred) 48">
+##FILTER=<ID=min_snvqual_71,Description="Minimum SNV Quality (Phred) 71">
+##FILTER=<ID=min_indelqual_57,Description="Minimum Indel Quality (Phred) 57">
+##FILTER=<ID=min_af_0.100000,Description="Minimum allele frequency 0.100000">
+##FILTER=<ID=min_dp_20,Description="Minimum Coverage 20">
+##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000">
+##SnpEffVersion="4.3t (build 2017-11-24 10:18), by Pablo Cingolani"
+##SnpEffCmd="SnpEff  -i vcf -o vcf -formatEff -classic -no-downstream -no-intergenic -no-intron -no-upstream -stats /data/jwd01/main/050/067/50067628/outputs/galaxy_dataset_776fff03-e254-4dfb-abbf-8d93b9cfb46b.dat -csvStats /data/jwd01/main/050/067/50067628/outputs/galaxy_dataset_fb58a8b5-8934-4d3e-9ea4-2b45f3933814.dat SARS-CoV-2 /data/dnb06/galaxy_db/files/7/6/b/dataset_76b4f78f-44ca-48ff-9ffb-46fda2231d70.dat "
+##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_Change| Amino_Acid_length | Gene_Name | Transcript_BioType | Gene_Coding | Transcript_ID | Exon_Rank  | Genotype [ | ERRORS | WARNINGS ] )' ">
+##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
+##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+NC_045512	509	.	GGTCATGTTA	G	15763.0	PASS	AF=0.991903;DP=494;DP4=25,25,293,197;HRUN=2;SB=6;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggtcatgttatg/gtg|GHVM82V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	670	.	T	G	19515.0	PASS	AF=0.969369;DP=555;DP4=0,0,280,275;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agT/agG|S135R|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	900	.	C	T	38595.0	PASS	AF=0.975285;DP=1052;DP4=5,2,514,531;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S212L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	1980	.	G	T	10895.0	PASS	AF=0.966443;DP=298;DP4=0,0,153,144;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gTa|G572V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	2790	.	C	T	15238.0	PASS	AF=0.966903;DP=423;DP4=0,0,204,219;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T842I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	3037	.	C	T	26967.0	PASS	AF=0.966533;DP=747;DP4=0,0,361,383;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	4184	.	G	A	10051.0	PASS	AF=0.978102;DP=274;DP4=0,0,162,112;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G1307S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
+NC_045512	4276	.	C	T	10845.0	PASS	AF=0.983051;DP=295;DP4=0,0,216,79;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y1337|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	4321	.	C	T	6431.0	PASS	AF=0.716475;DP=261;DP4=65,3,103,90;SB=108;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A1352|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	5628	.	C	T	3005.0	PASS	AF=0.293011;DP=372;DP4=113,147,57,54;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T1788M|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	6354	.	C	T	7773.0	PASS	AF=0.760274;DP=292;DP4=66,1,132,93;SB=113;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S2030L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	9344	.	C	T	20585.0	PASS	AF=0.982206;DP=562;DP4=0,0,283,279;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L3027F|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	9424	.	A	G	18743.0	PASS	AF=0.965779;DP=526;DP4=2,2,253,268;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V3053|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	9534	.	C	T	34480.0	PASS	AF=0.985808;DP=916;DP4=0,1,445,469;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T3090I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	9866	.	C	T	19606.0	PASS	AF=0.983114;DP=533;DP4=0,0,315,218;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L3201F|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	10029	.	C	T	23751.0	PASS	AF=0.944035;DP=679;DP4=0,1,306,372;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T3255I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	10198	.	C	T	19726.0	PASS	AF=0.990637;DP=534;DP4=0,0,281,253;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D3311|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	10447	.	G	A	11857.0	PASS	AF=0.951662;DP=331;DP4=0,0,164,165;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R3394|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
+NC_045512	10449	.	C	A	11818.0	PASS	AF=0.954407;DP=329;DP4=0,1,164,163;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cAc|P3395H|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
+NC_045512	11287	.	GTCTGGTTTT	G	6182.0	PASS	AF=0.994872;DP=195;DP4=21,21,89,105;HRUN=1;SB=1;INDEL;EFF=CODON_DELETION(MODERATE||tctggtttt/|SGF3675|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	12036	.	C	T	18290.0	PASS	AF=0.963178;DP=516;DP4=0,0,258,258;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A3924V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	12854	.	C	T	14548.0	PASS	AF=0.967172;DP=396;DP4=1,2,200,193;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P4197S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	12880	.	C	T	14683.0	PASS	AF=0.984810;DP=395;DP4=0,0,197,198;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I4205|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	14408	.	C	T	39342.0	PASS	AF=0.971216;DP=1077;DP4=1,2,531,543;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P4720L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	15451	.	G	A	26255.0	PASS	AF=0.969655;DP=725;DP4=0,0,411,313;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G5068S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|A)
+NC_045512	15714	.	C	T	21454.0	PASS	AF=0.972789;DP=588;DP4=0,0,282,306;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L5155|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	17410	.	C	T	9474.0	PASS	AF=0.984496;DP=258;DP4=0,0,127,131;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R5721C|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	18163	.	A	G	12021.0	PASS	AF=0.970326;DP=337;DP4=0,0,168,169;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I5972V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G)
+NC_045512	19955	.	C	T	28596.0	PASS	AF=0.973180;DP=783;DP4=0,0,463,318;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T6569I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	20055	.	A	G	11442.0	PASS	AF=0.968051;DP=313;DP4=0,0,156,157;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E6602|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G)
+NC_045512	20719	.	C	T	15802.0	PASS	AF=0.976798;DP=431;DP4=0,0,237,194;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L6824|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	21618	.	C	T	40675.0	PASS	AF=0.983441;DP=1087;DP4=1,2,533,551;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T19I|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	21632	.	TTACCCCCTG	T	32959.0	PASS	AF=0.983211;DP=953;DP4=39,46,461,476;HRUN=2;SB=2;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ttaccccctgca/tca|LPPA24S|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	21691	.	C	T	4169.0	PASS	AF=0.155660;DP=1060;DP4=430,461,81,88;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F43|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	21987	.	G	A	29742.0	PASS	AF=0.954816;DP=841;DP4=1,0,431,407;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G142D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22200	.	T	G	14370.0	PASS	AF=0.973105;DP=409;DP4=0,0,199,210;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gGg|V213G|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	22578	.	G	A	21245.0	PASS	AF=0.974790;DP=595;DP4=1,0,296,298;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G339D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22629	.	A	C	19866.0	PASS	AF=0.971377;DP=559;DP4=0,0,284,275;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aCg|K356T|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22664	.	C	A	20854.0	PASS	AF=0.972028;DP=572;DP4=0,0,277,292;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cta/Ata|L368I|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22674	.	C	T	20794.0	PASS	AF=0.974315;DP=584;DP4=0,0,280,303;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S371F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22679	.	T	C	20993.0	PASS	AF=0.976190;DP=588;DP4=0,0,286,302;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Cca|S373P|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22686	.	C	T	19322.0	PASS	AF=0.967332;DP=551;DP4=0,1,267,279;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S375F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22688	.	A	G	19389.0	PASS	AF=0.970588;DP=544;DP4=0,0,267,276;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T376A|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	22716	.	C	T	20710.0	PASS	AF=0.989267;DP=559;DP4=0,0,282,277;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T385I|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22775	.	G	A	42814.0	PASS	AF=0.980375;DP=1172;DP4=2,6,574,590;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D405N|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22786	.	A	C	43361.0	PASS	AF=0.963816;DP=1216;DP4=0,0,597,619;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agA/agC|R408S|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22792	.	C	T	46048.0	PASS	AF=0.977689;DP=1255;DP4=0,0,614,641;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I410|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22813	.	G	T	49314.0	PASS	AF=0.978801;DP=1368;DP4=0,0,679,686;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaG/aaT|K417N|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22882	.	T	G	38759.0	PASS	AF=0.966102;DP=1062;DP4=1,0,595,466;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N440K|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	22992	.	G	A	30675.0	PASS	AF=0.978873;DP=852;DP4=0,0,387,464;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S477N|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22995	.	C	A	30708.0	PASS	AF=0.978495;DP=837;DP4=0,0,384,453;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aAa|T478K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	23013	.	A	C	30583.0	PASS	AF=0.974760;DP=832;DP4=0,0,377,454;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gCa|E484A|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	23040	.	A	G	29750.0	PASS	AF=0.985240;DP=813;DP4=0,0,371,442;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q493R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23055	.	A	G	28119.0	PASS	AF=0.969620;DP=790;DP4=1,2,367,420;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q498R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23063	.	A	T	27561.0	PASS	AF=0.990553;DP=741;DP4=0,0,359,382;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Tat|N501Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	23075	.	T	C	26731.0	PASS	AF=0.960681;DP=763;DP4=2,2,379,380;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y505H|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	23403	.	A	G	14034.0	PASS	AF=0.966752;DP=391;DP4=0,0,179,212;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D614G|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23525	.	C	T	14033.0	PASS	AF=0.981771;DP=384;DP4=0,0,204,180;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H655Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	23589	.	C	A	5160.0	PASS	AF=0.188293;DP=1025;DP4=439,391,104,90;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aAt|T676N|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	23599	.	T	G	38164.0	PASS	AF=0.969466;DP=1048;DP4=0,1,549,497;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N679K|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23604	.	C	A	38022.0	PASS	AF=0.982592;DP=1034;DP4=0,1,541,490;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cAt|P681H|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	23854	.	C	A	21304.0	PASS	AF=0.960000;DP=600;DP4=0,1,283,315;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaC/aaA|N764K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	23948	.	G	T	22285.0	PASS	AF=0.971901;DP=605;DP4=0,0,315,290;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Tat|D796Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	24424	.	A	T	48760.0	PASS	AF=0.975392;DP=1341;DP4=1,1,682,657;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caA/caT|Q954H|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	24469	.	T	A	49314.0	PASS	AF=0.966245;DP=1422;DP4=0,2,719,698;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaA|N969K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	24966	.	A	G	30117.0	PASS	AF=0.970203;DP=839;DP4=0,0,399,437;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aGc|N1135S|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	25000	.	C	T	32463.0	PASS	AF=0.964126;DP=892;DP4=0,1,436,454;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D1146|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	25584	.	C	T	37535.0	PASS	AF=0.959499;DP=1037;DP4=0,1,579,457;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T64|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
+NC_045512	26060	.	C	T	43542.0	PASS	AF=0.979644;DP=1179;DP4=0,0,582,596;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T223I|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
+NC_045512	26195	.	C	T	18449.0	PASS	AF=0.959770;DP=522;DP4=1,0,262,258;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T268M|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
+NC_045512	26270	.	C	T	20039.0	PASS	AF=0.965704;DP=554;DP4=2,3,280,269;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T9I|75|E|protein_coding|CODING|GU280_gp04|1|T)
+NC_045512	26408	.	C	T	24554.0	PASS	AF=0.633469;DP=1225;DP4=225,182,408,383;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tTt|S55F|75|E|protein_coding|CODING|GU280_gp04|1|T)
+NC_045512	26577	.	C	G	24616.0	PASS	AF=0.974889;DP=677;DP4=2,1,309,364;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q19E|222|M|protein_coding|CODING|GU280_gp05|1|G)
+NC_045512	26709	.	G	A	47953.0	PASS	AF=0.966641;DP=1319;DP4=0,0,741,577;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A63T|222|M|protein_coding|CODING|GU280_gp05|1|A)
+NC_045512	26801	.	C	T	49314.0	PASS	AF=0.973983;DP=1499;DP4=0,1,758,740;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L93|222|M|protein_coding|CODING|GU280_gp05|1|T)
+NC_045512	26858	.	C	T	49314.0	PASS	AF=0.988078;DP=1342;DP4=0,0,605,737;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F112|222|M|protein_coding|CODING|GU280_gp05|1|T)
+NC_045512	27259	.	A	C	47693.0	PASS	AF=0.965004;DP=1343;DP4=3,5,560,770;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Agg/Cgg|R20|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
+NC_045512	27382	.	G	C	14516.0	PASS	AF=0.971795;DP=390;DP4=0,0,187,201;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Cat|D61H|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
+NC_045512	27383	.	A	T	14641.0	PASS	AF=0.981959;DP=388;DP4=0,0,187,201;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gTt|D61V|61|ORF6|protein_coding|CODING|GU280_gp06|1|T)
+NC_045512	27384	.	T	C	14550.0	PASS	AF=0.972010;DP=393;DP4=0,0,189,202;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D61|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
+NC_045512	27481	.	C	T	16357.0	PASS	AF=0.977728;DP=449;DP4=0,0,230,219;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L30F|121|ORF7a|protein_coding|CODING|GU280_gp07|1|T)
+NC_045512	27549	.	C	T	36762.0	PASS	AF=0.980080;DP=1004;DP4=1,0,512,489;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N52|121|ORF7a|protein_coding|CODING|GU280_gp07|1|T)
+NC_045512	27807	.	C	T	22385.0	PASS	AF=0.978723;DP=611;DP4=1,1,311,298;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L18|43|ORF7b|protein_coding|CODING|GU280_gp08|1|T)
+NC_045512	28271	.	A	T	49314.0	PASS	AF=0.973483;DP=1697;DP4=0,1,853,843;SB=3
+NC_045512	28311	.	C	T	49314.0	PASS	AF=0.939506;DP=1620;DP4=0,2,794,819;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cTc|P13L|419|N|protein_coding|CODING|GU280_gp10|1|T)
+NC_045512	28361	.	GGAGAACGCA	G	37520.0	PASS	AF=0.786337;DP=1376;DP4=247,53,394,688;HRUN=2;SB=465;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggagaacgcagt/ggt|GERS30G|419|N|protein_coding|CODING|GU280_gp10|1|G|INFO_REALIGN_3_PRIME)
+NC_045512	28657	.	C	T	45171.0	PASS	AF=0.964511;DP=1268;DP4=1,1,668,597;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D128|419|N|protein_coding|CODING|GU280_gp10|1|T)
+NC_045512	28881	.	G	A	20403.0	PASS	AF=0.960714;DP=560;DP4=1,1,271,287;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aAg|R203K|419|N|protein_coding|CODING|GU280_gp10|1|A)
+NC_045512	28882	.	G	A	19828.0	PASS	AF=0.942755;DP=559;DP4=0,0,271,287;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R203|419|N|protein_coding|CODING|GU280_gp10|1|A)
+NC_045512	28883	.	G	C	20716.0	PASS	AF=0.970280;DP=572;DP4=0,0,277,295;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gga/Cga|G204R|419|N|protein_coding|CODING|GU280_gp10|1|C)
+NC_045512	29510	.	A	C	49314.0	PASS	AF=0.966520;DP=1822;DP4=0,0,792,1028;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agt/Cgt|S413R|419|N|protein_coding|CODING|GU280_gp10|1|C)
+NC_045512	29733	.	CGAGGCCACGCGGAGTACGATCGAGTG	C	21485.0	PASS	AF=0.981550;DP=542;DP4=94,101,189,343;HRUN=1;SB=25;INDEL
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/day_4.vcf	Wed May 15 13:37:49 2024 +0000
@@ -0,0 +1,113 @@
+##fileformat=VCFv4.0
+##fileDate=20221107
+##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 20 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.001 --bonf dynamic --no-default-filter --no-default-filter -r NC_045512:1-7475 -o /data/jwd01/main/051/983/51983885/tmp/lofreq2_call_parallelwl6gca3r/0.vcf.gz reads.bam
+##reference=reference.fa
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth">
+##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
+##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias at this position">
+##INFO=<ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">
+##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position">
+##FILTER=<ID=min_snvqual_67,Description="Minimum SNV Quality (Phred) 67">
+##FILTER=<ID=min_indelqual_52,Description="Minimum Indel Quality (Phred) 52">
+##FILTER=<ID=min_snvqual_75,Description="Minimum SNV Quality (Phred) 75">
+##FILTER=<ID=min_indelqual_59,Description="Minimum Indel Quality (Phred) 59">
+##FILTER=<ID=min_af_0.100000,Description="Minimum allele frequency 0.100000">
+##FILTER=<ID=min_dp_20,Description="Minimum Coverage 20">
+##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000">
+##SnpEffVersion="4.3t (build 2017-11-24 10:18), by Pablo Cingolani"
+##SnpEffCmd="SnpEff  -i vcf -o vcf -formatEff -classic -no-downstream -no-intergenic -no-intron -no-upstream -stats /data/jwd/main/051/984/51984230/outputs/galaxy_dataset_bbc88d99-200c-4bf8-9fbe-465c91367b69.dat -csvStats /data/jwd/main/051/984/51984230/outputs/galaxy_dataset_4d617348-b84f-4c0c-b5e7-08cdfba66ba9.dat SARS-CoV-2 /data/dnb06/galaxy_db/files/8/3/1/dataset_831b536b-ae98-4f42-beca-a2ed99cd2af3.dat "
+##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_Change| Amino_Acid_length | Gene_Name | Transcript_BioType | Gene_Coding | Transcript_ID | Exon_Rank  | Genotype [ | ERRORS | WARNINGS ] )' ">
+##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
+##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+NC_045512	241	.	C	T	1624.0	PASS	AF=0.978261;DP=46;DP4=0,0,24,22;SB=0
+NC_045512	509	.	GGTCATGTTA	G	47743.0	PASS	AF=0.983237;DP=1551;DP4=104,108,805,720;HRUN=2;SB=4;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggtcatgttatg/gtg|GHVM82V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	670	.	T	G	46964.0	PASS	AF=0.927311;DP=1417;DP4=1,0,710,704;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agT/agG|S135R|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	900	.	C	T	49314.0	PASS	AF=0.948932;DP=2761;DP4=0,0,1399,1357;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S212L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	1980	.	G	T	17443.0	PASS	AF=0.927308;DP=509;DP4=1,0,250,256;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gTa|G572V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	2790	.	C	T	33283.0	PASS	AF=0.944211;DP=950;DP4=0,0,466,481;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T842I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	3037	.	C	T	49314.0	PASS	AF=0.939726;DP=1460;DP4=1,2,719,732;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	4184	.	G	A	34956.0	PASS	AF=0.943227;DP=1004;DP4=3,2,559,439;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G1307S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
+NC_045512	4276	.	C	T	16152.0	PASS	AF=0.479167;DP=1104;DP4=369,183,379,172;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y1337|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	4321	.	C	T	22108.0	PASS	AF=0.684265;DP=966;DP4=256,4,362,344;SB=531;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A1352|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	6318	.	C	T	8299.0	PASS	AF=0.227941;DP=1360;DP4=755,275,231,92;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCa/cTa|P2018L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	6354	.	C	T	7263.0	PASS	AF=0.238657;DP=1102;DP4=649,164,162,124;SB=128;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S2030L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	9344	.	C	T	48430.0	PASS	AF=0.958211;DP=1364;DP4=0,0,674,685;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L3027F|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	9424	.	A	G	41396.0	PASS	AF=0.926591;DP=1226;DP4=0,0,601,620;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V3053|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	9534	.	C	T	49314.0	PASS	AF=0.948826;DP=2599;DP4=1,0,1294,1295;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T3090I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	9866	.	C	T	41727.0	PASS	AF=0.943333;DP=1200;DP4=2,2,652,541;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L3201F|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	10029	.	C	T	49314.0	PASS	AF=0.907692;DP=2145;DP4=1,2,1037,1098;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T3255I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	10198	.	C	T	49314.0	PASS	AF=0.953225;DP=1411;DP4=2,1,707,700;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D3311|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	10447	.	G	A	28453.0	PASS	AF=0.909524;DP=840;DP4=1,0,416,419;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R3394|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
+NC_045512	10449	.	C	A	28281.0	PASS	AF=0.900235;DP=852;DP4=1,2,424,419;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cAc|P3395H|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
+NC_045512	11287	.	GTCTGGTTTT	G	17479.0	PASS	AF=0.987589;DP=564;DP4=41,39,264,293;HRUN=1;SB=2;INDEL;EFF=CODON_DELETION(MODERATE||tctggtttt/|SGF3675|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	12036	.	C	T	16708.0	PASS	AF=0.413247;DP=1389;DP4=369,386,311,320;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A3924V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	12854	.	C	T	14178.0	PASS	AF=0.520325;DP=861;DP4=199,179,242,237;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P4197S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	12880	.	C	T	29212.0	PASS	AF=0.942099;DP=829;DP4=0,0,416,411;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I4205|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	14408	.	C	T	49314.0	PASS	AF=0.945489;DP=2660;DP4=1,2,1282,1369;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P4720L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	15451	.	G	A	24631.0	PASS	AF=0.457675;DP=1772;DP4=472,418,465,411;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G5068S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|A)
+NC_045512	15714	.	C	T	42630.0	PASS	AF=0.937908;DP=1224;DP4=0,0,608,612;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L5155|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	17410	.	C	T	21877.0	PASS	AF=0.950241;DP=623;DP4=0,1,313,305;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R5721C|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	18163	.	A	G	22663.0	PASS	AF=0.926362;DP=679;DP4=1,1,342,333;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I5972V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G)
+NC_045512	19955	.	C	T	49314.0	PASS	AF=0.937285;DP=2902;DP4=3,6,1484,1397;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T6569I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	20055	.	A	G	26437.0	PASS	AF=0.882927;DP=820;DP4=28,0,388,402;SB=82;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E6602|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G)
+NC_045512	20719	.	C	T	24589.0	PASS	AF=0.917469;DP=727;DP4=0,0,390,334;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L6824|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	21618	.	C	T	49314.0	PASS	AF=0.952261;DP=2388;DP4=1,0,1162,1219;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T19I|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	21632	.	TTACCCCCTG	T	49314.0	PASS	AF=0.985252;DP=2102;DP4=104,87,978,1093;HRUN=2;SB=12;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ttaccccctgca/tca|LPPA24S|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	21987	.	G	A	49314.0	PASS	AF=0.901728;DP=1852;DP4=3,1,944,895;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G142D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22200	.	T	G	33452.0	PASS	AF=0.914767;DP=1009;DP4=1,3,466,537;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gGg|V213G|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	22578	.	G	A	49314.0	PASS	AF=0.914653;DP=1945;DP4=1,0,944,988;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G339D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22629	.	A	C	49314.0	PASS	AF=0.925228;DP=1645;DP4=1,0,799,840;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aCg|K356T|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22664	.	C	A	49314.0	PASS	AF=0.940945;DP=1524;DP4=1,2,716,796;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cta/Ata|L368I|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22674	.	C	T	49314.0	PASS	AF=0.921333;DP=1500;DP4=0,0,704,793;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S371F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22679	.	T	C	49314.0	PASS	AF=0.929708;DP=1508;DP4=1,4,717,783;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Cca|S373P|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22686	.	C	T	46674.0	PASS	AF=0.929078;DP=1410;DP4=0,3,676,722;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S375F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22688	.	A	G	45642.0	PASS	AF=0.907923;DP=1401;DP4=3,3,678,713;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T376A|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	22716	.	C	T	47711.0	PASS	AF=0.931933;DP=1381;DP4=1,0,691,684;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T385I|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22775	.	G	A	49314.0	PASS	AF=0.765402;DP=3295;DP4=309,363,1159,1456;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D405N|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22786	.	A	C	49314.0	PASS	AF=0.900539;DP=2785;DP4=8,18,1223,1523;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agA/agC|R408S|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22792	.	C	T	49314.0	PASS	AF=0.943945;DP=2783;DP4=0,0,1240,1539;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I410|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22813	.	G	T	49314.0	PASS	AF=0.948471;DP=3008;DP4=0,3,1355,1643;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaG/aaT|K417N|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22882	.	T	G	49314.0	PASS	AF=0.905708;DP=1962;DP4=7,2,1020,929;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N440K|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	22992	.	G	A	49314.0	PASS	AF=0.952740;DP=1989;DP4=0,0,955,1031;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S477N|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22995	.	C	A	49314.0	PASS	AF=0.948847;DP=1994;DP4=4,0,957,1030;SB=12;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aAa|T478K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	23013	.	A	C	49314.0	PASS	AF=0.924191;DP=2071;DP4=7,8,981,1069;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gCa|E484A|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	23040	.	A	G	49314.0	PASS	AF=0.936407;DP=1887;DP4=1,0,891,991;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q493R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23055	.	A	G	49314.0	PASS	AF=0.926287;DP=1845;DP4=1,0,876,967;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q498R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23063	.	A	T	49314.0	PASS	AF=0.960481;DP=1746;DP4=2,1,841,900;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Tat|N501Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	23075	.	T	C	49314.0	PASS	AF=0.925448;DP=1784;DP4=3,0,876,903;SB=9;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y505H|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	23403	.	A	G	18992.0	PASS	AF=0.938517;DP=553;DP4=0,0,264,285;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D614G|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23525	.	C	T	15396.0	PASS	AF=0.927765;DP=443;DP4=0,0,219,222;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H655Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	23599	.	T	G	49314.0	PASS	AF=0.941716;DP=1527;DP4=4,1,769,752;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N679K|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23604	.	C	A	49314.0	PASS	AF=0.933113;DP=1510;DP4=0,1,763,743;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cAt|P681H|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	23854	.	C	A	35654.0	PASS	AF=0.928166;DP=1058;DP4=5,1,527,518;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaC/aaA|N764K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	23948	.	G	T	48560.0	PASS	AF=0.945788;DP=1365;DP4=0,0,683,680;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Tat|D796Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	24424	.	A	T	49314.0	PASS	AF=0.945769;DP=2600;DP4=2,10,1349,1239;SB=17;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caA/caT|Q954H|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	24469	.	T	A	49314.0	PASS	AF=0.937872;DP=3026;DP4=5,1,1532,1478;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaA|N969K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	24966	.	A	G	49314.0	PASS	AF=0.918567;DP=1842;DP4=2,0,910,921;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aGc|N1135S|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	25000	.	C	T	49314.0	PASS	AF=0.929784;DP=1709;DP4=0,0,866,835;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D1146|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	25584	.	C	T	49314.0	PASS	AF=0.885308;DP=2110;DP4=7,8,1108,978;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T64|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
+NC_045512	26060	.	C	T	49314.0	PASS	AF=0.948015;DP=2443;DP4=1,1,1228,1209;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T223I|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
+NC_045512	26270	.	C	T	38261.0	PASS	AF=0.941284;DP=1090;DP4=0,0,541,549;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T9I|75|E|protein_coding|CODING|GU280_gp04|1|T)
+NC_045512	26577	.	C	G	45906.0	PASS	AF=0.943482;DP=1327;DP4=0,1,666,658;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q19E|222|M|protein_coding|CODING|GU280_gp05|1|G)
+NC_045512	26709	.	G	A	49314.0	PASS	AF=0.939802;DP=2525;DP4=0,2,1287,1226;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A63T|222|M|protein_coding|CODING|GU280_gp05|1|A)
+NC_045512	26801	.	C	T	49314.0	PASS	AF=0.939266;DP=2371;DP4=4,3,1150,1206;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L93|222|M|protein_coding|CODING|GU280_gp05|1|T)
+NC_045512	26858	.	C	T	49314.0	PASS	AF=0.946081;DP=2003;DP4=1,2,957,1038;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F112|222|M|protein_coding|CODING|GU280_gp05|1|T)
+NC_045512	27259	.	A	C	49314.0	PASS	AF=0.926424;DP=2827;DP4=10,13,1321,1480;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Agg/Cgg|R20|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
+NC_045512	27382	.	G	C	30546.0	PASS	AF=0.911534;DP=893;DP4=0,0,430,456;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Cat|D61H|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
+NC_045512	27383	.	A	T	30542.0	PASS	AF=0.919226;DP=879;DP4=0,3,426,448;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gTt|D61V|61|ORF6|protein_coding|CODING|GU280_gp06|1|T)
+NC_045512	27384	.	T	C	30931.0	PASS	AF=0.920493;DP=893;DP4=1,1,434,456;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D61|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
+NC_045512	27481	.	C	T	33066.0	PASS	AF=0.937500;DP=960;DP4=2,2,482,470;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L30F|121|ORF7a|protein_coding|CODING|GU280_gp07|1|T)
+NC_045512	27549	.	C	T	49314.0	PASS	AF=0.953926;DP=2496;DP4=0,1,1264,1226;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N52|121|ORF7a|protein_coding|CODING|GU280_gp07|1|T)
+NC_045512	27807	.	C	T	38044.0	PASS	AF=0.943223;DP=1092;DP4=1,0,534,551;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L18|43|ORF7b|protein_coding|CODING|GU280_gp08|1|T)
+NC_045512	28271	.	A	T	49314.0	PASS	AF=0.937521;DP=3025;DP4=3,14,1501,1504;SB=19
+NC_045512	28311	.	C	T	49314.0	PASS	AF=0.864715;DP=3075;DP4=2,18,1526,1516;SB=34;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cTc|P13L|419|N|protein_coding|CODING|GU280_gp10|1|T)
+NC_045512	28361	.	GGAGAACGCA	G	49314.0	PASS	AF=0.792256;DP=2402;DP4=326,206,852,1051;HRUN=2;SB=106;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggagaacgcagt/ggt|GERS30G|419|N|protein_coding|CODING|GU280_gp10|1|G|INFO_REALIGN_3_PRIME)
+NC_045512	28657	.	C	T	44422.0	PASS	AF=0.447055;DP=3277;DP4=879,800,815,768;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D128|419|N|protein_coding|CODING|GU280_gp10|1|T)
+NC_045512	28881	.	G	A	49314.0	PASS	AF=0.943983;DP=1446;DP4=0,0,704,741;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aAg|R203K|419|N|protein_coding|CODING|GU280_gp10|1|A)
+NC_045512	28882	.	G	A	49314.0	PASS	AF=0.919668;DP=1444;DP4=0,2,703,737;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R203|419|N|protein_coding|CODING|GU280_gp10|1|A)
+NC_045512	28883	.	G	C	49314.0	PASS	AF=0.949256;DP=1478;DP4=0,1,721,755;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gga/Cga|G204R|419|N|protein_coding|CODING|GU280_gp10|1|C)
+NC_045512	29510	.	A	C	49314.0	PASS	AF=0.941703;DP=3688;DP4=0,2,1728,1951;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agt/Cgt|S413R|419|N|protein_coding|CODING|GU280_gp10|1|C)
+NC_045512	29733	.	CGAGGCCACGCGGAGTACGATCGAGTG	C	49314.0	PASS	AF=0.987190;DP=1249;DP4=233,253,539,694;HRUN=1;SB=9;INDEL
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/day_47.vcf	Wed May 15 13:37:49 2024 +0000
@@ -0,0 +1,113 @@
+##fileformat=VCFv4.0
+##fileDate=20220830
+##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 20 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.001 --bonf dynamic --no-default-filter --no-default-filter -r NC_045512:1-7475 -o /data/jwd01/main/050/077/50077831/tmp/lofreq2_call_paralleljx9ag7ty/0.vcf.gz reads.bam
+##reference=reference.fa
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth">
+##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
+##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias at this position">
+##INFO=<ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">
+##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position">
+##FILTER=<ID=min_snvqual_67,Description="Minimum SNV Quality (Phred) 67">
+##FILTER=<ID=min_indelqual_53,Description="Minimum Indel Quality (Phred) 53">
+##FILTER=<ID=min_snvqual_75,Description="Minimum SNV Quality (Phred) 75">
+##FILTER=<ID=min_indelqual_60,Description="Minimum Indel Quality (Phred) 60">
+##FILTER=<ID=min_af_0.100000,Description="Minimum allele frequency 0.100000">
+##FILTER=<ID=min_dp_20,Description="Minimum Coverage 20">
+##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000">
+##SnpEffVersion="4.3t (build 2017-11-24 10:18), by Pablo Cingolani"
+##SnpEffCmd="SnpEff  -i vcf -o vcf -formatEff -classic -no-downstream -no-intergenic -no-intron -no-upstream -stats /data/jwd/main/050/078/50078067/outputs/galaxy_dataset_3981ca66-013f-4fe6-8c99-424941590985.dat -csvStats /data/jwd/main/050/078/50078067/outputs/galaxy_dataset_ece32d7c-1cdc-4631-83b6-ceeb0925fd3d.dat SARS-CoV-2 /data/dnb07/galaxy_db/files/9/1/e/dataset_91ea8736-9635-4c9f-9eea-3585f33f19b3.dat "
+##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_Change| Amino_Acid_length | Gene_Name | Transcript_BioType | Gene_Coding | Transcript_ID | Exon_Rank  | Genotype [ | ERRORS | WARNINGS ] )' ">
+##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
+##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+NC_045512	509	.	GGTCATGTTA	G	49314.0	PASS	AF=0.964711;DP=2437;DP4=125,110,1642,709;HRUN=2;SB=63;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggtcatgttatg/gtg|GHVM82V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	670	.	T	G	49314.0	PASS	AF=0.984314;DP=1785;DP4=0,1,862,920;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agT/agG|S135R|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	900	.	C	T	49314.0	PASS	AF=0.989156;DP=5902;DP4=1,1,2941,2956;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S212L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	1980	.	G	T	25695.0	PASS	AF=0.995588;DP=680;DP4=0,1,359,320;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gTa|G572V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	2790	.	C	T	42437.0	PASS	AF=0.991424;DP=1166;DP4=0,0,584,582;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T842I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	3037	.	C	T	49314.0	PASS	AF=0.987794;DP=3277;DP4=0,1,1559,1711;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	4184	.	G	A	47607.0	PASS	AF=0.985981;DP=1284;DP4=1,1,857,425;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G1307S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
+NC_045512	4276	.	C	T	43481.0	PASS	AF=0.988176;DP=1184;DP4=1,2,884,297;SB=7;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y1337|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	4321	.	C	T	19908.0	PASS	AF=0.658863;DP=897;DP4=286,7,297,307;SB=565;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A1352|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	5628	.	C	T	41106.0	PASS	AF=0.990257;DP=1129;DP4=1,1,556,571;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T1788M|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	6354	.	C	T	33710.0	PASS	AF=0.635502;DP=1583;DP4=569,0,650,364;SB=829;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S2030L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	9344	.	C	T	49314.0	PASS	AF=0.993193;DP=1763;DP4=0,0,891,871;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L3027F|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	9424	.	A	G	49314.0	PASS	AF=0.989374;DP=1788;DP4=4,2,952,830;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V3053|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	9534	.	C	T	49314.0	PASS	AF=0.993327;DP=4046;DP4=0,2,1808,2236;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T3090I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	9866	.	C	T	49314.0	PASS	AF=0.987175;DP=3119;DP4=2,2,2060,1054;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L3201F|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	10029	.	C	T	49314.0	PASS	AF=0.971262;DP=2923;DP4=0,1,1186,1734;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T3255I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	10198	.	C	T	49314.0	PASS	AF=0.991991;DP=1748;DP4=0,0,918,829;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D3311|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	10447	.	G	A	45437.0	PASS	AF=0.979658;DP=1229;DP4=1,0,572,654;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R3394|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
+NC_045512	10449	.	C	A	45018.0	PASS	AF=0.980231;DP=1214;DP4=1,1,572,640;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cAc|P3395H|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
+NC_045512	11287	.	GTCTGGTTTT	G	27011.0	PASS	AF=0.990279;DP=823;DP4=62,70,362,453;HRUN=1;SB=1;INDEL;EFF=CODON_DELETION(MODERATE||tctggtttt/|SGF3675|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	12036	.	C	T	49314.0	PASS	AF=0.981526;DP=1678;DP4=1,1,786,887;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A3924V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	12854	.	C	T	45502.0	PASS	AF=0.975923;DP=1246;DP4=0,1,585,660;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P4197S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	12880	.	C	T	45131.0	PASS	AF=0.985950;DP=1210;DP4=0,0,567,643;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I4205|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	14408	.	C	T	49314.0	PASS	AF=0.989749;DP=4585;DP4=1,2,2275,2306;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P4720L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	15451	.	G	A	49314.0	PASS	AF=0.983557;DP=3649;DP4=6,2,2381,1260;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G5068S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|A)
+NC_045512	15714	.	C	T	49314.0	PASS	AF=0.990524;DP=1794;DP4=0,1,896,897;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L5155|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	17410	.	C	T	30355.0	PASS	AF=0.992656;DP=817;DP4=0,1,406,410;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R5721C|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	18163	.	A	G	30799.0	PASS	AF=0.989349;DP=845;DP4=1,1,422,421;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I5972V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G)
+NC_045512	19955	.	C	T	49314.0	PASS	AF=0.990399;DP=1354;DP4=0,0,954,400;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T6569I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	20055	.	A	G	29180.0	PASS	AF=0.943981;DP=839;DP4=39,1,363,435;SB=113;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E6602|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G)
+NC_045512	20719	.	C	T	33653.0	PASS	AF=0.986784;DP=908;DP4=0,0,498,409;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L6824|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	21618	.	C	T	49314.0	PASS	AF=0.994356;DP=3898;DP4=0,2,1788,2108;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T19I|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	21632	.	TTACCCCCTG	T	49314.0	PASS	AF=0.986514;DP=3411;DP4=138,132,1502,1863;HRUN=2;SB=13;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ttaccccctgca/tca|LPPA24S|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	21987	.	G	A	49314.0	PASS	AF=0.984083;DP=3644;DP4=0,0,2146,1497;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G142D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22200	.	T	G	49314.0	PASS	AF=0.985459;DP=1513;DP4=0,0,715,797;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gGg|V213G|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	22578	.	G	A	45997.0	PASS	AF=0.994377;DP=1245;DP4=0,0,624,621;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G339D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22629	.	A	C	42289.0	PASS	AF=0.980508;DP=1180;DP4=1,1,602,572;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aCg|K356T|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22664	.	C	A	39901.0	PASS	AF=0.968326;DP=1105;DP4=0,0,578,505;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cta/Ata|L368I|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22674	.	C	T	41351.0	PASS	AF=0.976440;DP=1146;DP4=0,1,612,533;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S371F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22679	.	T	C	42146.0	PASS	AF=0.981116;DP=1165;DP4=0,0,630,535;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Cca|S373P|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22686	.	C	T	40448.0	PASS	AF=0.978629;DP=1123;DP4=1,4,619,494;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S375F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22688	.	A	G	40481.0	PASS	AF=0.981149;DP=1114;DP4=1,0,619,493;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T376A|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	22716	.	C	T	44859.0	PASS	AF=0.987593;DP=1209;DP4=1,1,668,538;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T385I|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22775	.	G	A	42117.0	PASS	AF=0.714412;DP=2255;DP4=11,624,492,1128;SB=643;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D405N|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22786	.	A	C	49314.0	PASS	AF=0.977541;DP=1692;DP4=0,2,505,1181;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agA/agC|R408S|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22792	.	C	T	49314.0	PASS	AF=0.991515;DP=1650;DP4=1,2,484,1162;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I410|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22813	.	G	T	49314.0	PASS	AF=0.992745;DP=1654;DP4=0,0,483,1171;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaG/aaT|K417N|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22882	.	T	G	884.0	AmpliconRemoval	AF=1.000000;DP=24;DP4=0,0,15,9;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N440K|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	22992	.	G	A	823.0	PASS	AF=1.000000;DP=25;DP4=0,0,12,13;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S477N|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22995	.	C	A	781.0	PASS	AF=1.000000;DP=21;DP4=0,0,10,11;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aAa|T478K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	23013	.	A	C	859.0	PASS	AF=1.000000;DP=23;DP4=0,0,12,11;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gCa|E484A|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	23040	.	A	G	903.0	PASS	AF=1.000000;DP=24;DP4=0,0,14,10;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q493R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23055	.	A	G	973.0	PASS	AF=1.000000;DP=26;DP4=0,0,13,13;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q498R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23063	.	A	T	962.0	PASS	AF=0.961538;DP=26;DP4=0,0,13,13;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Tat|N501Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	23075	.	T	C	1043.0	PASS	AF=1.000000;DP=31;DP4=0,0,16,15;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y505H|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	23403	.	A	G	17428.0	PASS	AF=0.981092;DP=476;DP4=0,0,222,254;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D614G|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23525	.	C	T	16461.0	PASS	AF=0.982063;DP=446;DP4=0,0,242,204;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H655Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	23599	.	T	G	49314.0	PASS	AF=0.988860;DP=3411;DP4=0,0,1979,1432;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N679K|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23604	.	C	A	49314.0	PASS	AF=0.992007;DP=3378;DP4=0,0,1954,1422;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cAt|P681H|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	23854	.	C	A	49314.0	PASS	AF=0.984864;DP=1916;DP4=2,3,933,973;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaC/aaA|N764K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	23948	.	G	T	49314.0	PASS	AF=0.989320;DP=1779;DP4=0,0,955,823;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Tat|D796Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	24424	.	A	T	49314.0	PASS	AF=0.987671;DP=5191;DP4=3,4,2781,2401;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caA/caT|Q954H|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	24469	.	T	A	49314.0	PASS	AF=0.984535;DP=5367;DP4=2,1,2818,2541;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaA|N969K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	24966	.	A	G	49314.0	PASS	AF=0.978797;DP=2028;DP4=3,2,925,1083;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aGc|N1135S|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	25000	.	C	T	49314.0	PASS	AF=0.983463;DP=2056;DP4=0,2,966,1086;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D1146|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	25584	.	C	T	49314.0	PASS	AF=0.983101;DP=3373;DP4=0,3,2086,1284;SB=12;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T64|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
+NC_045512	26060	.	C	T	49314.0	PASS	AF=0.990775;DP=4661;DP4=2,2,2481,2176;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T223I|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
+NC_045512	26195	.	C	T	49314.0	PASS	AF=0.984024;DP=1690;DP4=0,2,825,863;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T268M|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
+NC_045512	26270	.	C	T	49314.0	PASS	AF=0.988365;DP=1633;DP4=0,1,882,749;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T9I|75|E|protein_coding|CODING|GU280_gp04|1|T)
+NC_045512	26577	.	C	G	49314.0	PASS	AF=0.986207;DP=1595;DP4=0,0,726,868;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q19E|222|M|protein_coding|CODING|GU280_gp05|1|G)
+NC_045512	26709	.	G	A	49314.0	PASS	AF=0.987324;DP=4970;DP4=4,2,3093,1869;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A63T|222|M|protein_coding|CODING|GU280_gp05|1|A)
+NC_045512	26801	.	C	T	49314.0	PASS	AF=0.983907;DP=5779;DP4=1,2,3024,2713;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L93|222|M|protein_coding|CODING|GU280_gp05|1|T)
+NC_045512	26858	.	C	T	49314.0	PASS	AF=0.995163;DP=4548;DP4=0,0,1849,2696;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F112|222|M|protein_coding|CODING|GU280_gp05|1|T)
+NC_045512	27259	.	A	C	49314.0	PASS	AF=0.976766;DP=5423;DP4=15,39,1838,3523;SB=4;EFF=SYNONYMOUS_CODING(LOW|SILENT|Agg/Cgg|R20|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
+NC_045512	27382	.	G	C	32997.0	PASS	AF=0.982916;DP=878;DP4=0,0,452,425;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Cat|D61H|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
+NC_045512	27383	.	A	T	33140.0	PASS	AF=0.991926;DP=867;DP4=0,0,448,419;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gTt|D61V|61|ORF6|protein_coding|CODING|GU280_gp06|1|T)
+NC_045512	27384	.	T	C	33260.0	PASS	AF=0.985327;DP=886;DP4=0,0,456,430;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D61|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
+NC_045512	27481	.	C	T	36096.0	PASS	AF=0.977114;DP=1005;DP4=2,1,563,425;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L30F|121|ORF7a|protein_coding|CODING|GU280_gp07|1|T)
+NC_045512	27549	.	C	T	49314.0	PASS	AF=0.990227;DP=4400;DP4=0,1,2333,2063;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N52|121|ORF7a|protein_coding|CODING|GU280_gp07|1|T)
+NC_045512	27807	.	C	T	49314.0	PASS	AF=0.988889;DP=1890;DP4=1,1,975,913;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L18|43|ORF7b|protein_coding|CODING|GU280_gp08|1|T)
+NC_045512	28271	.	A	T	49314.0	PASS	AF=0.991431;DP=8286;DP4=4,4,4119,4155;SB=0
+NC_045512	28311	.	C	T	49314.0	PASS	AF=0.973481;DP=8145;DP4=0,7,3952,4182;SB=17;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cTc|P13L|419|N|protein_coding|CODING|GU280_gp10|1|T)
+NC_045512	28361	.	GGAGAACGCA	G	49314.0	PASS	AF=0.746176;DP=7387;DP4=1654,249,1767,3745;HRUN=2;SB=2147483647;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggagaacgcagt/ggt|GERS30G|419|N|protein_coding|CODING|GU280_gp10|1|G|INFO_REALIGN_3_PRIME)
+NC_045512	28657	.	C	T	49314.0	PASS	AF=0.981710;DP=6889;DP4=0,4,3498,3382;SB=12;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D128|419|N|protein_coding|CODING|GU280_gp10|1|T)
+NC_045512	28881	.	G	A	49314.0	PASS	AF=0.989726;DP=1752;DP4=0,0,868,883;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aAg|R203K|419|N|protein_coding|CODING|GU280_gp10|1|A)
+NC_045512	28882	.	G	A	49314.0	PASS	AF=0.985673;DP=1745;DP4=0,1,863,881;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R203|419|N|protein_coding|CODING|GU280_gp10|1|A)
+NC_045512	28883	.	G	C	49314.0	PASS	AF=0.986947;DP=1762;DP4=0,0,871,890;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gga/Cga|G204R|419|N|protein_coding|CODING|GU280_gp10|1|C)
+NC_045512	29510	.	A	C	49314.0	PASS	AF=0.983741;DP=6827;DP4=2,1,2748,4074;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agt/Cgt|S413R|419|N|protein_coding|CODING|GU280_gp10|1|C)
+NC_045512	29733	.	CGAGGCCACGCGGAGTACGATCGAGTG	C	49314.0	PASS	AF=0.992764;DP=3455;DP4=343,324,779,2651;HRUN=1;SB=468;INDEL
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/day_55.vcf	Wed May 15 13:37:49 2024 +0000
@@ -0,0 +1,116 @@
+##fileformat=VCFv4.0
+##fileDate=20220901
+##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 20 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.001 --bonf dynamic --no-default-filter --no-default-filter -r NC_045512:1-7475 -o /data/jwd/main/050/129/50129874/tmp/lofreq2_call_parallel_4m1yhf9/0.vcf.gz reads.bam
+##reference=reference.fa
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth">
+##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
+##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias at this position">
+##INFO=<ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">
+##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position">
+##FILTER=<ID=min_snvqual_69,Description="Minimum SNV Quality (Phred) 69">
+##FILTER=<ID=min_indelqual_54,Description="Minimum Indel Quality (Phred) 54">
+##FILTER=<ID=min_snvqual_76,Description="Minimum SNV Quality (Phred) 76">
+##FILTER=<ID=min_indelqual_62,Description="Minimum Indel Quality (Phred) 62">
+##FILTER=<ID=min_af_0.100000,Description="Minimum allele frequency 0.100000">
+##FILTER=<ID=min_dp_20,Description="Minimum Coverage 20">
+##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000">
+##SnpEffVersion="4.3t (build 2017-11-24 10:18), by Pablo Cingolani"
+##SnpEffCmd="SnpEff  -i vcf -o vcf -formatEff -classic -no-downstream -no-intergenic -no-intron -no-upstream -stats /data/jwd01/main/050/130/50130117/outputs/galaxy_dataset_54d75f13-335c-4bee-9f56-a8cc78951a0e.dat -csvStats /data/jwd01/main/050/130/50130117/outputs/galaxy_dataset_a4477757-f597-48ad-a763-e3d57c7946ec.dat SARS-CoV-2 /data/dnb06/galaxy_db/files/a/9/a/dataset_a9aee115-dacc-4ec4-a915-a667c1f8b549.dat "
+##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_Change| Amino_Acid_length | Gene_Name | Transcript_BioType | Gene_Coding | Transcript_ID | Exon_Rank  | Genotype [ | ERRORS | WARNINGS ] )' ">
+##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
+##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+NC_045512	241	.	C	T	2150.0	PASS	AF=0.983607;DP=61;DP4=0,0,30,31;SB=0
+NC_045512	509	.	GGTCATGTTA	G	49314.0	PASS	AF=0.990594;DP=2339;DP4=136,167,1257,1060;HRUN=2;SB=26;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggtcatgttatg/gtg|GHVM82V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	670	.	T	G	49314.0	PASS	AF=0.977359;DP=2915;DP4=0,0,1471,1444;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agT/agG|S135R|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	900	.	C	T	49314.0	PASS	AF=0.982265;DP=6428;DP4=27,23,3221,3157;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S212L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	1980	.	G	T	34404.0	PASS	AF=0.983871;DP=930;DP4=0,0,458,468;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gTa|G572V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	2790	.	C	T	49314.0	PASS	AF=0.982153;DP=1793;DP4=0,0,892,897;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T842I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	3037	.	C	T	49314.0	PASS	AF=0.981051;DP=4433;DP4=0,0,2205,2220;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	4184	.	G	A	49314.0	PASS	AF=0.988202;DP=2119;DP4=3,2,1183,931;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G1307S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
+NC_045512	4276	.	C	T	49314.0	PASS	AF=0.981818;DP=1980;DP4=1,1,1403,575;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y1337|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	4321	.	C	T	40010.0	PASS	AF=0.657609;DP=1840;DP4=596,8,635,599;SB=1173;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A1352|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	5628	.	C	T	49314.0	PASS	AF=0.966059;DP=1974;DP4=22,20,938,994;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T1788M|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	6354	.	C	T	30043.0	PASS	AF=0.541788;DP=1711;DP4=774,1,530,406;SB=1263;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S2030L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	8109	.	C	T	49314.0	PASS	AF=0.968127;DP=2008;DP4=19,16,1017,956;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T2615I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	9344	.	C	T	49314.0	PASS	AF=0.988103;DP=3194;DP4=1,0,1583,1609;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L3027F|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	9424	.	A	G	49314.0	PASS	AF=0.976721;DP=3050;DP4=1,1,1520,1528;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V3053|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	9534	.	C	T	49314.0	PASS	AF=0.987535;DP=5054;DP4=0,0,2472,2582;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T3090I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	9866	.	C	T	49314.0	PASS	AF=0.980011;DP=3652;DP4=5,6,1966,1674;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L3201F|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	10029	.	C	T	49314.0	PASS	AF=0.957557;DP=4241;DP4=1,1,2025,2212;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T3255I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	10198	.	C	T	49314.0	PASS	AF=0.984712;DP=2878;DP4=1,1,1450,1423;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D3311|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	10447	.	G	A	49314.0	PASS	AF=0.981521;DP=1894;DP4=1,1,920,971;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R3394|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
+NC_045512	10449	.	C	A	49314.0	PASS	AF=0.981142;DP=1909;DP4=0,3,934,971;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cAc|P3395H|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
+NC_045512	11287	.	GTCTGGTTTT	G	44284.0	PASS	AF=0.994074;DP=1350;DP4=118,131,668,674;HRUN=1;SB=3;INDEL;EFF=CODON_DELETION(MODERATE||tctggtttt/|SGF3675|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	12036	.	C	T	49314.0	PASS	AF=0.977939;DP=3037;DP4=1,0,1500,1533;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A3924V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	12854	.	C	T	49314.0	PASS	AF=0.978914;DP=1897;DP4=1,0,953,942;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P4197S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	12880	.	C	T	49314.0	PASS	AF=0.984450;DP=1865;DP4=1,1,927,936;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I4205|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	14408	.	C	T	49314.0	PASS	AF=0.987194;DP=5232;DP4=2,3,2604,2622;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P4720L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	15451	.	G	A	49314.0	PASS	AF=0.973996;DP=3884;DP4=4,4,2076,1798;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G5068S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|A)
+NC_045512	15714	.	C	T	49314.0	PASS	AF=0.982387;DP=2555;DP4=0,1,1249,1301;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L5155|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	17410	.	C	T	49314.0	PASS	AF=0.983071;DP=1713;DP4=0,0,872,838;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R5721C|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	18163	.	A	G	49314.0	PASS	AF=0.981366;DP=1771;DP4=0,0,876,895;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I5972V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G)
+NC_045512	19955	.	C	T	49314.0	PASS	AF=0.983919;DP=5410;DP4=0,0,2706,2704;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T6569I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	20055	.	A	G	49314.0	PASS	AF=0.878327;DP=1578;DP4=168,1,696,713;SB=454;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E6602|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G)
+NC_045512	20719	.	C	T	49314.0	PASS	AF=0.983268;DP=1793;DP4=1,1,931,860;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L6824|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	21618	.	C	T	49314.0	PASS	AF=0.992293;DP=4282;DP4=2,3,2045,2232;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T19I|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	21632	.	TTACCCCCTG	T	49314.0	PASS	AF=0.971920;DP=3490;DP4=211,224,1595,1797;HRUN=2;SB=2;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ttaccccctgca/tca|LPPA24S|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	21987	.	G	A	49314.0	PASS	AF=0.976943;DP=3860;DP4=1,0,2009,1848;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G142D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22200	.	T	G	49314.0	PASS	AF=0.978495;DP=2232;DP4=2,3,1064,1163;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gGg|V213G|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	22578	.	G	A	49314.0	PASS	AF=0.976501;DP=3830;DP4=2,1,1895,1932;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G339D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22629	.	A	C	49314.0	PASS	AF=0.980153;DP=3527;DP4=0,0,1757,1763;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aCg|K356T|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22664	.	C	A	49314.0	PASS	AF=0.977541;DP=3384;DP4=5,4,1661,1711;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cta/Ata|L368I|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22674	.	C	T	49314.0	PASS	AF=0.974561;DP=3420;DP4=0,1,1667,1752;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S371F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22679	.	T	C	49314.0	PASS	AF=0.976274;DP=3414;DP4=2,5,1668,1739;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Cca|S373P|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22686	.	C	T	49314.0	PASS	AF=0.976059;DP=3258;DP4=4,5,1593,1651;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S375F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22688	.	A	G	49314.0	PASS	AF=0.977301;DP=3216;DP4=5,4,1586,1618;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T376A|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	22716	.	C	T	49314.0	PASS	AF=0.985468;DP=3303;DP4=0,1,1676,1625;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T385I|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22775	.	G	A	49314.0	PASS	AF=0.853479;DP=8579;DP4=496,663,3330,4089;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D405N|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22786	.	A	C	49314.0	PASS	AF=0.965444;DP=7524;DP4=19,20,3305,4170;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agA/agC|R408S|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22792	.	C	T	49314.0	PASS	AF=0.983602;DP=7501;DP4=2,1,3333,4164;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I410|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22813	.	G	T	49314.0	PASS	AF=0.986985;DP=7914;DP4=0,0,3588,4319;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaG/aaT|K417N|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22882	.	T	G	49314.0	PASS	AF=0.976932;DP=5072;DP4=4,8,2639,2420;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N440K|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	22992	.	G	A	49314.0	PASS	AF=0.983352;DP=4385;DP4=2,3,2107,2272;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S477N|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22995	.	C	A	49314.0	PASS	AF=0.985318;DP=4359;DP4=1,0,2105,2251;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aAa|T478K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	23013	.	A	C	49314.0	PASS	AF=0.971480;DP=4453;DP4=17,16,2118,2294;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gCa|E484A|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	23040	.	A	G	49314.0	PASS	AF=0.986637;DP=4490;DP4=0,2,2153,2335;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q493R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23055	.	A	G	49314.0	PASS	AF=0.983106;DP=4262;DP4=1,1,2069,2191;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q498R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23063	.	A	T	49314.0	PASS	AF=0.992556;DP=4030;DP4=0,0,1975,2053;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Tat|N501Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	23075	.	T	C	49314.0	PASS	AF=0.975079;DP=4093;DP4=2,2,2038,2047;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y505H|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	23403	.	A	G	32080.0	PASS	AF=0.981756;DP=877;DP4=0,0,411,466;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D614G|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23525	.	C	T	31898.0	PASS	AF=0.982916;DP=878;DP4=1,0,442,434;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H655Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	23599	.	T	G	49314.0	PASS	AF=0.984131;DP=3970;DP4=1,1,2073,1895;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N679K|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23604	.	C	A	49314.0	PASS	AF=0.984480;DP=3866;DP4=0,1,2017,1845;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cAt|P681H|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	23854	.	C	A	49314.0	PASS	AF=0.975383;DP=3006;DP4=5,5,1472,1519;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaC/aaA|N764K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	23948	.	G	T	49314.0	PASS	AF=0.978654;DP=3045;DP4=0,0,1551,1490;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Tat|D796Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	24424	.	A	T	49314.0	PASS	AF=0.984966;DP=6585;DP4=3,3,3360,3219;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caA/caT|Q954H|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	24469	.	T	A	49314.0	PASS	AF=0.981200;DP=7181;DP4=0,0,3618,3562;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaA|N969K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	24966	.	A	G	49314.0	PASS	AF=0.969872;DP=3983;DP4=3,5,1951,2000;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aGc|N1135S|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	25000	.	C	T	49314.0	PASS	AF=0.982474;DP=3937;DP4=0,2,1940,1995;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D1146|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	25584	.	C	T	49314.0	PASS	AF=0.969027;DP=4972;DP4=2,2,2628,2338;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T64|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
+NC_045512	26060	.	C	T	49314.0	PASS	AF=0.984340;DP=4917;DP4=3,3,2409,2502;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T223I|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
+NC_045512	26195	.	C	T	49314.0	PASS	AF=0.978567;DP=1773;DP4=1,1,889,882;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T268M|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
+NC_045512	26270	.	C	T	49314.0	PASS	AF=0.986331;DP=1829;DP4=1,0,942,885;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T9I|75|E|protein_coding|CODING|GU280_gp04|1|T)
+NC_045512	26571	.	C	T	19089.0	PASS	AF=0.257871;DP=2668;DP4=957,1013,332,366;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L17F|222|M|protein_coding|CODING|GU280_gp05|1|T)
+NC_045512	26577	.	C	G	49314.0	PASS	AF=0.972893;DP=2693;DP4=0,0,1280,1374;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q19E|222|M|protein_coding|CODING|GU280_gp05|1|G)
+NC_045512	26709	.	G	A	49314.0	PASS	AF=0.977913;DP=5433;DP4=4,3,2855,2569;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A63T|222|M|protein_coding|CODING|GU280_gp05|1|A)
+NC_045512	26801	.	C	T	49314.0	PASS	AF=0.983187;DP=5829;DP4=1,0,2894,2931;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L93|222|M|protein_coding|CODING|GU280_gp05|1|T)
+NC_045512	26858	.	C	T	49314.0	PASS	AF=0.989801;DP=5687;DP4=3,3,2686,2994;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F112|222|M|protein_coding|CODING|GU280_gp05|1|T)
+NC_045512	27259	.	A	C	49314.0	PASS	AF=0.973431;DP=5721;DP4=14,21,2604,3071;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|Agg/Cgg|R20|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
+NC_045512	27382	.	G	C	49314.0	PASS	AF=0.987069;DP=1624;DP4=0,0,798,826;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Cat|D61H|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
+NC_045512	27383	.	A	T	49314.0	PASS	AF=0.974439;DP=1604;DP4=0,0,788,816;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gTt|D61V|61|ORF6|protein_coding|CODING|GU280_gp06|1|T)
+NC_045512	27384	.	T	C	49314.0	PASS	AF=0.985339;DP=1637;DP4=2,0,807,828;SB=6;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D61|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
+NC_045512	27481	.	C	T	49314.0	PASS	AF=0.984321;DP=1722;DP4=0,0,863,858;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L30F|121|ORF7a|protein_coding|CODING|GU280_gp07|1|T)
+NC_045512	27549	.	C	T	49314.0	PASS	AF=0.986065;DP=4234;DP4=1,0,2141,2076;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N52|121|ORF7a|protein_coding|CODING|GU280_gp07|1|T)
+NC_045512	27807	.	C	T	49314.0	PASS	AF=0.985981;DP=2354;DP4=1,1,1167,1184;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L18|43|ORF7b|protein_coding|CODING|GU280_gp08|1|T)
+NC_045512	28271	.	A	T	49314.0	PASS	AF=0.985745;DP=7857;DP4=8,11,3861,3975;SB=1
+NC_045512	28311	.	C	T	49314.0	PASS	AF=0.957243;DP=7297;DP4=7,4,3570,3710;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cTc|P13L|419|N|protein_coding|CODING|GU280_gp10|1|T)
+NC_045512	28361	.	GGAGAACGCA	G	49314.0	PASS	AF=0.830892;DP=6280;DP4=717,401,2253,2965;HRUN=2;SB=365;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggagaacgcagt/ggt|GERS30G|419|N|protein_coding|CODING|GU280_gp10|1|G|INFO_REALIGN_3_PRIME)
+NC_045512	28657	.	C	T	49314.0	PASS	AF=0.975592;DP=5531;DP4=3,2,2828,2694;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D128|419|N|protein_coding|CODING|GU280_gp10|1|T)
+NC_045512	28881	.	G	A	49314.0	PASS	AF=0.977910;DP=2354;DP4=0,0,1161,1193;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aAg|R203K|419|N|protein_coding|CODING|GU280_gp10|1|A)
+NC_045512	28882	.	G	A	49314.0	PASS	AF=0.978916;DP=2324;DP4=0,2,1147,1175;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R203|419|N|protein_coding|CODING|GU280_gp10|1|A)
+NC_045512	28883	.	G	C	49314.0	PASS	AF=0.981528;DP=2382;DP4=0,0,1174,1207;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gga/Cga|G204R|419|N|protein_coding|CODING|GU280_gp10|1|C)
+NC_045512	29510	.	A	C	49314.0	PASS	AF=0.977301;DP=7181;DP4=2,2,3340,3833;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agt/Cgt|S413R|419|N|protein_coding|CODING|GU280_gp10|1|C)
+NC_045512	29733	.	CGAGGCCACGCGGAGTACGATCGAGTG	C	49314.0	PASS	AF=0.991870;DP=2091;DP4=516,513,868,1206;HRUN=1;SB=48;INDEL
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/day_60.vcf	Wed May 15 13:37:49 2024 +0000
@@ -0,0 +1,126 @@
+##fileformat=VCFv4.0
+##fileDate=20220906
+##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 20 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.001 --bonf dynamic --no-default-filter --no-default-filter -r NC_045512:1-7475 -o /data/jwd01/main/050/269/50269464/tmp/lofreq2_call_parallel15a3xw5c/0.vcf.gz reads.bam
+##reference=reference.fa
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth">
+##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
+##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias at this position">
+##INFO=<ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">
+##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position">
+##FILTER=<ID=min_snvqual_66,Description="Minimum SNV Quality (Phred) 66">
+##FILTER=<ID=min_indelqual_50,Description="Minimum Indel Quality (Phred) 50">
+##FILTER=<ID=min_snvqual_74,Description="Minimum SNV Quality (Phred) 74">
+##FILTER=<ID=min_indelqual_58,Description="Minimum Indel Quality (Phred) 58">
+##FILTER=<ID=min_af_0.100000,Description="Minimum allele frequency 0.100000">
+##FILTER=<ID=min_dp_20,Description="Minimum Coverage 20">
+##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000">
+##SnpEffVersion="4.3t (build 2017-11-24 10:18), by Pablo Cingolani"
+##SnpEffCmd="SnpEff  -i vcf -o vcf -formatEff -classic -no-downstream -no-intergenic -no-intron -no-upstream -stats /data/jwd01/main/050/269/50269699/outputs/galaxy_dataset_4f76b3c9-c65b-440c-b6eb-7c0658803d91.dat -csvStats /data/jwd01/main/050/269/50269699/outputs/galaxy_dataset_80517e55-786a-45d8-bef0-754a8780e1a9.dat SARS-CoV-2 /data/dnb06/galaxy_db/files/9/4/9/dataset_94943b16-6476-4636-83c0-5f7d8cfc524c.dat "
+##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_Change| Amino_Acid_length | Gene_Name | Transcript_BioType | Gene_Coding | Transcript_ID | Exon_Rank  | Genotype [ | ERRORS | WARNINGS ] )' ">
+##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
+##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+NC_045512	59	.	C	A	1760.0	PASS	AF=0.854545;DP=55;DP4=0,0,37,18;SB=0
+NC_045512	509	.	GGTCATGTTA	G	49314.0	PASS	AF=0.978667;DP=1875;DP4=75,82,1053,782;HRUN=2;SB=16;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggtcatgttatg/gtg|GHVM82V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	670	.	T	G	42432.0	PASS	AF=0.920869;DP=1289;DP4=0,2,647,637;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agT/agG|S135R|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	900	.	C	T	49314.0	PASS	AF=0.941725;DP=2145;DP4=0,1,1107,1034;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S212L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	1821	.	G	A	1189.0	PASS	AF=0.125604;DP=414;DP4=159,197,31,27;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G519D|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
+NC_045512	1980	.	G	T	8919.0	PASS	AF=0.895522;DP=268;DP4=0,0,134,134;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gTa|G572V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	2790	.	C	T	19472.0	PASS	AF=0.935201;DP=571;DP4=1,1,278,288;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T842I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	3037	.	C	T	28976.0	PASS	AF=0.941805;DP=842;DP4=1,1,419,418;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	4184	.	G	A	9009.0	PASS	AF=0.907407;DP=270;DP4=0,0,167,103;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G1307S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
+NC_045512	4276	.	C	T	14849.0	PASS	AF=0.911565;DP=441;DP4=3,3,290,145;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y1337|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	4321	.	C	T	12472.0	PASS	AF=0.790068;DP=443;DP4=63,0,197,182;SB=159;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A1352|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	5628	.	C	T	17261.0	PASS	AF=0.911488;DP=531;DP4=2,1,237,289;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T1788M|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	6048	.	T	C	1355.0	PASS	AF=0.155425;DP=341;DP4=141,141,30,29;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTt/tCt|F1928S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|C)
+NC_045512	6083	.	G	T	751.0	PASS	AF=0.110000;DP=300;DP4=143,118,19,18;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Tat|D1940Y|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	6354	.	C	T	8316.0	PASS	AF=0.771987;DP=307;DP4=48,0,157,100;SB=89;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S2030L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	7246	.	G	GT	2323.0	PASS	AF=0.105200;DP=827;DP4=349,424,45,42;HRUN=5;SB=5;INDEL;EFF=FRAME_SHIFT(HIGH||ttg/ttTg|L2329F?|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|GT|INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|1|1.00)
+NC_045512	8109	.	C	T	22999.0	PASS	AF=0.936937;DP=666;DP4=1,2,345,316;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T2615I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	8537	.	A	G	1413.0	PASS	AF=0.117647;DP=493;DP4=216,213,25,36;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I2758V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	9344	.	C	T	46680.0	PASS	AF=0.949165;DP=1318;DP4=0,0,682,633;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L3027F|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	9424	.	A	G	42834.0	PASS	AF=0.944844;DP=1251;DP4=0,1,635,614;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V3053|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	9534	.	C	T	49314.0	PASS	AF=0.940808;DP=2078;DP4=0,1,941,1132;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T3090I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	9866	.	C	T	29696.0	PASS	AF=0.889010;DP=919;DP4=23,13,543,339;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L3201F|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	10029	.	C	T	49314.0	PASS	AF=0.815325;DP=1814;DP4=0,9,851,950;SB=23;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T3255I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	10198	.	C	T	38164.0	PASS	AF=0.823036;DP=1311;DP4=65,61,619,561;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D3311|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	10447	.	G	A	22164.0	PASS	AF=0.884164;DP=682;DP4=1,0,330,347;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R3394|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
+NC_045512	10449	.	C	A	21817.0	PASS	AF=0.863836;DP=683;DP4=0,7,336,337;SB=18;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cAc|P3395H|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
+NC_045512	10687	.	TG	T	2233.0	PASS	AF=0.103405;DP=793;DP4=408,325,48,34;HRUN=1;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||gtt/|V3475|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T);LOF=(ORF1ab|GU280_gp01|1|1.00)
+NC_045512	11287	.	GTCTGGTTTT	G	5267.0	PASS	AF=0.988764;DP=178;DP4=11,9,86,90;HRUN=1;SB=1;INDEL;EFF=CODON_DELETION(MODERATE||tctggtttt/|SGF3675|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	12036	.	C	T	33687.0	PASS	AF=0.897411;DP=1043;DP4=0,0,506,531;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A3924V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	12854	.	C	T	17843.0	PASS	AF=0.868231;DP=554;DP4=0,0,297,257;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P4197S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	12880	.	C	T	20579.0	PASS	AF=0.948542;DP=583;DP4=0,0,295,286;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I4205|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	14408	.	C	T	49314.0	PASS	AF=0.941292;DP=1533;DP4=1,0,668,860;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P4720L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	15451	.	G	A	28015.0	PASS	AF=0.827736;DP=923;DP4=1,1,546,368;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G5068S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|A)
+NC_045512	15714	.	C	T	37696.0	PASS	AF=0.953774;DP=1060;DP4=0,0,510,545;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L5155|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	17137	.	T	C	3063.0	PASS	AF=0.134361;DP=908;DP4=402,366,77,56;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tct/Cct|S5630P|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|C)
+NC_045512	17410	.	C	T	10881.0	PASS	AF=0.893939;DP=330;DP4=0,0,164,163;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R5721C|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	18163	.	A	G	13707.0	PASS	AF=0.927536;DP=414;DP4=0,0,208,205;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I5972V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G)
+NC_045512	18778	.	TGGG	T	3602.0	PASS	AF=0.123062;DP=1032;DP4=415,495,56,71;HRUN=4;SB=1;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||tggggt/tgt|WG6177C|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T|INFO_REALIGN_3_PRIME)
+NC_045512	19955	.	C	T	36425.0	PASS	AF=0.943961;DP=1035;DP4=0,0,521,511;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T6569I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	20055	.	A	G	9643.0	PASS	AF=0.897611;DP=293;DP4=14,0,127,151;SB=45;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E6602|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G)
+NC_045512	20719	.	C	T	5731.0	PASS	AF=0.906977;DP=172;DP4=0,0,108,62;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L6824|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	21618	.	C	T	32230.0	PASS	AF=0.917204;DP=930;DP4=0,0,436,488;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T19I|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	21632	.	TTACCCCCTG	T	30504.0	PASS	AF=0.992299;DP=909;DP4=26,13,413,489;HRUN=2;SB=18;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ttaccccctgca/tca|LPPA24S|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	21987	.	G	A	15467.0	PASS	AF=0.794340;DP=530;DP4=3,0,280,244;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G142D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22200	.	T	G	7938.0	PASS	AF=0.908333;DP=240;DP4=0,0,96,142;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gGg|V213G|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	22578	.	G	A	27298.0	PASS	AF=0.891892;DP=851;DP4=0,0,414,434;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G339D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22629	.	A	C	24933.0	PASS	AF=0.903567;DP=757;DP4=1,0,356,400;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aCg|K356T|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22664	.	C	A	24562.0	PASS	AF=0.917695;DP=729;DP4=1,2,307,414;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cta/Ata|L368I|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22674	.	C	T	21334.0	PASS	AF=0.846705;DP=698;DP4=0,4,285,408;SB=8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S371F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22679	.	T	C	22897.0	PASS	AF=0.938346;DP=665;DP4=0,0,267,397;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Cca|S373P|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22686	.	C	T	19116.0	PASS	AF=0.869984;DP=623;DP4=0,2,262,358;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S375F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22688	.	A	G	19590.0	PASS	AF=0.901695;DP=590;DP4=0,0,249,340;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T376A|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	22716	.	C	T	16916.0	PASS	AF=0.941788;DP=481;DP4=1,1,224,254;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T385I|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22775	.	G	A	27898.0	PASS	AF=0.691026;DP=1560;DP4=186,237,577,559;SB=17;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D405N|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22786	.	A	C	45143.0	PASS	AF=0.890287;DP=1431;DP4=0,1,760,664;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agA/agC|R408S|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22792	.	C	T	49314.0	PASS	AF=0.931681;DP=1493;DP4=0,1,805,681;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I410|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22813	.	G	T	49314.0	PASS	AF=0.910685;DP=1825;DP4=0,1,1008,810;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaG/aaT|K417N|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22882	.	T	G	49314.0	PASS	AF=0.899664;DP=1784;DP4=2,2,1005,768;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N440K|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	22992	.	G	A	49314.0	PASS	AF=0.931250;DP=1760;DP4=1,1,767,986;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S477N|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22995	.	C	A	49314.0	PASS	AF=0.953356;DP=1758;DP4=0,0,771,985;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aAa|T478K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	23013	.	A	C	49314.0	PASS	AF=0.907710;DP=1712;DP4=5,3,734,967;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gCa|E484A|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	23040	.	A	G	49314.0	PASS	AF=0.895874;DP=1527;DP4=0,4,663,859;SB=8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q493R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23055	.	A	G	44772.0	PASS	AF=0.903039;DP=1382;DP4=2,1,608,770;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q498R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23063	.	A	T	47115.0	PASS	AF=0.939597;DP=1341;DP4=0,3,617,719;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Tat|N501Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	23075	.	T	C	41610.0	PASS	AF=0.911007;DP=1281;DP4=1,0,619,660;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y505H|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	23403	.	A	G	8353.0	PASS	AF=0.939516;DP=248;DP4=1,0,116,131;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D614G|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23525	.	C	T	7115.0	PASS	AF=0.871560;DP=218;DP4=0,1,102,113;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H655Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	23599	.	T	G	22781.0	PASS	AF=0.932229;DP=664;DP4=0,0,346,315;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N679K|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23604	.	C	A	22524.0	PASS	AF=0.925982;DP=662;DP4=1,1,345,313;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cAt|P681H|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	23854	.	C	A	11753.0	PASS	AF=0.933333;DP=345;DP4=0,3,173,169;SB=9;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaC/aaA|N764K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	23948	.	G	T	14977.0	PASS	AF=0.911364;DP=440;DP4=0,1,226,210;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Tat|D796Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	24318	.	A	ACC	556.0	PASS	AF=0.107356;DP=503;DP4=226,224,27,27;HRUN=2;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||caa/cCCaa|Q920P?|1273|S|protein_coding|CODING|GU280_gp02|1|ACC|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00)
+NC_045512	24320	.	CAAA	C	548.0	PASS	AF=0.108652;DP=497;DP4=237,225,27,27;HRUN=5;SB=0;INDEL;EFF=CODON_DELETION(MODERATE||aaa/|K921|1273|S|protein_coding|CODING|GU280_gp02|1|C|INFO_REALIGN_3_PRIME)
+NC_045512	24424	.	A	T	49314.0	PASS	AF=0.909987;DP=1522;DP4=0,5,853,661;SB=17;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caA/caT|Q954H|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	24469	.	T	A	49314.0	PASS	AF=0.922658;DP=1836;DP4=2,1,1000,830;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaA|N969K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	24951	.	TAG	T	3457.0	PASS	AF=0.100924;DP=1298;DP4=509,678,57,74;HRUN=1;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||atagga/|IG1130|1273|S|protein_coding|CODING|GU280_gp02|1|T);LOF=(S|GU280_gp02|1|1.00)
+NC_045512	24966	.	A	G	41334.0	PASS	AF=0.887944;DP=1294;DP4=1,1,548,722;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aGc|N1135S|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	25000	.	C	T	39557.0	PASS	AF=0.924282;DP=1149;DP4=0,0,560,586;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D1146|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	25584	.	C	T	49314.0	PASS	AF=0.816110;DP=1887;DP4=42,43,1024,772;SB=7;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T64|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
+NC_045512	26060	.	C	T	34411.0	PASS	AF=0.949640;DP=973;DP4=0,0,464,508;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T223I|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
+NC_045512	26195	.	C	T	9159.0	PASS	AF=0.878893;DP=289;DP4=0,0,148,140;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T268M|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
+NC_045512	26270	.	C	T	12517.0	PASS	AF=0.917808;DP=365;DP4=1,0,193,170;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T9I|75|E|protein_coding|CODING|GU280_gp04|1|T)
+NC_045512	26577	.	C	G	29585.0	PASS	AF=0.898210;DP=894;DP4=0,0,456,435;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q19E|222|M|protein_coding|CODING|GU280_gp05|1|G)
+NC_045512	26709	.	G	A	49314.0	PASS	AF=0.924149;DP=1938;DP4=2,0,982,939;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A63T|222|M|protein_coding|CODING|GU280_gp05|1|A)
+NC_045512	26801	.	C	T	49314.0	PASS	AF=0.889426;DP=1863;DP4=1,0,935,918;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L93|222|M|protein_coding|CODING|GU280_gp05|1|T)
+NC_045512	26858	.	C	T	39423.0	PASS	AF=0.890110;DP=1183;DP4=1,2,564,608;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F112|222|M|protein_coding|CODING|GU280_gp05|1|T)
+NC_045512	27259	.	A	C	49314.0	PASS	AF=0.901362;DP=2129;DP4=1,2,859,1262;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Agg/Cgg|R20|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
+NC_045512	27382	.	G	C	18534.0	PASS	AF=0.875886;DP=564;DP4=0,1,279,281;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Cat|D61H|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
+NC_045512	27383	.	A	T	18084.0	PASS	AF=0.860465;DP=559;DP4=1,1,278,278;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gTt|D61V|61|ORF6|protein_coding|CODING|GU280_gp06|1|T)
+NC_045512	27384	.	T	C	19016.0	PASS	AF=0.900709;DP=564;DP4=4,0,277,281;SB=9;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D61|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
+NC_045512	27481	.	C	T	23583.0	PASS	AF=0.956845;DP=672;DP4=2,0,317,353;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L30F|121|ORF7a|protein_coding|CODING|GU280_gp07|1|T)
+NC_045512	27549	.	C	T	49314.0	PASS	AF=0.888954;DP=1720;DP4=0,2,914,791;SB=6;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N52|121|ORF7a|protein_coding|CODING|GU280_gp07|1|T)
+NC_045512	27807	.	C	T	31266.0	PASS	AF=0.941694;DP=909;DP4=2,1,457,448;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L18|43|ORF7b|protein_coding|CODING|GU280_gp08|1|T)
+NC_045512	28271	.	A	T	49314.0	PASS	AF=0.856293;DP=2185;DP4=3,14,1036,1059;SB=19
+NC_045512	28311	.	C	T	49314.0	PASS	AF=0.795816;DP=2581;DP4=60,65,1233,1220;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cTc|P13L|419|N|protein_coding|CODING|GU280_gp10|1|T)
+NC_045512	28361	.	GGAGAACGCA	G	48884.0	PASS	AF=0.710514;DP=2197;DP4=425,228,710,851;HRUN=2;SB=164;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggagaacgcagt/ggt|GERS30G|419|N|protein_coding|CODING|GU280_gp10|1|G|INFO_REALIGN_3_PRIME)
+NC_045512	28657	.	C	T	49314.0	PASS	AF=0.856894;DP=3445;DP4=30,41,1789,1544;SB=11;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D128|419|N|protein_coding|CODING|GU280_gp10|1|T)
+NC_045512	28881	.	G	A	49314.0	PASS	AF=0.936155;DP=1441;DP4=0,1,675,763;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aAg|R203K|419|N|protein_coding|CODING|GU280_gp10|1|A)
+NC_045512	28882	.	G	A	47438.0	PASS	AF=0.895543;DP=1436;DP4=0,1,669,749;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R203|419|N|protein_coding|CODING|GU280_gp10|1|A)
+NC_045512	28883	.	G	C	48607.0	PASS	AF=0.905024;DP=1453;DP4=0,0,674,774;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gga/Cga|G204R|419|N|protein_coding|CODING|GU280_gp10|1|C)
+NC_045512	29510	.	A	C	49314.0	PASS	AF=0.913119;DP=4017;DP4=2,5,1794,2208;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agt/Cgt|S413R|419|N|protein_coding|CODING|GU280_gp10|1|C)
+NC_045512	29733	.	CGAGGCCACGCGGAGTACGATCGAGTG	C	49314.0	PASS	AF=0.991364;DP=2200;DP4=197,163,758,1423;HRUN=1;SB=119;INDEL
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/day_76.vcf	Wed May 15 13:37:49 2024 +0000
@@ -0,0 +1,119 @@
+##fileformat=VCFv4.0
+##fileDate=20220901
+##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 20 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.001 --bonf dynamic --no-default-filter --no-default-filter -r NC_045512:1-7475 -o /data/jwd/main/050/129/50129877/tmp/lofreq2_call_parallelyczniu8l/0.vcf.gz reads.bam
+##reference=reference.fa
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth">
+##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
+##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias at this position">
+##INFO=<ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">
+##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position">
+##FILTER=<ID=min_snvqual_67,Description="Minimum SNV Quality (Phred) 67">
+##FILTER=<ID=min_indelqual_51,Description="Minimum Indel Quality (Phred) 51">
+##FILTER=<ID=min_snvqual_75,Description="Minimum SNV Quality (Phred) 75">
+##FILTER=<ID=min_indelqual_60,Description="Minimum Indel Quality (Phred) 60">
+##FILTER=<ID=min_af_0.100000,Description="Minimum allele frequency 0.100000">
+##FILTER=<ID=min_dp_20,Description="Minimum Coverage 20">
+##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000">
+##SnpEffVersion="4.3t (build 2017-11-24 10:18), by Pablo Cingolani"
+##SnpEffCmd="SnpEff  -i vcf -o vcf -formatEff -classic -no-downstream -no-intergenic -no-intron -no-upstream -stats /data/jwd/main/050/130/50130120/outputs/galaxy_dataset_edd6311e-29d6-44ea-9c53-1de8b934c9f0.dat -csvStats /data/jwd/main/050/130/50130120/outputs/galaxy_dataset_bd832d92-3d90-4ea9-b282-63f08d89a4f1.dat SARS-CoV-2 /data/dnb07/galaxy_db/files/d/7/9/dataset_d7970cc4-d845-4970-858e-02f7ba5eadd1.dat "
+##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_Change| Amino_Acid_length | Gene_Name | Transcript_BioType | Gene_Coding | Transcript_ID | Exon_Rank  | Genotype [ | ERRORS | WARNINGS ] )' ">
+##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
+##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+NC_045512	509	.	GGTCATGTTA	G	42184.0	PASS	AF=0.982707;DP=1330;DP4=85,104,722,585;HRUN=2;SB=20;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggtcatgttatg/gtg|GHVM82V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	670	.	T	G	49290.0	PASS	AF=0.977012;DP=1392;DP4=0,0,702,690;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agT/agG|S135R|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	900	.	C	T	49314.0	PASS	AF=0.987725;DP=3340;DP4=1,1,1672,1666;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S212L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	1980	.	G	T	19250.0	PASS	AF=0.977230;DP=527;DP4=1,1,252,273;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gTa|G572V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	2790	.	C	T	31461.0	PASS	AF=0.980210;DP=859;DP4=0,0,428,429;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T842I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	3037	.	C	T	49314.0	PASS	AF=0.981888;DP=2098;DP4=0,0,1045,1051;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	4184	.	G	A	32697.0	PASS	AF=0.973154;DP=894;DP4=2,3,504,385;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G1307S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
+NC_045512	4276	.	C	T	29741.0	PASS	AF=0.981949;DP=831;DP4=1,1,639,190;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y1337|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	4321	.	C	T	12804.0	PASS	AF=0.520703;DP=797;DP4=367,11,216,203;SB=544;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A1352|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	5302	.	A	G	4149.0	PASS	AF=0.116610;DP=1475;DP4=650,648,89,87;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A1679|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	5628	.	C	T	28094.0	PASS	AF=0.989704;DP=777;DP4=0,0,379,398;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T1788M|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	6354	.	C	T	14031.0	PASS	AF=0.694915;DP=590;DP4=174,0,236,179;SB=336;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S2030L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	9344	.	C	T	49314.0	PASS	AF=0.993553;DP=1551;DP4=0,0,768,783;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L3027F|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	9424	.	A	G	49314.0	PASS	AF=0.977535;DP=1558;DP4=0,1,793,764;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V3053|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	9534	.	C	T	49314.0	PASS	AF=0.984412;DP=2502;DP4=1,1,1200,1299;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T3090I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	9866	.	C	T	49314.0	PASS	AF=0.981550;DP=1355;DP4=2,2,734,616;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L3201F|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	10029	.	C	T	49314.0	PASS	AF=0.945828;DP=1606;DP4=0,0,781,821;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T3255I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	10198	.	C	T	46438.0	PASS	AF=0.985793;DP=1267;DP4=0,0,642,625;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D3311|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	10447	.	G	A	33471.0	PASS	AF=0.975877;DP=912;DP4=0,0,449,462;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R3394|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
+NC_045512	10449	.	C	A	33190.0	PASS	AF=0.975664;DP=904;DP4=0,0,444,455;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cAc|P3395H|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
+NC_045512	11287	.	GTCTGGTTTT	G	13350.0	PASS	AF=0.997555;DP=409;DP4=29,38,202,206;HRUN=1;SB=4;INDEL;EFF=CODON_DELETION(MODERATE||tctggtttt/|SGF3675|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	12036	.	C	T	49314.0	PASS	AF=0.974949;DP=1477;DP4=3,0,709,764;SB=9;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A3924V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	12854	.	C	T	32749.0	PASS	AF=0.979821;DP=892;DP4=1,1,436,454;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P4197S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	12880	.	C	T	32911.0	PASS	AF=0.976562;DP=896;DP4=0,0,433,463;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I4205|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	14408	.	C	T	49314.0	PASS	AF=0.984702;DP=3007;DP4=2,3,1458,1542;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P4720L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	15451	.	G	A	49314.0	PASS	AF=0.978308;DP=2305;DP4=2,1,1246,1053;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G5068S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|A)
+NC_045512	15714	.	C	T	49314.0	PASS	AF=0.980050;DP=1604;DP4=0,0,796,808;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L5155|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	17410	.	C	T	21331.0	PASS	AF=0.975904;DP=581;DP4=2,2,289,288;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R5721C|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	18163	.	A	G	25394.0	PASS	AF=0.974719;DP=712;DP4=0,0,343,369;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I5972V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G)
+NC_045512	19955	.	C	T	49314.0	PASS	AF=0.986418;DP=2577;DP4=0,0,1302,1273;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T6569I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	20055	.	A	G	27353.0	PASS	AF=0.914945;DP=823;DP4=45,0,388,388;SB=128;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E6602|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G)
+NC_045512	20719	.	C	T	34374.0	PASS	AF=0.987013;DP=924;DP4=0,0,475,449;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L6824|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	21618	.	C	T	49314.0	PASS	AF=0.991832;DP=2816;DP4=3,4,1412,1397;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T19I|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	21632	.	TTACCCCCTG	T	49314.0	PASS	AF=0.969520;DP=2395;DP4=157,157,1149,1173;HRUN=2;SB=0;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ttaccccctgca/tca|LPPA24S|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	21987	.	G	A	49314.0	PASS	AF=0.971223;DP=2363;DP4=4,1,1204,1153;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G142D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22200	.	T	G	37578.0	PASS	AF=0.973535;DP=1058;DP4=1,1,493,563;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gGg|V213G|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	22578	.	G	A	49314.0	PASS	AF=0.979866;DP=1788;DP4=1,0,898,889;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G339D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22599	.	G	C	49314.0	PASS	AF=0.984492;DP=1741;DP4=0,0,869,869;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGa/aCa|R346T|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22629	.	A	C	49314.0	PASS	AF=0.977650;DP=1745;DP4=0,0,863,879;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aCg|K356T|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22664	.	C	A	49314.0	PASS	AF=0.981829;DP=1651;DP4=0,0,808,843;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cta/Ata|L368I|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22674	.	C	T	49314.0	PASS	AF=0.976661;DP=1671;DP4=0,0,814,857;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S371F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22679	.	T	C	49314.0	PASS	AF=0.980392;DP=1683;DP4=0,1,831,851;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Cca|S373P|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22686	.	C	T	49314.0	PASS	AF=0.977444;DP=1596;DP4=3,2,784,805;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S375F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22688	.	A	G	49314.0	PASS	AF=0.977960;DP=1588;DP4=3,2,783,800;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T376A|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	22716	.	C	T	49314.0	PASS	AF=0.987611;DP=1695;DP4=1,0,852,840;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T385I|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22775	.	G	A	49314.0	PASS	AF=0.866976;DP=4954;DP4=264,337,2050,2303;SB=8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D405N|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22786	.	A	C	49314.0	PASS	AF=0.966713;DP=4326;DP4=8,11,1994,2310;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agA/agC|R408S|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22792	.	C	T	49314.0	PASS	AF=0.985711;DP=4269;DP4=3,2,1982,2282;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I410|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22813	.	G	T	49314.0	PASS	AF=0.985740;DP=4418;DP4=0,0,2060,2350;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaG/aaT|K417N|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22882	.	T	G	49314.0	PASS	AF=0.971882;DP=3023;DP4=8,10,1590,1412;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N440K|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	22992	.	G	A	49314.0	PASS	AF=0.984755;DP=2427;DP4=0,0,1149,1278;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S477N|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22995	.	C	A	49314.0	PASS	AF=0.977565;DP=2407;DP4=1,1,1144,1261;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aAa|T478K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	23013	.	A	C	49314.0	PASS	AF=0.972462;DP=2433;DP4=7,5,1146,1275;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gCa|E484A|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	23040	.	A	G	49314.0	PASS	AF=0.981124;DP=2437;DP4=2,1,1148,1286;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q493R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23055	.	A	G	49314.0	PASS	AF=0.979228;DP=2359;DP4=1,2,1113,1242;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q498R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23063	.	A	T	49314.0	PASS	AF=0.989863;DP=2269;DP4=0,0,1091,1177;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Tat|N501Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	23075	.	T	C	49314.0	PASS	AF=0.978643;DP=2388;DP4=2,2,1173,1210;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y505H|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	23403	.	A	G	33624.0	PASS	AF=0.978655;DP=937;DP4=0,0,452,483;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D614G|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23525	.	C	T	34230.0	PASS	AF=0.987097;DP=930;DP4=1,2,472,454;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H655Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	23599	.	T	G	49314.0	PASS	AF=0.981453;DP=2588;DP4=0,0,1324,1264;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N679K|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23604	.	C	A	49314.0	PASS	AF=0.981782;DP=2525;DP4=2,1,1287,1234;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cAt|P681H|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	23781	.	T	C	49314.0	PASS	AF=0.984828;DP=1450;DP4=2,0,697,751;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M740T|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	23854	.	C	A	49314.0	PASS	AF=0.975335;DP=1419;DP4=0,0,708,705;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaC/aaA|N764K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	23948	.	G	T	49314.0	PASS	AF=0.979577;DP=1420;DP4=1,1,728,689;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Tat|D796Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	24424	.	A	T	49314.0	PASS	AF=0.981157;DP=3715;DP4=4,4,1876,1829;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caA/caT|Q954H|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	24469	.	T	A	49314.0	PASS	AF=0.979514;DP=3954;DP4=6,6,2000,1940;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaA|N969K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	24966	.	A	G	49314.0	PASS	AF=0.974262;DP=2370;DP4=2,2,1177,1184;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aGc|N1135S|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	25000	.	C	T	49314.0	PASS	AF=0.978199;DP=2477;DP4=1,2,1230,1244;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D1146|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	25584	.	C	T	49314.0	PASS	AF=0.966142;DP=2924;DP4=1,2,1570,1348;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T64|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
+NC_045512	26060	.	C	T	49314.0	PASS	AF=0.980381;DP=3466;DP4=2,1,1700,1759;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T223I|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
+NC_045512	26195	.	C	T	45258.0	PASS	AF=0.964899;DP=1282;DP4=0,0,652,630;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T268M|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
+NC_045512	26270	.	C	T	44918.0	PASS	AF=0.989274;DP=1212;DP4=1,0,615,596;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T9I|75|E|protein_coding|CODING|GU280_gp04|1|T)
+NC_045512	26408	.	C	T	49314.0	PASS	AF=0.954265;DP=3564;DP4=0,0,1797,1657;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tTt|S55F|75|E|protein_coding|CODING|GU280_gp04|1|T)
+NC_045512	26577	.	C	G	49314.0	PASS	AF=0.982902;DP=1930;DP4=1,1,933,994;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q19E|222|M|protein_coding|CODING|GU280_gp05|1|G)
+NC_045512	26709	.	G	A	49314.0	PASS	AF=0.987394;DP=4125;DP4=1,0,2163,1959;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A63T|222|M|protein_coding|CODING|GU280_gp05|1|A)
+NC_045512	26801	.	C	T	49314.0	PASS	AF=0.980411;DP=4237;DP4=0,3,2119,2106;SB=9;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L93|222|M|protein_coding|CODING|GU280_gp05|1|T)
+NC_045512	26858	.	C	T	49314.0	PASS	AF=0.991272;DP=4010;DP4=2,1,1898,2106;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F112|222|M|protein_coding|CODING|GU280_gp05|1|T)
+NC_045512	27259	.	A	C	49314.0	PASS	AF=0.973996;DP=4730;DP4=11,18,2124,2568;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|Agg/Cgg|R20|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
+NC_045512	27382	.	G	C	48109.0	PASS	AF=0.977519;DP=1290;DP4=0,1,637,650;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Cat|D61H|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
+NC_045512	27383	.	A	T	48059.0	PASS	AF=0.980408;DP=1276;DP4=0,0,631,645;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gTt|D61V|61|ORF6|protein_coding|CODING|GU280_gp06|1|T)
+NC_045512	27384	.	T	C	48678.0	PASS	AF=0.985362;DP=1298;DP4=1,0,642,655;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D61|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
+NC_045512	27481	.	C	A	49314.0	PASS	AF=0.985457;DP=1444;DP4=0,0,724,717;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Att|L30I|121|ORF7a|protein_coding|CODING|GU280_gp07|1|A)
+NC_045512	27549	.	C	T	49314.0	PASS	AF=0.988926;DP=3251;DP4=0,0,1620,1630;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N52|121|ORF7a|protein_coding|CODING|GU280_gp07|1|T)
+NC_045512	27807	.	C	T	49314.0	PASS	AF=0.987966;DP=1745;DP4=0,0,868,877;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L18|43|ORF7b|protein_coding|CODING|GU280_gp08|1|T)
+NC_045512	28271	.	A	T	49314.0	PASS	AF=0.984275;DP=5596;DP4=3,6,2769,2811;SB=2
+NC_045512	28307	.	G	A	49314.0	PASS	AF=0.977890;DP=5337;DP4=3,5,2621,2706;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A12T|419|N|protein_coding|CODING|GU280_gp10|1|A)
+NC_045512	28311	.	C	T	49314.0	PASS	AF=0.933372;DP=5178;DP4=9,4,2537,2621;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cTc|P13L|419|N|protein_coding|CODING|GU280_gp10|1|T)
+NC_045512	28361	.	GGAGAACGCA	G	49314.0	PASS	AF=0.836136;DP=4638;DP4=550,230,1660,2218;HRUN=2;SB=453;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggagaacgcagt/ggt|GERS30G|419|N|protein_coding|CODING|GU280_gp10|1|G|INFO_REALIGN_3_PRIME)
+NC_045512	28483	.	A	G	49314.0	PASS	AF=0.967772;DP=2141;DP4=0,1,1061,1079;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q70|419|N|protein_coding|CODING|GU280_gp10|1|G)
+NC_045512	28657	.	C	T	49314.0	PASS	AF=0.979384;DP=4511;DP4=0,0,2307,2200;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D128|419|N|protein_coding|CODING|GU280_gp10|1|T)
+NC_045512	28881	.	G	A	49314.0	PASS	AF=0.983315;DP=1858;DP4=0,1,934,923;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aAg|R203K|419|N|protein_coding|CODING|GU280_gp10|1|A)
+NC_045512	28882	.	G	A	49314.0	PASS	AF=0.980572;DP=1853;DP4=0,0,933,920;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R203|419|N|protein_coding|CODING|GU280_gp10|1|A)
+NC_045512	28883	.	G	C	49314.0	PASS	AF=0.982465;DP=1882;DP4=0,0,949,933;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gga/Cga|G204R|419|N|protein_coding|CODING|GU280_gp10|1|C)
+NC_045512	29510	.	A	C	49314.0	PASS	AF=0.975827;DP=5833;DP4=1,2,2720,3107;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agt/Cgt|S413R|419|N|protein_coding|CODING|GU280_gp10|1|C)
+NC_045512	29733	.	CGAGGCCACGCGGAGTACGATCGAGTG	C	49314.0	PASS	AF=0.987166;DP=1870;DP4=377,353,741,1105;HRUN=1;SB=68;INDEL
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/day_83.vcf	Wed May 15 13:37:49 2024 +0000
@@ -0,0 +1,121 @@
+##fileformat=VCFv4.0
+##fileDate=20220906
+##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 20 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.001 --bonf dynamic --no-default-filter --no-default-filter -r NC_045512:1-7475 -o /data/jwd/main/050/269/50269466/tmp/lofreq2_call_parallelbsw9y3ln/0.vcf.gz reads.bam
+##reference=reference.fa
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth">
+##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
+##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias at this position">
+##INFO=<ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">
+##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position">
+##FILTER=<ID=min_snvqual_66,Description="Minimum SNV Quality (Phred) 66">
+##FILTER=<ID=min_indelqual_50,Description="Minimum Indel Quality (Phred) 50">
+##FILTER=<ID=min_snvqual_74,Description="Minimum SNV Quality (Phred) 74">
+##FILTER=<ID=min_indelqual_58,Description="Minimum Indel Quality (Phred) 58">
+##FILTER=<ID=min_af_0.100000,Description="Minimum allele frequency 0.100000">
+##FILTER=<ID=min_dp_20,Description="Minimum Coverage 20">
+##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000">
+##SnpEffVersion="4.3t (build 2017-11-24 10:18), by Pablo Cingolani"
+##SnpEffCmd="SnpEff  -i vcf -o vcf -formatEff -classic -no-downstream -no-intergenic -no-intron -no-upstream -stats /data/jwd01/main/050/269/50269701/outputs/galaxy_dataset_ef5dc3b4-139d-4ea2-92d6-0eee2b2185ce.dat -csvStats /data/jwd01/main/050/269/50269701/outputs/galaxy_dataset_e009b109-f15c-434d-af07-16d0fbe31d3c.dat SARS-CoV-2 /data/dnb07/galaxy_db/files/f/0/8/dataset_f08a98f8-5b31-4629-83fd-0bc9698a48ac.dat "
+##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_Change| Amino_Acid_length | Gene_Name | Transcript_BioType | Gene_Coding | Transcript_ID | Exon_Rank  | Genotype [ | ERRORS | WARNINGS ] )' ">
+##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
+##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+NC_045512	509	.	GGTCATGTTA	G	44081.0	PASS	AF=0.977320;DP=1455;DP4=71,87,803,619;HRUN=2;SB=21;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggtcatgttatg/gtg|GHVM82V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	670	.	T	G	28402.0	PASS	AF=0.924065;DP=856;DP4=2,1,417,436;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agT/agG|S135R|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	900	.	C	T	49314.0	PASS	AF=0.949196;DP=1555;DP4=0,0,790,764;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S212L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	1980	.	G	T	12662.0	PASS	AF=0.872774;DP=393;DP4=2,1,193,195;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gTa|G572V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	2790	.	C	T	23573.0	PASS	AF=0.950599;DP=668;DP4=1,0,337,328;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T842I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	3037	.	C	T	28907.0	PASS	AF=0.959559;DP=816;DP4=0,0,402,413;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	4184	.	G	A	9720.0	PASS	AF=0.929329;DP=283;DP4=0,0,153,129;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G1307S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
+NC_045512	4276	.	C	T	14067.0	PASS	AF=0.935644;DP=404;DP4=2,0,271,131;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y1337|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	4321	.	C	T	11408.0	PASS	AF=0.787589;DP=419;DP4=70,2,176,171;SB=153;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A1352|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	6354	.	C	T	8379.0	PASS	AF=0.702312;DP=346;DP4=80,0,164,100;SB=136;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S2030L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	9344	.	C	T	26816.0	PASS	AF=0.952191;DP=753;DP4=0,0,369,375;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L3027F|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	9424	.	A	G	25123.0	PASS	AF=0.950207;DP=723;DP4=0,1,356,364;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V3053|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	9495	.	T	C	24939.0	PASS	AF=0.798876;DP=890;DP4=12,102,395,380;SB=171;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTa/gCa|V3077A|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|C)
+NC_045512	9534	.	C	T	36433.0	PASS	AF=0.945894;DP=1035;DP4=1,1,363,670;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T3090I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	9866	.	C	T	18660.0	PASS	AF=0.938889;DP=540;DP4=3,3,316,216;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L3201F|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	10029	.	C	T	29070.0	PASS	AF=0.902746;DP=874;DP4=3,3,586,282;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T3255I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	10198	.	C	T	27766.0	PASS	AF=0.922030;DP=808;DP4=1,1,413,392;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D3311|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	10447	.	G	A	16235.0	PASS	AF=0.908714;DP=482;DP4=1,1,246,232;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R3394|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
+NC_045512	10449	.	C	A	16642.0	PASS	AF=0.910180;DP=501;DP4=1,2,258,240;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cAc|P3395H|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
+NC_045512	11287	.	GTCTGGTTTT	G	10180.0	PASS	AF=0.990991;DP=333;DP4=26,17,169,161;HRUN=1;SB=5;INDEL;EFF=CODON_DELETION(MODERATE||tctggtttt/|SGF3675|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	12036	.	C	T	24427.0	PASS	AF=0.913514;DP=740;DP4=0,0,352,382;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A3924V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	12854	.	C	T	14545.0	PASS	AF=0.905530;DP=434;DP4=1,2,228,202;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P4197S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	12880	.	C	T	15074.0	PASS	AF=0.959716;DP=422;DP4=0,0,211,209;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I4205|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	14408	.	C	T	49314.0	PASS	AF=0.942193;DP=1505;DP4=0,0,711,788;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P4720L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	15451	.	G	A	29209.0	PASS	AF=0.851222;DP=941;DP4=1,1,518,419;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G5068S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|A)
+NC_045512	15714	.	C	T	27739.0	PASS	AF=0.955243;DP=782;DP4=0,1,378,401;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L5155|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	17410	.	C	T	12584.0	PASS	AF=0.899736;DP=379;DP4=0,1,192,183;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R5721C|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	18163	.	A	G	16936.0	PASS	AF=0.931507;DP=511;DP4=1,0,247,260;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I5972V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G)
+NC_045512	19955	.	C	T	41409.0	PASS	AF=0.948936;DP=1175;DP4=0,0,609,564;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T6569I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	20055	.	A	G	8915.0	PASS	AF=0.880866;DP=277;DP4=17,0,116,143;SB=56;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E6602|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G)
+NC_045512	20719	.	C	T	10033.0	PASS	AF=0.916107;DP=298;DP4=1,0,179,113;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L6824|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	21441	.	T	C	19924.0	PASS	AF=0.894569;DP=626;DP4=9,8,346,263;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S7064|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|C)
+NC_045512	21618	.	C	T	45561.0	PASS	AF=0.910189;DP=1325;DP4=1,0,618,685;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T19I|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	21632	.	TTACCCCCTG	T	42692.0	PASS	AF=0.986760;DP=1284;DP4=40,19,574,693;HRUN=2;SB=31;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ttaccccctgca/tca|LPPA24S|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	21773	.	T	C	10733.0	PASS	AF=0.922601;DP=323;DP4=2,2,146,172;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tct/Cct|S71P|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	21987	.	G	A	34993.0	PASS	AF=0.787603;DP=1210;DP4=7,0,669,526;SB=16;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G142D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22200	.	T	G	23440.0	PASS	AF=0.945827;DP=683;DP4=0,0,284,396;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gGg|V213G|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	22578	.	G	A	31260.0	PASS	AF=0.876152;DP=977;DP4=1,0,462,510;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G339D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22599	.	G	C	32998.0	PASS	AF=0.953813;DP=931;DP4=0,0,437,491;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGa/aCa|R346T|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22629	.	A	C	27981.0	PASS	AF=0.895540;DP=852;DP4=0,0,405,445;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aCg|K356T|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22664	.	C	A	24854.0	PASS	AF=0.891247;DP=754;DP4=3,1,325,424;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cta/Ata|L368I|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22674	.	C	T	21228.0	PASS	AF=0.806540;DP=734;DP4=0,1,306,426;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S371F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22679	.	T	C	24327.0	PASS	AF=0.947592;DP=706;DP4=0,0,294,410;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Cca|S373P|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22686	.	C	T	19403.0	PASS	AF=0.858915;DP=645;DP4=0,2,271,370;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S375F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22688	.	A	G	19658.0	PASS	AF=0.885950;DP=605;DP4=1,0,255,349;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T376A|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	22716	.	C	T	17060.0	PASS	AF=0.964135;DP=474;DP4=0,0,218,256;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T385I|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22775	.	G	A	27032.0	PASS	AF=0.759106;DP=1208;DP4=110,126,463,508;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D405N|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22786	.	A	C	38537.0	PASS	AF=0.878986;DP=1223;DP4=3,6,600,609;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agA/agC|R408S|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22792	.	C	T	42345.0	PASS	AF=0.900631;DP=1268;DP4=1,3,633,628;SB=4;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I410|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22813	.	G	T	49314.0	PASS	AF=0.890789;DP=1520;DP4=2,1,791,723;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaG/aaT|K417N|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22882	.	T	G	41212.0	PASS	AF=0.893515;DP=1249;DP4=6,4,704,533;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N440K|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	22992	.	G	A	41603.0	PASS	AF=0.922204;DP=1234;DP4=6,8,527,682;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S477N|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22995	.	C	A	44039.0	PASS	AF=0.955538;DP=1237;DP4=0,1,538,695;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aAa|T478K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	23013	.	A	C	39440.0	PASS	AF=0.865539;DP=1242;DP4=7,8,527,697;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gCa|E484A|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	23040	.	A	G	36321.0	PASS	AF=0.893789;DP=1111;DP4=3,2,482,622;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q493R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23055	.	A	G	32481.0	PASS	AF=0.900802;DP=998;DP4=3,0,450,542;SB=10;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q498R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23063	.	A	T	34000.0	PASS	AF=0.937628;DP=978;DP4=3,4,450,521;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Tat|N501Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	23075	.	T	C	29355.0	PASS	AF=0.894168;DP=926;DP4=4,3,455,462;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y505H|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	23403	.	A	G	12242.0	PASS	AF=0.927419;DP=372;DP4=0,0,162,210;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D614G|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23525	.	C	T	9334.0	PASS	AF=0.890071;DP=282;DP4=2,1,135,144;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H655Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	23599	.	T	G	34424.0	PASS	AF=0.939394;DP=990;DP4=1,0,523,466;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N679K|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23604	.	C	A	32027.0	PASS	AF=0.885396;DP=986;DP4=3,0,515,468;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cAt|P681H|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	23854	.	C	A	20408.0	PASS	AF=0.932432;DP=592;DP4=1,2,284,305;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaC/aaA|N764K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	23948	.	G	T	29879.0	PASS	AF=0.920507;DP=868;DP4=1,2,443,419;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Tat|D796Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	24424	.	A	T	47659.0	PASS	AF=0.901191;DP=1427;DP4=2,14,769,642;SB=31;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caA/caT|Q954H|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	24469	.	T	A	49314.0	PASS	AF=0.939541;DP=1654;DP4=2,0,884,763;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaA|N969K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	24966	.	A	G	33803.0	PASS	AF=0.894434;DP=1042;DP4=3,1,460,569;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aGc|N1135S|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	25000	.	C	T	32268.0	PASS	AF=0.937773;DP=916;DP4=0,1,455,455;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D1146|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	25584	.	C	T	42188.0	PASS	AF=0.841246;DP=1348;DP4=2,8,756,578;SB=16;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T64|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
+NC_045512	26060	.	C	T	49314.0	PASS	AF=0.957550;DP=1437;DP4=0,2,737,694;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T223I|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
+NC_045512	26195	.	C	T	25026.0	PASS	AF=0.914667;DP=750;DP4=3,2,391,352;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T268M|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
+NC_045512	26270	.	C	T	31607.0	PASS	AF=0.924342;DP=912;DP4=0,1,470,440;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T9I|75|E|protein_coding|CODING|GU280_gp04|1|T)
+NC_045512	26324	.	T	C	2986.0	PASS	AF=0.146732;DP=811;DP4=353,331,66,57;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTg/tCg|L27S|75|E|protein_coding|CODING|GU280_gp04|1|C)
+NC_045512	26333	.	C	T	20679.0	PASS	AF=0.768638;DP=778;DP4=71,56,346,305;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T30I|75|E|protein_coding|CODING|GU280_gp04|1|T)
+NC_045512	26550	.	G	A	4831.0	PASS	AF=0.223039;DP=816;DP4=308,306,100,101;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V10I|222|M|protein_coding|CODING|GU280_gp05|1|A)
+NC_045512	26577	.	C	G	31868.0	PASS	AF=0.906152;DP=959;DP4=0,1,489,466;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q19E|222|M|protein_coding|CODING|GU280_gp05|1|G)
+NC_045512	26709	.	G	A	49314.0	PASS	AF=0.920627;DP=2041;DP4=3,3,994,1025;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A63T|222|M|protein_coding|CODING|GU280_gp05|1|A)
+NC_045512	26728	.	C	T	5102.0	PASS	AF=0.110196;DP=1942;DP4=855,852,118,113;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A69V|222|M|protein_coding|CODING|GU280_gp05|1|T)
+NC_045512	26801	.	C	T	49314.0	PASS	AF=0.887376;DP=1616;DP4=4,4,765,828;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L93|222|M|protein_coding|CODING|GU280_gp05|1|T)
+NC_045512	26858	.	C	T	27420.0	PASS	AF=0.846238;DP=917;DP4=15,20,417,458;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F112|222|M|protein_coding|CODING|GU280_gp05|1|T)
+NC_045512	26985	.	C	T	12028.0	PASS	AF=0.361871;DP=1133;DP4=334,325,236,233;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H155Y|222|M|protein_coding|CODING|GU280_gp05|1|T)
+NC_045512	27259	.	A	C	49314.0	PASS	AF=0.883410;DP=2170;DP4=6,12,916,1230;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|Agg/Cgg|R20|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
+NC_045512	27382	.	G	C	24097.0	PASS	AF=0.903090;DP=712;DP4=0,0,351,357;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Cat|D61H|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
+NC_045512	27383	.	A	T	23587.0	PASS	AF=0.887006;DP=708;DP4=0,0,351,353;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gTt|D61V|61|ORF6|protein_coding|CODING|GU280_gp06|1|T)
+NC_045512	27384	.	T	C	24162.0	PASS	AF=0.898187;DP=717;DP4=0,0,355,359;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D61|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
+NC_045512	27481	.	C	T	29456.0	PASS	AF=0.954654;DP=838;DP4=1,1,402,428;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L30F|121|ORF7a|protein_coding|CODING|GU280_gp07|1|T)
+NC_045512	27549	.	C	T	49314.0	PASS	AF=0.900465;DP=2150;DP4=0,0,1090,1037;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N52|121|ORF7a|protein_coding|CODING|GU280_gp07|1|T)
+NC_045512	27807	.	C	T	33703.0	PASS	AF=0.934827;DP=982;DP4=2,3,465,505;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L18|43|ORF7b|protein_coding|CODING|GU280_gp08|1|T)
+NC_045512	28271	.	A	T	49314.0	PASS	AF=0.878304;DP=1627;DP4=1,15,781,826;SB=32
+NC_045512	28311	.	C	T	49314.0	PASS	AF=0.812185;DP=1986;DP4=5,15,972,988;SB=13;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cTc|P13L|419|N|protein_coding|CODING|GU280_gp10|1|T)
+NC_045512	28361	.	GGAGAACGCA	G	36912.0	PASS	AF=0.764169;DP=1535;DP4=239,128,540,633;HRUN=2;SB=97;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggagaacgcagt/ggt|GERS30G|419|N|protein_coding|CODING|GU280_gp10|1|G|INFO_REALIGN_3_PRIME)
+NC_045512	28657	.	C	T	49314.0	PASS	AF=0.882603;DP=2828;DP4=5,5,1516,1283;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D128|419|N|protein_coding|CODING|GU280_gp10|1|T)
+NC_045512	28881	.	G	A	44587.0	PASS	AF=0.945774;DP=1254;DP4=0,1,574,678;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aAg|R203K|419|N|protein_coding|CODING|GU280_gp10|1|A)
+NC_045512	28882	.	G	A	42098.0	PASS	AF=0.911788;DP=1247;DP4=0,2,570,668;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R203|419|N|protein_coding|CODING|GU280_gp10|1|A)
+NC_045512	28883	.	G	C	42990.0	PASS	AF=0.922586;DP=1253;DP4=0,0,570,681;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gga/Cga|G204R|419|N|protein_coding|CODING|GU280_gp10|1|C)
+NC_045512	29510	.	A	C	49314.0	PASS	AF=0.922913;DP=2815;DP4=12,12,1232,1545;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agt/Cgt|S413R|419|N|protein_coding|CODING|GU280_gp10|1|C)
+NC_045512	29733	.	CGAGGCCACGCGGAGTACGATCGAGTG	C	49314.0	PASS	AF=0.989508;DP=1239;DP4=124,107,440,786;HRUN=1;SB=61;INDEL
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/day_85.vcf	Wed May 15 13:37:49 2024 +0000
@@ -0,0 +1,119 @@
+##fileformat=VCFv4.0
+##fileDate=20220927
+##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 20 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.001 --bonf dynamic --no-default-filter --no-default-filter -r NC_045512:1-7475 -o /data/jwd01/main/050/996/50996339/tmp/lofreq2_call_parallel_00t3eed/0.vcf.gz reads.bam
+##reference=reference.fa
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth">
+##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
+##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias at this position">
+##INFO=<ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">
+##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position">
+##FILTER=<ID=min_snvqual_68,Description="Minimum SNV Quality (Phred) 68">
+##FILTER=<ID=min_indelqual_52,Description="Minimum Indel Quality (Phred) 52">
+##FILTER=<ID=min_snvqual_75,Description="Minimum SNV Quality (Phred) 75">
+##FILTER=<ID=min_indelqual_60,Description="Minimum Indel Quality (Phred) 60">
+##FILTER=<ID=min_af_0.100000,Description="Minimum allele frequency 0.100000">
+##FILTER=<ID=min_dp_20,Description="Minimum Coverage 20">
+##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000">
+##SnpEffVersion="4.3t (build 2017-11-24 10:18), by Pablo Cingolani"
+##SnpEffCmd="SnpEff  -i vcf -o vcf -formatEff -classic -no-downstream -no-intergenic -no-intron -no-upstream -stats /data/jwd01/main/050/996/50996574/outputs/galaxy_dataset_61c05207-723c-481f-a33c-93acf8a6685f.dat -csvStats /data/jwd01/main/050/996/50996574/outputs/galaxy_dataset_609dc569-c14e-4725-861e-c0faa56ea1a3.dat SARS-CoV-2 /data/dnb07/galaxy_db/files/3/d/e/dataset_3dec9a4b-cd72-4350-9252-e3ac4947f31b.dat "
+##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_Change| Amino_Acid_length | Gene_Name | Transcript_BioType | Gene_Coding | Transcript_ID | Exon_Rank  | Genotype [ | ERRORS | WARNINGS ] )' ">
+##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
+##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+NC_045512	509	.	GGTCATGTTA	G	24816.0	PASS	AF=0.969084;DP=841;DP4=72,85,462,353;HRUN=2;SB=18;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggtcatgttatg/gtg|GHVM82V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	670	.	T	G	25606.0	PASS	AF=0.942105;DP=760;DP4=1,0,393,363;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agT/agG|S135R|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	900	.	C	T	49314.0	PASS	AF=0.949125;DP=1828;DP4=2,2,914,905;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S212L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	1980	.	G	T	10608.0	PASS	AF=0.895062;DP=324;DP4=0,3,167,153;SB=9;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gTa|G572V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	2790	.	C	T	11585.0	PASS	AF=0.924419;DP=344;DP4=0,0,172,170;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T842I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	3037	.	C	T	32298.0	PASS	AF=0.957929;DP=927;DP4=1,2,464,457;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	4184	.	G	A	17648.0	PASS	AF=0.933464;DP=511;DP4=0,0,288,218;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G1307S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
+NC_045512	4276	.	C	T	14453.0	PASS	AF=0.856838;DP=468;DP4=0,0,358,106;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y1337|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	4321	.	C	T	4973.0	PASS	AF=0.407229;DP=415;DP4=233,1,92,89;SB=373;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A1352|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	5302	.	A	G	2648.0	PASS	AF=0.153736;DP=696;DP4=281,288,58,66;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A1679|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	5628	.	C	T	14736.0	PASS	AF=0.923077;DP=442;DP4=2,2,214,221;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T1788M|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	6354	.	C	T	9316.0	PASS	AF=0.575453;DP=497;DP4=194,0,181,121;SB=310;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S2030L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	9344	.	C	T	21975.0	PASS	AF=0.939778;DP=631;DP4=0,0,309,319;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L3027F|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	9424	.	A	G	20883.0	PASS	AF=0.922204;DP=617;DP4=0,1,312,300;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V3053|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	9534	.	C	T	44514.0	PASS	AF=0.894855;DP=1341;DP4=1,0,686,648;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T3090I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	9866	.	C	T	31818.0	PASS	AF=0.954190;DP=895;DP4=1,1,504,388;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L3201F|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	10029	.	C	T	40172.0	PASS	AF=0.923801;DP=1168;DP4=0,0,542,624;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T3255I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	10198	.	C	T	19006.0	PASS	AF=0.917563;DP=558;DP4=0,0,290,264;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D3311|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	10447	.	G	A	14949.0	PASS	AF=0.899329;DP=447;DP4=0,0,220,225;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R3394|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
+NC_045512	10449	.	C	A	14477.0	PASS	AF=0.861538;DP=455;DP4=4,11,222,217;SB=9;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cAc|P3395H|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
+NC_045512	11287	.	GTCTGGTTTT	G	8782.0	PASS	AF=0.975694;DP=288;DP4=30,31,138,143;HRUN=1;SB=0;INDEL;EFF=CODON_DELETION(MODERATE||tctggtttt/|SGF3675|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	12036	.	C	T	20280.0	PASS	AF=0.917742;DP=620;DP4=1,1,282,333;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A3924V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	12854	.	C	T	14821.0	PASS	AF=0.845992;DP=474;DP4=0,6,234,233;SB=15;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P4197S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	12880	.	C	T	17325.0	PASS	AF=0.968685;DP=479;DP4=0,1,232,246;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I4205|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	14408	.	C	T	49314.0	PASS	AF=0.949393;DP=1482;DP4=0,3,709,768;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P4720L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	15451	.	G	A	36768.0	PASS	AF=0.911172;DP=1092;DP4=1,0,606,468;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G5068S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|A)
+NC_045512	15714	.	C	T	21744.0	PASS	AF=0.948136;DP=617;DP4=1,3,318,293;SB=4;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L5155|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	17410	.	C	T	7745.0	PASS	AF=0.928889;DP=225;DP4=0,0,107,117;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R5721C|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	18163	.	A	G	13119.0	PASS	AF=0.891626;DP=406;DP4=1,1,199,203;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I5972V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G)
+NC_045512	19955	.	C	T	49314.0	PASS	AF=0.947122;DP=1494;DP4=0,0,747,741;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T6569I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	20055	.	A	G	10686.0	PASS	AF=0.902141;DP=327;DP4=20,0,148,159;SB=59;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E6602|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G)
+NC_045512	20719	.	C	T	10811.0	PASS	AF=0.932692;DP=312;DP4=1,2,166,141;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L6824|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	21618	.	C	T	37364.0	PASS	AF=0.888987;DP=1135;DP4=0,6,560,553;SB=18;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T19I|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	21632	.	TTACCCCCTG	T	32441.0	PASS	AF=0.980080;DP=1004;DP4=55,42,469,515;HRUN=2;SB=9;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ttaccccctgca/tca|LPPA24S|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	21987	.	G	A	36002.0	PASS	AF=0.907493;DP=1081;DP4=0,1,557,519;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G142D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22200	.	T	G	16165.0	PASS	AF=0.924843;DP=479;DP4=3,0,211,263;SB=10;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gGg|V213G|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	22578	.	G	A	19580.0	PASS	AF=0.824508;DP=661;DP4=0,0,301,343;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G339D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22599	.	G	C	20362.0	PASS	AF=0.902280;DP=614;DP4=0,0,300,306;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGa/aCa|R346T|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22629	.	A	C	19818.0	PASS	AF=0.902156;DP=603;DP4=0,1,307,293;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aCg|K356T|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22664	.	C	A	18689.0	PASS	AF=0.893428;DP=563;DP4=2,1,281,277;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cta/Ata|L368I|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22674	.	C	T	18845.0	PASS	AF=0.926916;DP=561;DP4=0,0,275,284;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S371F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22679	.	T	C	19011.0	PASS	AF=0.926056;DP=568;DP4=1,0,288,278;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Cca|S373P|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22686	.	C	T	17628.0	PASS	AF=0.950851;DP=529;DP4=0,3,273,253;SB=9;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S375F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22688	.	A	G	16023.0	PASS	AF=0.869141;DP=512;DP4=0,1,269,238;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T376A|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	22716	.	C	T	19370.0	PASS	AF=0.939068;DP=558;DP4=0,0,301,254;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T385I|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22775	.	G	A	49314.0	PASS	AF=0.797604;DP=2337;DP4=173,208,921,1033;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D405N|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22786	.	A	C	49314.0	PASS	AF=0.895996;DP=1923;DP4=4,10,908,996;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agA/agC|R408S|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22792	.	C	T	49314.0	PASS	AF=0.946617;DP=1892;DP4=0,1,900,987;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I410|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22813	.	G	T	49314.0	PASS	AF=0.922457;DP=1986;DP4=2,1,957,1014;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaG/aaT|K417N|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22882	.	T	G	37187.0	PASS	AF=0.825487;DP=1232;DP4=5,2,668,550;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N440K|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	22992	.	G	A	39520.0	PASS	AF=0.943478;DP=1150;DP4=0,0,533,607;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S477N|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22995	.	C	A	41015.0	PASS	AF=0.971831;DP=1136;DP4=0,0,539,597;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aAa|T478K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	23013	.	A	C	39263.0	PASS	AF=0.911243;DP=1183;DP4=7,7,556,609;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gCa|E484A|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	23040	.	A	G	38673.0	PASS	AF=0.916594;DP=1151;DP4=2,5,543,597;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q493R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23055	.	A	G	35683.0	PASS	AF=0.902992;DP=1103;DP4=2,2,535,559;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q498R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23063	.	A	T	37185.0	PASS	AF=0.957733;DP=1041;DP4=0,0,521,520;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Tat|N501Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	23075	.	T	C	33766.0	PASS	AF=0.872827;DP=1093;DP4=5,2,561,522;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y505H|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	23403	.	A	G	13054.0	PASS	AF=0.951743;DP=373;DP4=0,1,178,194;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D614G|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23525	.	C	T	10850.0	PASS	AF=0.873900;DP=341;DP4=1,0,165,171;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H655Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	23599	.	T	G	44250.0	PASS	AF=0.941223;DP=1276;DP4=3,1,664,607;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N679K|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23604	.	C	A	41230.0	PASS	AF=0.902244;DP=1248;DP4=0,0,651,595;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cAt|P681H|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	23781	.	T	C	24650.0	PASS	AF=0.918256;DP=734;DP4=0,0,354,379;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M740T|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	23854	.	C	A	18022.0	PASS	AF=0.911071;DP=551;DP4=0,3,263,285;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaC/aaA|N764K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	23948	.	G	T	18412.0	PASS	AF=0.883929;DP=560;DP4=0,0,271,284;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Tat|D796Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	24424	.	A	T	44012.0	PASS	AF=0.835790;DP=1425;DP4=6,32,729,656;SB=53;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caA/caT|Q954H|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	24469	.	T	A	49314.0	PASS	AF=0.941802;DP=1598;DP4=4,0,824,765;SB=9;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaA|N969K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	24966	.	A	G	25737.0	PASS	AF=0.916237;DP=776;DP4=0,4,362,405;SB=8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aGc|N1135S|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	25000	.	C	T	23128.0	PASS	AF=0.932836;DP=670;DP4=0,0,336,332;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D1146|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	25584	.	C	T	34714.0	PASS	AF=0.843556;DP=1125;DP4=1,17,617,486;SB=49;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T64|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
+NC_045512	26060	.	C	T	48795.0	PASS	AF=0.959004;DP=1366;DP4=0,2,689,673;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T223I|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
+NC_045512	26195	.	C	T	17410.0	PASS	AF=0.867621;DP=559;DP4=0,1,274,279;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T268M|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
+NC_045512	26270	.	C	T	16029.0	PASS	AF=0.877264;DP=497;DP4=1,1,252,235;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T9I|75|E|protein_coding|CODING|GU280_gp04|1|T)
+NC_045512	26408	.	C	T	37918.0	PASS	AF=0.924915;DP=1172;DP4=0,0,574,561;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tTt|S55F|75|E|protein_coding|CODING|GU280_gp04|1|T)
+NC_045512	26577	.	C	G	23695.0	PASS	AF=0.921316;DP=699;DP4=1,0,337,354;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q19E|222|M|protein_coding|CODING|GU280_gp05|1|G)
+NC_045512	26709	.	G	A	49314.0	PASS	AF=0.946639;DP=1443;DP4=0,0,767,673;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A63T|222|M|protein_coding|CODING|GU280_gp05|1|A)
+NC_045512	26801	.	C	T	47205.0	PASS	AF=0.941005;DP=1373;DP4=2,1,682,684;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L93|222|M|protein_coding|CODING|GU280_gp05|1|T)
+NC_045512	26858	.	C	T	41810.0	PASS	AF=0.962835;DP=1157;DP4=0,0,532,623;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F112|222|M|protein_coding|CODING|GU280_gp05|1|T)
+NC_045512	27259	.	A	C	49314.0	PASS	AF=0.903539;DP=1752;DP4=0,4,732,1001;SB=8;EFF=SYNONYMOUS_CODING(LOW|SILENT|Agg/Cgg|R20|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
+NC_045512	27382	.	G	C	16412.0	PASS	AF=0.903292;DP=486;DP4=1,0,237,242;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Cat|D61H|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
+NC_045512	27383	.	A	T	15885.0	PASS	AF=0.877083;DP=480;DP4=0,1,238,233;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gTt|D61V|61|ORF6|protein_coding|CODING|GU280_gp06|1|T)
+NC_045512	27384	.	T	C	16182.0	PASS	AF=0.877800;DP=491;DP4=1,0,245,242;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D61|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
+NC_045512	27481	.	C	A	21747.0	PASS	AF=0.949429;DP=613;DP4=1,2,314,294;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Att|L30I|121|ORF7a|protein_coding|CODING|GU280_gp07|1|A)
+NC_045512	27549	.	C	T	49314.0	PASS	AF=0.901484;DP=1482;DP4=0,0,746,720;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N52|121|ORF7a|protein_coding|CODING|GU280_gp07|1|T)
+NC_045512	27807	.	C	T	16022.0	PASS	AF=0.916143;DP=477;DP4=1,0,240,234;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L18|43|ORF7b|protein_coding|CODING|GU280_gp08|1|T)
+NC_045512	28271	.	A	T	49314.0	PASS	AF=0.923592;DP=1793;DP4=1,10,893,886;SB=19
+NC_045512	28307	.	G	A	49314.0	PASS	AF=0.852097;DP=1812;DP4=3,2,884,890;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A12T|419|N|protein_coding|CODING|GU280_gp10|1|A)
+NC_045512	28311	.	C	T	49314.0	PASS	AF=0.829309;DP=1781;DP4=5,24,875,873;SB=32;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cTc|P13L|419|N|protein_coding|CODING|GU280_gp10|1|T)
+NC_045512	28361	.	GGAGAACGCA	G	40362.0	PASS	AF=0.788374;DP=1531;DP4=239,97,491,716;HRUN=2;SB=226;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggagaacgcagt/ggt|GERS30G|419|N|protein_coding|CODING|GU280_gp10|1|G|INFO_REALIGN_3_PRIME)
+NC_045512	28483	.	A	G	24535.0	PASS	AF=0.917663;DP=753;DP4=3,4,354,387;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q70|419|N|protein_coding|CODING|GU280_gp10|1|G)
+NC_045512	28657	.	C	T	49314.0	PASS	AF=0.927105;DP=1948;DP4=3,2,1064,862;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D128|419|N|protein_coding|CODING|GU280_gp10|1|T)
+NC_045512	28881	.	G	A	29591.0	PASS	AF=0.964242;DP=811;DP4=0,1,411,397;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aAg|R203K|419|N|protein_coding|CODING|GU280_gp10|1|A)
+NC_045512	28882	.	G	A	27445.0	PASS	AF=0.918216;DP=807;DP4=0,1,408,394;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R203|419|N|protein_coding|CODING|GU280_gp10|1|A)
+NC_045512	28883	.	G	C	27530.0	PASS	AF=0.907317;DP=820;DP4=2,0,413,402;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gga/Cga|G204R|419|N|protein_coding|CODING|GU280_gp10|1|C)
+NC_045512	29510	.	A	C	49314.0	PASS	AF=0.902691;DP=1932;DP4=1,1,877,1050;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agt/Cgt|S413R|419|N|protein_coding|CODING|GU280_gp10|1|C)
+NC_045512	29733	.	CGAGGCCACGCGGAGTACGATCGAGTG	C	30334.0	PASS	AF=0.994702;DP=755;DP4=144,132,273,478;HRUN=1;SB=52;INDEL
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/day_91.vcf	Wed May 15 13:37:49 2024 +0000
@@ -0,0 +1,120 @@
+##fileformat=VCFv4.0
+##fileDate=20220927
+##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 20 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.001 --bonf dynamic --no-default-filter --no-default-filter -r NC_045512:1-7475 -o /data/jwd01/main/050/996/50996340/tmp/lofreq2_call_parallel6ivdou83/0.vcf.gz reads.bam
+##reference=reference.fa
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth">
+##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
+##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias at this position">
+##INFO=<ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">
+##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position">
+##FILTER=<ID=min_snvqual_66,Description="Minimum SNV Quality (Phred) 66">
+##FILTER=<ID=min_indelqual_50,Description="Minimum Indel Quality (Phred) 50">
+##FILTER=<ID=min_snvqual_74,Description="Minimum SNV Quality (Phred) 74">
+##FILTER=<ID=min_indelqual_59,Description="Minimum Indel Quality (Phred) 59">
+##FILTER=<ID=min_af_0.100000,Description="Minimum allele frequency 0.100000">
+##FILTER=<ID=min_dp_20,Description="Minimum Coverage 20">
+##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000">
+##SnpEffVersion="4.3t (build 2017-11-24 10:18), by Pablo Cingolani"
+##SnpEffCmd="SnpEff  -i vcf -o vcf -formatEff -classic -no-downstream -no-intergenic -no-intron -no-upstream -stats /data/jwd/main/050/996/50996575/outputs/galaxy_dataset_75872de2-697f-40a3-8fc1-615981f550e3.dat -csvStats /data/jwd/main/050/996/50996575/outputs/galaxy_dataset_5f2c1e84-2d8b-4128-b50b-2f94725c3fa8.dat SARS-CoV-2 /data/dnb07/galaxy_db/files/4/4/b/dataset_44b78fc2-2fd9-4e6c-91ce-81aba326a225.dat "
+##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_Change| Amino_Acid_length | Gene_Name | Transcript_BioType | Gene_Coding | Transcript_ID | Exon_Rank  | Genotype [ | ERRORS | WARNINGS ] )' ">
+##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
+##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+NC_045512	509	.	GGTCATGTTA	G	21124.0	PASS	AF=0.984195;DP=696;DP4=32,39,423,262;HRUN=2;SB=21;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggtcatgttatg/gtg|GHVM82V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	670	.	T	G	19287.0	PASS	AF=0.922680;DP=582;DP4=1,1,272,307;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agT/agG|S135R|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	900	.	C	T	49314.0	PASS	AF=0.937765;DP=1414;DP4=2,1,730,675;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S212L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	1980	.	G	T	7272.0	PASS	AF=0.865217;DP=230;DP4=0,1,115,113;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gTa|G572V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	2790	.	C	T	9638.0	PASS	AF=0.925795;DP=283;DP4=0,0,135,145;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T842I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	3037	.	C	T	21293.0	PASS	AF=0.960133;DP=602;DP4=0,1,299,302;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	3683	.	C	A	238.0	PASS	AF=0.105263;DP=95;DP4=49,36,6,4;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cag/Aag|Q1140K|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
+NC_045512	4184	.	G	A	9755.0	PASS	AF=0.925532;DP=282;DP4=0,0,172,109;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G1307S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
+NC_045512	4276	.	C	T	8500.0	PASS	AF=0.882576;DP=264;DP4=0,0,210,53;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y1337|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	4321	.	C	T	3039.0	PASS	AF=0.375000;DP=280;DP4=166,2,60,52;SB=217;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A1352|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	5302	.	A	G	14543.0	PASS	AF=0.849899;DP=493;DP4=12,15,227,233;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A1679|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	5628	.	C	T	6181.0	PASS	AF=0.870647;DP=201;DP4=1,0,99,98;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T1788M|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	6354	.	C	T	4745.0	PASS	AF=0.496667;DP=300;DP4=136,0,97,67;SB=209;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S2030L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	9344	.	C	T	14163.0	PASS	AF=0.929612;DP=412;DP4=0,0,204,205;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L3027F|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	9424	.	A	G	16090.0	PASS	AF=0.906504;DP=492;DP4=0,1,250,237;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V3053|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	9534	.	C	T	30931.0	PASS	AF=0.851434;DP=976;DP4=0,0,476,492;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T3090I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	9866	.	C	T	21641.0	PASS	AF=0.936204;DP=627;DP4=2,3,352,268;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L3201F|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	10029	.	C	T	24390.0	PASS	AF=0.919220;DP=718;DP4=0,0,327,385;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T3255I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	10198	.	C	T	13719.0	PASS	AF=0.859447;DP=434;DP4=0,0,227,200;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D3311|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	10447	.	G	A	6728.0	PASS	AF=0.915000;DP=200;DP4=0,0,101,99;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R3394|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
+NC_045512	10449	.	C	A	6479.0	PASS	AF=0.875000;DP=200;DP4=1,0,101,97;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cAc|P3395H|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
+NC_045512	11287	.	GTCTGGTTTT	G	5414.0	PASS	AF=0.988372;DP=172;DP4=12,15,87,83;HRUN=1;SB=2;INDEL;EFF=CODON_DELETION(MODERATE||tctggtttt/|SGF3675|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	12036	.	C	T	13967.0	PASS	AF=0.908879;DP=428;DP4=0,0,191,236;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A3924V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	12854	.	C	T	8084.0	PASS	AF=0.850980;DP=255;DP4=1,4,121,129;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P4197S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	12880	.	C	T	9293.0	PASS	AF=0.953668;DP=259;DP4=0,0,122,137;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I4205|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	14408	.	C	T	30442.0	PASS	AF=0.945790;DP=867;DP4=1,1,421,444;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P4720L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	15451	.	G	A	32619.0	PASS	AF=0.917191;DP=954;DP4=2,0,570,378;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G5068S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|A)
+NC_045512	15714	.	C	T	16193.0	PASS	AF=0.944326;DP=467;DP4=0,0,232,235;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L5155|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	17410	.	C	T	4679.0	PASS	AF=0.927007;DP=137;DP4=0,0,61,76;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R5721C|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	18163	.	A	G	8692.0	PASS	AF=0.853147;DP=286;DP4=1,2,138,143;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I5972V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G)
+NC_045512	19955	.	C	T	34314.0	PASS	AF=0.954825;DP=974;DP4=0,1,461,509;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T6569I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	20055	.	A	G	4430.0	PASS	AF=0.811321;DP=159;DP4=21,1,66,71;SB=48;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E6602|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G)
+NC_045512	20719	.	C	T	8638.0	PASS	AF=0.950820;DP=244;DP4=1,1,135,107;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L6824|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	21618	.	C	T	23086.0	PASS	AF=0.871329;DP=715;DP4=0,2,339,365;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T19I|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	21632	.	TTACCCCCTG	T	20809.0	PASS	AF=0.990581;DP=637;DP4=37,20,286,345;HRUN=2;SB=22;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ttaccccctgca/tca|LPPA24S|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	21987	.	G	A	27221.0	PASS	AF=0.915545;DP=817;DP4=2,0,449,362;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G142D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22200	.	T	G	11644.0	PASS	AF=0.940120;DP=334;DP4=0,0,146,188;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gGg|V213G|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	22578	.	G	A	11598.0	PASS	AF=0.782082;DP=413;DP4=0,1,190,214;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G339D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22599	.	G	C	10927.0	PASS	AF=0.865330;DP=349;DP4=0,0,163,183;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGa/aCa|R346T|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22629	.	A	C	10965.0	PASS	AF=0.875000;DP=352;DP4=0,0,160,192;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aCg|K356T|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22664	.	C	A	10461.0	PASS	AF=0.896552;DP=319;DP4=1,0,139,176;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cta/Ata|L368I|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22674	.	C	T	10533.0	PASS	AF=0.945338;DP=311;DP4=0,0,142,169;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S371F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22679	.	T	C	10381.0	PASS	AF=0.919872;DP=312;DP4=0,0,146,164;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Cca|S373P|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22686	.	C	T	9882.0	PASS	AF=0.922297;DP=296;DP4=1,2,139,152;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S375F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22688	.	A	G	9752.0	PASS	AF=0.880645;DP=310;DP4=0,0,149,159;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T376A|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	22716	.	C	T	10414.0	PASS	AF=0.923588;DP=301;DP4=0,0,156,141;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T385I|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22775	.	G	A	32099.0	PASS	AF=0.611635;DP=2544;DP4=422,472,857,792;SB=16;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D405N|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22786	.	A	C	49314.0	PASS	AF=0.911746;DP=1541;DP4=3,6,803,727;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agA/agC|R408S|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22792	.	C	T	49314.0	PASS	AF=0.944075;DP=1502;DP4=1,0,788,709;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I410|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22813	.	G	T	49314.0	PASS	AF=0.928571;DP=1610;DP4=1,0,841,763;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaG/aaT|K417N|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22882	.	T	G	32587.0	PASS	AF=0.774221;DP=1156;DP4=8,5,629,510;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N440K|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	22992	.	G	A	31454.0	PASS	AF=0.921758;DP=933;DP4=1,0,411,514;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S477N|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22995	.	C	A	33366.0	PASS	AF=0.967672;DP=928;DP4=0,0,417,509;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aAa|T478K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	23013	.	A	C	32717.0	PASS	AF=0.891304;DP=1012;DP4=6,5,461,535;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gCa|E484A|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	23040	.	A	G	33801.0	PASS	AF=0.914086;DP=1001;DP4=0,2,465,528;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q493R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23055	.	A	G	31971.0	PASS	AF=0.904908;DP=978;DP4=0,2,465,509;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q498R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23063	.	A	T	34081.0	PASS	AF=0.953271;DP=963;DP4=0,0,466,496;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Tat|N501Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	23075	.	T	C	30581.0	PASS	AF=0.886715;DP=971;DP4=7,0,480,481;SB=18;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y505H|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	23403	.	A	G	6624.0	PASS	AF=0.937500;DP=192;DP4=0,1,88,103;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D614G|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23525	.	C	T	5738.0	PASS	AF=0.885057;DP=174;DP4=0,0,87,85;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H655Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	23599	.	T	G	34087.0	PASS	AF=0.924623;DP=995;DP4=2,2,543,443;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N679K|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23604	.	C	A	32266.0	PASS	AF=0.891019;DP=991;DP4=0,7,541,438;SB=24;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cAt|P681H|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	23781	.	T	C	19378.0	PASS	AF=0.926829;DP=574;DP4=0,0,258,315;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M740T|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	23854	.	C	A	15863.0	PASS	AF=0.935484;DP=465;DP4=1,1,224,237;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaC/aaA|N764K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	23948	.	G	T	14150.0	PASS	AF=0.882217;DP=433;DP4=0,0,213,209;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Tat|D796Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	24424	.	A	T	34766.0	PASS	AF=0.852834;DP=1094;DP4=0,17,579,496;SB=56;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caA/caT|Q954H|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	24469	.	T	A	40157.0	PASS	AF=0.926871;DP=1176;DP4=8,0,614,554;SB=20;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaA|N969K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	24966	.	A	G	15404.0	PASS	AF=0.884058;DP=483;DP4=0,3,223,250;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aGc|N1135S|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	25000	.	C	T	14885.0	PASS	AF=0.932870;DP=432;DP4=0,0,207,224;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D1146|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	25584	.	C	T	31362.0	PASS	AF=0.853000;DP=1000;DP4=2,13,580,402;SB=31;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T64|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
+NC_045512	26060	.	C	T	47532.0	PASS	AF=0.955157;DP=1338;DP4=1,2,679,652;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T223I|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
+NC_045512	26195	.	C	T	14674.0	PASS	AF=0.876356;DP=461;DP4=0,0,225,233;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T268M|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
+NC_045512	26270	.	C	T	14524.0	PASS	AF=0.882353;DP=442;DP4=0,0,233,207;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T9I|75|E|protein_coding|CODING|GU280_gp04|1|T)
+NC_045512	26408	.	C	T	33813.0	PASS	AF=0.922710;DP=1048;DP4=1,1,506,514;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tTt|S55F|75|E|protein_coding|CODING|GU280_gp04|1|T)
+NC_045512	26577	.	C	G	16529.0	PASS	AF=0.903808;DP=499;DP4=1,2,247,245;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q19E|222|M|protein_coding|CODING|GU280_gp05|1|G)
+NC_045512	26709	.	G	A	45733.0	PASS	AF=0.942308;DP=1300;DP4=0,1,719,575;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A63T|222|M|protein_coding|CODING|GU280_gp05|1|A)
+NC_045512	26801	.	C	T	44080.0	PASS	AF=0.932558;DP=1290;DP4=1,3,645,637;SB=4;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L93|222|M|protein_coding|CODING|GU280_gp05|1|T)
+NC_045512	26858	.	C	T	37583.0	PASS	AF=0.949763;DP=1055;DP4=0,2,470,579;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F112|222|M|protein_coding|CODING|GU280_gp05|1|T)
+NC_045512	27259	.	A	C	49314.0	PASS	AF=0.894131;DP=1823;DP4=3,9,728,1075;SB=4;EFF=SYNONYMOUS_CODING(LOW|SILENT|Agg/Cgg|R20|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
+NC_045512	27382	.	G	C	14584.0	PASS	AF=0.904651;DP=430;DP4=1,0,211,214;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Cat|D61H|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
+NC_045512	27383	.	A	T	13812.0	PASS	AF=0.862150;DP=428;DP4=0,1,214,211;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gTt|D61V|61|ORF6|protein_coding|CODING|GU280_gp06|1|T)
+NC_045512	27384	.	T	C	13802.0	PASS	AF=0.844037;DP=436;DP4=1,3,216,215;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D61|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
+NC_045512	27481	.	C	A	18804.0	PASS	AF=0.951402;DP=535;DP4=2,0,272,259;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Att|L30I|121|ORF7a|protein_coding|CODING|GU280_gp07|1|A)
+NC_045512	27549	.	C	T	45982.0	PASS	AF=0.876333;DP=1407;DP4=1,1,717,658;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N52|121|ORF7a|protein_coding|CODING|GU280_gp07|1|T)
+NC_045512	27807	.	C	T	18061.0	PASS	AF=0.931035;DP=522;DP4=0,0,252,269;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L18|43|ORF7b|protein_coding|CODING|GU280_gp08|1|T)
+NC_045512	28271	.	A	T	49314.0	PASS	AF=0.915477;DP=1751;DP4=1,17,884,845;SB=42
+NC_045512	28307	.	G	A	49314.0	PASS	AF=0.796053;DP=1824;DP4=5,3,896,871;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A12T|419|N|protein_coding|CODING|GU280_gp10|1|A)
+NC_045512	28311	.	C	T	49314.0	PASS	AF=0.756948;DP=1835;DP4=2,45,917,862;SB=114;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cTc|P13L|419|N|protein_coding|CODING|GU280_gp10|1|T)
+NC_045512	28361	.	GGAGAACGCA	G	40606.0	PASS	AF=0.766583;DP=1598;DP4=305,87,454,771;HRUN=2;SB=455;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggagaacgcagt/ggt|GERS30G|419|N|protein_coding|CODING|GU280_gp10|1|G|INFO_REALIGN_3_PRIME)
+NC_045512	28483	.	A	G	24461.0	PASS	AF=0.905512;DP=762;DP4=1,4,364,386;SB=4;EFF=SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q70|419|N|protein_coding|CODING|GU280_gp10|1|G)
+NC_045512	28657	.	C	T	49314.0	PASS	AF=0.916149;DP=2254;DP4=1,3,1298,932;SB=5;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D128|419|N|protein_coding|CODING|GU280_gp10|1|T)
+NC_045512	28881	.	G	A	30935.0	PASS	AF=0.969194;DP=844;DP4=0,0,406,437;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aAg|R203K|419|N|protein_coding|CODING|GU280_gp10|1|A)
+NC_045512	28882	.	G	A	28482.0	PASS	AF=0.916667;DP=840;DP4=0,2,402,433;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R203|419|N|protein_coding|CODING|GU280_gp10|1|A)
+NC_045512	28883	.	G	C	28643.0	PASS	AF=0.906033;DP=862;DP4=0,1,415,438;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gga/Cga|G204R|419|N|protein_coding|CODING|GU280_gp10|1|C)
+NC_045512	29510	.	A	C	49314.0	PASS	AF=0.892053;DP=2177;DP4=1,1,945,1228;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agt/Cgt|S413R|419|N|protein_coding|CODING|GU280_gp10|1|C)
+NC_045512	29733	.	CGAGGCCACGCGGAGTACGATCGAGTG	C	38545.0	PASS	AF=0.984359;DP=959;DP4=153,130,300,644;HRUN=1;SB=105;INDEL
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/day_96.vcf	Wed May 15 13:37:49 2024 +0000
@@ -0,0 +1,125 @@
+##fileformat=VCFv4.0
+##fileDate=20220927
+##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 20 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.001 --bonf dynamic --no-default-filter --no-default-filter -r NC_045512:1-7475 -o /data/jwd01/main/050/996/50996341/tmp/lofreq2_call_parallelkbk_8g6w/0.vcf.gz reads.bam
+##reference=reference.fa
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth">
+##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
+##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias at this position">
+##INFO=<ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">
+##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position">
+##FILTER=<ID=min_snvqual_67,Description="Minimum SNV Quality (Phred) 67">
+##FILTER=<ID=min_indelqual_51,Description="Minimum Indel Quality (Phred) 51">
+##FILTER=<ID=min_snvqual_74,Description="Minimum SNV Quality (Phred) 74">
+##FILTER=<ID=min_indelqual_59,Description="Minimum Indel Quality (Phred) 59">
+##FILTER=<ID=min_af_0.100000,Description="Minimum allele frequency 0.100000">
+##FILTER=<ID=min_dp_20,Description="Minimum Coverage 20">
+##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000">
+##SnpEffVersion="4.3t (build 2017-11-24 10:18), by Pablo Cingolani"
+##SnpEffCmd="SnpEff  -i vcf -o vcf -formatEff -classic -no-downstream -no-intergenic -no-intron -no-upstream -stats /data/jwd01/main/050/996/50996576/outputs/galaxy_dataset_7134dc8f-2717-4c53-9401-0608f3cc8edd.dat -csvStats /data/jwd01/main/050/996/50996576/outputs/galaxy_dataset_2d827137-0272-431c-b364-f79cadd4a78e.dat SARS-CoV-2 /data/dnb06/galaxy_db/files/5/0/4/dataset_504f8e70-d9aa-40dc-bcad-7013ecb50497.dat "
+##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_Change| Amino_Acid_length | Gene_Name | Transcript_BioType | Gene_Coding | Transcript_ID | Exon_Rank  | Genotype [ | ERRORS | WARNINGS ] )' ">
+##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
+##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+NC_045512	509	.	GGTCATGTTA	G	17835.0	PASS	AF=0.981605;DP=598;DP4=54,68,369,218;HRUN=2;SB=37;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggtcatgttatg/gtg|GHVM82V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	670	.	T	G	21430.0	PASS	AF=0.938389;DP=633;DP4=2,0,307,322;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agT/agG|S135R|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	900	.	C	T	49314.0	PASS	AF=0.929595;DP=1605;DP4=8,8,813,769;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S212L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	1059	.	C	A	2369.0	PASS	AF=0.169912;DP=565;DP4=225,228,49,63;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aAc|T265N|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
+NC_045512	1980	.	G	T	9721.0	PASS	AF=0.913194;DP=288;DP4=0,1,152,134;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gTa|G572V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	2790	.	C	T	10797.0	PASS	AF=0.928349;DP=321;DP4=0,0,158,162;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T842I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	3037	.	C	T	26954.0	PASS	AF=0.964520;DP=761;DP4=1,0,374,384;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	4184	.	G	A	15491.0	PASS	AF=0.960920;DP=435;DP4=1,0,269,164;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G1307S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
+NC_045512	4276	.	C	T	12820.0	PASS	AF=0.867647;DP=408;DP4=0,1,309,96;SB=6;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y1337|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	4321	.	C	T	4723.0	PASS	AF=0.432133;DP=361;DP4=193,2,83,83;SB=312;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A1352|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	5302	.	A	G	3100.0	PASS	AF=0.207815;DP=563;DP4=214,212,58,74;SB=6;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A1679|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	5628	.	C	T	11175.0	PASS	AF=0.923077;DP=338;DP4=1,1,167,168;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T1788M|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	6354	.	C	T	5649.0	PASS	AF=0.501401;DP=357;DP4=170,0,112,75;SB=249;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S2030L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	9344	.	C	T	18651.0	PASS	AF=0.943503;DP=531;DP4=0,0,268,261;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L3027F|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	9424	.	A	G	16423.0	PASS	AF=0.928425;DP=489;DP4=0,0,263,222;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V3053|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	9534	.	C	T	36641.0	PASS	AF=0.865435;DP=1137;DP4=0,0,546,584;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T3090I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	9866	.	C	T	23590.0	PASS	AF=0.955023;DP=667;DP4=2,3,389,273;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L3201F|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	10029	.	C	T	30341.0	PASS	AF=0.925223;DP=896;DP4=2,2,410,481;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T3255I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	10198	.	C	T	15723.0	PASS	AF=0.899582;DP=478;DP4=0,0,252,223;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D3311|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	10447	.	G	A	12304.0	PASS	AF=0.913279;DP=369;DP4=0,0,178,187;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R3394|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
+NC_045512	10449	.	C	A	11276.0	PASS	AF=0.841962;DP=367;DP4=5,4,176,179;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cAc|P3395H|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
+NC_045512	11287	.	GTCTGGTTTT	G	6950.0	PASS	AF=0.986667;DP=225;DP4=20,19,112,110;HRUN=1;SB=0;INDEL;EFF=CODON_DELETION(MODERATE||tctggtttt/|SGF3675|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
+NC_045512	12036	.	C	T	18341.0	PASS	AF=0.938069;DP=549;DP4=0,0,263,284;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A3924V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	12624	.	C	A	1944.0	PASS	AF=0.175105;DP=474;DP4=158,219,47,48;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cAt|P4120H|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
+NC_045512	12854	.	C	T	10807.0	PASS	AF=0.845070;DP=355;DP4=1,6,177,171;SB=11;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P4197S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	12880	.	C	T	12842.0	PASS	AF=0.950413;DP=363;DP4=1,1,168,192;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I4205|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
+NC_045512	14408	.	C	T	42858.0	PASS	AF=0.960866;DP=1201;DP4=0,1,581,619;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P4720L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	15451	.	G	A	33250.0	PASS	AF=0.926577;DP=967;DP4=3,0,564,397;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G5068S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|A)
+NC_045512	15714	.	C	T	18071.0	PASS	AF=0.955253;DP=514;DP4=1,0,253,260;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L5155|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	17410	.	C	T	7942.0	PASS	AF=0.941964;DP=224;DP4=0,1,106,116;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R5721C|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	18163	.	A	G	10968.0	PASS	AF=0.891496;DP=341;DP4=0,0,172,165;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I5972V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G)
+NC_045512	19955	.	C	T	44996.0	PASS	AF=0.948113;DP=1272;DP4=0,0,626,643;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T6569I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	20055	.	A	G	9573.0	PASS	AF=0.892256;DP=297;DP4=19,0,130,148;SB=56;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E6602|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G)
+NC_045512	20719	.	C	T	13503.0	PASS	AF=0.931122;DP=392;DP4=0,0,215,175;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L6824|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
+NC_045512	21604	.	G	T	3845.0	PASS	AF=0.164516;DP=930;DP4=377,374,89,85;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caG/caT|Q14H|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	21618	.	C	T	29895.0	PASS	AF=0.867884;DP=931;DP4=1,6,462,443;SB=11;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T19I|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	21632	.	TTACCCCCTG	T	26031.0	PASS	AF=0.982565;DP=803;DP4=44,28,379,410;HRUN=2;SB=14;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ttaccccctgca/tca|LPPA24S|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	21851	.	A	C	1949.0	PASS	AF=0.289796;DP=245;DP4=87,83,38,37;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aag/Cag|K97Q|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	21987	.	G	A	25306.0	PASS	AF=0.916340;DP=765;DP4=4,3,403,352;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G142D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22200	.	T	G	12774.0	PASS	AF=0.949062;DP=373;DP4=0,0,161,211;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gGg|V213G|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	22578	.	G	A	21127.0	PASS	AF=0.841727;DP=695;DP4=0,1,333,353;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G339D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22599	.	G	C	20259.0	PASS	AF=0.906710;DP=611;DP4=1,1,302,302;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGa/aCa|R346T|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22629	.	A	C	20204.0	PASS	AF=0.913540;DP=613;DP4=0,4,302,306;SB=9;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aCg|K356T|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22664	.	C	A	18684.0	PASS	AF=0.922101;DP=552;DP4=0,0,270,279;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cta/Ata|L368I|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22674	.	C	T	18575.0	PASS	AF=0.919065;DP=556;DP4=0,0,271,285;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S371F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22679	.	T	C	18765.0	PASS	AF=0.935484;DP=558;DP4=0,0,280,277;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Cca|S373P|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22686	.	C	T	17116.0	PASS	AF=0.939335;DP=511;DP4=0,1,262,248;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S375F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22688	.	A	G	15732.0	PASS	AF=0.867735;DP=499;DP4=1,1,258,236;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T376A|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	22716	.	C	T	17520.0	PASS	AF=0.921722;DP=511;DP4=1,0,275,229;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T385I|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22775	.	G	A	49314.0	PASS	AF=0.820296;DP=2365;DP4=149,170,1020,1022;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D405N|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22786	.	A	C	49314.0	PASS	AF=0.921507;DP=1911;DP4=3,6,948,947;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agA/agC|R408S|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	22792	.	C	T	49314.0	PASS	AF=0.950347;DP=1873;DP4=1,2,934,927;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I410|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22813	.	G	T	49314.0	PASS	AF=0.924974;DP=1946;DP4=2,0,964,969;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaG/aaT|K417N|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	22882	.	T	G	34196.0	PASS	AF=0.795763;DP=1180;DP4=7,2,635,531;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N440K|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	22992	.	G	A	33850.0	PASS	AF=0.923535;DP=1007;DP4=0,0,465,538;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S477N|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	22995	.	C	A	36099.0	PASS	AF=0.975952;DP=998;DP4=0,0,470,528;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aAa|T478K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	23013	.	A	C	34866.0	PASS	AF=0.899152;DP=1061;DP4=7,7,493,550;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gCa|E484A|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	23040	.	A	G	33790.0	PASS	AF=0.894277;DP=1031;DP4=2,4,479,544;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q493R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23055	.	A	G	33032.0	PASS	AF=0.907646;DP=1007;DP4=0,2,475,527;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q498R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23063	.	A	T	33942.0	PASS	AF=0.947040;DP=963;DP4=0,0,464,496;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Tat|N501Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	23075	.	T	C	32040.0	PASS	AF=0.894527;DP=1005;DP4=5,1,495,501;SB=9;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y505H|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	23403	.	A	G	9001.0	PASS	AF=0.950000;DP=260;DP4=0,0,123,137;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D614G|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23525	.	C	T	8188.0	PASS	AF=0.924370;DP=238;DP4=0,0,115,122;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H655Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	23599	.	T	G	38741.0	PASS	AF=0.922603;DP=1137;DP4=2,2,599,528;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N679K|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	23604	.	C	A	36017.0	PASS	AF=0.886282;DP=1108;DP4=0,0,586,520;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cAt|P681H|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	23781	.	T	C	21116.0	PASS	AF=0.887195;DP=656;DP4=2,1,316,335;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M740T|1273|S|protein_coding|CODING|GU280_gp02|1|C)
+NC_045512	23854	.	C	A	16899.0	PASS	AF=0.921260;DP=508;DP4=3,4,238,262;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaC/aaA|N764K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	23948	.	G	T	18143.0	PASS	AF=0.890311;DP=547;DP4=2,1,265,273;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Tat|D796Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	24424	.	A	T	41776.0	PASS	AF=0.859435;DP=1309;DP4=1,17,665,626;SB=42;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caA/caT|Q954H|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	24469	.	T	A	47759.0	PASS	AF=0.940331;DP=1391;DP4=5,1,696,688;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaA|N969K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512	24821	.	G	T	49314.0	PASS	AF=0.656224;DP=2362;DP4=332,304,911,808;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Tca|A1087S|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	24966	.	A	G	26912.0	PASS	AF=0.887707;DP=846;DP4=2,8,377,455;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aGc|N1135S|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512	25000	.	C	T	27316.0	PASS	AF=0.939009;DP=787;DP4=0,1,369,415;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D1146|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512	25584	.	C	T	31496.0	PASS	AF=0.852912;DP=1013;DP4=0,21,586,405;SB=80;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T64|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
+NC_045512	26060	.	C	T	38253.0	PASS	AF=0.959925;DP=1073;DP4=1,0,533,538;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T223I|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
+NC_045512	26195	.	C	T	11120.0	PASS	AF=0.846995;DP=366;DP4=0,1,185,176;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T268M|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
+NC_045512	26270	.	C	T	13678.0	PASS	AF=0.936387;DP=393;DP4=0,0,200,192;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T9I|75|E|protein_coding|CODING|GU280_gp04|1|T)
+NC_045512	26408	.	C	T	31278.0	PASS	AF=0.922118;DP=963;DP4=1,1,481,455;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tTt|S55F|75|E|protein_coding|CODING|GU280_gp04|1|T)
+NC_045512	26577	.	C	G	18200.0	PASS	AF=0.907407;DP=540;DP4=1,0,258,278;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q19E|222|M|protein_coding|CODING|GU280_gp05|1|G)
+NC_045512	26709	.	G	A	42976.0	PASS	AF=0.956703;DP=1201;DP4=0,0,635,564;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A63T|222|M|protein_coding|CODING|GU280_gp05|1|A)
+NC_045512	26801	.	C	T	39142.0	PASS	AF=0.947462;DP=1123;DP4=0,0,556,566;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L93|222|M|protein_coding|CODING|GU280_gp05|1|T)
+NC_045512	26858	.	C	T	38024.0	PASS	AF=0.947761;DP=1072;DP4=1,0,489,576;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F112|222|M|protein_coding|CODING|GU280_gp05|1|T)
+NC_045512	27259	.	A	C	47862.0	PASS	AF=0.806818;DP=1760;DP4=100,107,630,913;SB=13;EFF=SYNONYMOUS_CODING(LOW|SILENT|Agg/Cgg|R20|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
+NC_045512	27382	.	G	C	13532.0	PASS	AF=0.905707;DP=403;DP4=0,0,202,196;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Cat|D61H|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
+NC_045512	27383	.	A	T	12580.0	PASS	AF=0.854220;DP=391;DP4=1,1,200,187;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gTt|D61V|61|ORF6|protein_coding|CODING|GU280_gp06|1|T)
+NC_045512	27384	.	T	C	12931.0	PASS	AF=0.870558;DP=394;DP4=4,0,200,190;SB=9;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D61|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
+NC_045512	27481	.	C	A	15550.0	PASS	AF=0.961009;DP=436;DP4=0,0,227,208;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Att|L30I|121|ORF7a|protein_coding|CODING|GU280_gp07|1|A)
+NC_045512	27549	.	C	T	36336.0	PASS	AF=0.892040;DP=1093;DP4=0,0,540,542;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N52|121|ORF7a|protein_coding|CODING|GU280_gp07|1|T)
+NC_045512	27807	.	C	T	11735.0	PASS	AF=0.923754;DP=341;DP4=0,0,173,164;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L18|43|ORF7b|protein_coding|CODING|GU280_gp08|1|T)
+NC_045512	28271	.	A	T	49314.0	PASS	AF=0.924107;DP=1568;DP4=3,14,792,754;SB=21
+NC_045512	28307	.	G	A	46522.0	PASS	AF=0.822322;DP=1559;DP4=2,0,766,752;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A12T|419|N|protein_coding|CODING|GU280_gp10|1|A)
+NC_045512	28311	.	C	T	43345.0	PASS	AF=0.783117;DP=1540;DP4=3,29,764,739;SB=56;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cTc|P13L|419|N|protein_coding|CODING|GU280_gp10|1|T)
+NC_045512	28361	.	GGAGAACGCA	G	35243.0	PASS	AF=0.759166;DP=1391;DP4=263,96,409,647;HRUN=2;SB=293;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggagaacgcagt/ggt|GERS30G|419|N|protein_coding|CODING|GU280_gp10|1|G|INFO_REALIGN_3_PRIME)
+NC_045512	28483	.	A	G	9278.0	PASS	AF=0.504092;DP=611;DP4=0,6,165,174;SB=15;EFF=SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q70|419|N|protein_coding|CODING|GU280_gp10|1|G)
+NC_045512	28483	.	A	T	6655.0	PASS	AF=0.386252;DP=611;DP4=0,6,130,136;SB=15;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caA/caT|Q70H|419|N|protein_coding|CODING|GU280_gp10|1|T)
+NC_045512	28657	.	C	T	49314.0	PASS	AF=0.912524;DP=1589;DP4=7,8,902,653;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D128|419|N|protein_coding|CODING|GU280_gp10|1|T)
+NC_045512	28881	.	G	A	21838.0	PASS	AF=0.978003;DP=591;DP4=0,0,297,294;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aAg|R203K|419|N|protein_coding|CODING|GU280_gp10|1|A)
+NC_045512	28882	.	G	A	20034.0	PASS	AF=0.919932;DP=587;DP4=0,0,294,292;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R203|419|N|protein_coding|CODING|GU280_gp10|1|A)
+NC_045512	28883	.	G	C	20532.0	PASS	AF=0.931667;DP=600;DP4=0,0,300,297;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gga/Cga|G204R|419|N|protein_coding|CODING|GU280_gp10|1|C)
+NC_045512	29510	.	A	C	49314.0	PASS	AF=0.902601;DP=1653;DP4=2,1,735,914;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agt/Cgt|S413R|419|N|protein_coding|CODING|GU280_gp10|1|C)
+NC_045512	29733	.	CGAGGCCACGCGGAGTACGATCGAGTG	C	27833.0	PASS	AF=0.994203;DP=690;DP4=128,105,232,454;HRUN=1;SB=77;INDEL
Binary file test-data/example.png has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/virheat.xml	Wed May 15 13:37:49 2024 +0000
@@ -0,0 +1,185 @@
+<tool id="virheat" name="VirHEAT: visualize allele frequencies"
+      version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"
+      profile="@PROFILE@">
+    <description>
+        from VCFs as a heatmap and map mutations to respective genes
+    </description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="biotools"/>
+    <expand macro="requirements"/>
+    <expand macro="version"/>
+    <command detect_errors="exit_code"><![CDATA[
+#import re
+#set $vcfs_dir = 'vcfs_dir/'
+mkdir -p $vcfs_dir &&
+mkdir -p ./output_dir &&
+#set $outfile = 'tmp_output.' + str($advanced.output_type)
+#for $input_file in $sinputs
+    #set $file_path = $vcfs_dir + re.sub('[^\s\w\-\\.]', '_', str($input_file.element_identifier))
+    ln -s '$input_file' '$file_path' &&
+#end for
+#set $output_dir = 'output_dir/'
+virheat
+    '$vcfs_dir'
+    '$output_dir'
+    --name '$outfile'
+    #if $genome_data.choice == 'length'
+        -l $genome_data.genome_length
+    #else
+        -g '$genome_data.gff3_file'
+    #end if
+    #if $varfreq
+        -t $varfreq
+    #end if
+    $delete
+    -n $delete_n
+    #if $zoom.choice == 'yes'
+        -z $zoom.zoom_start $zoom.zoom_stop
+    #end if
+    $sort
+    --min-cov $min_cov
+    ]]></command>
+    <inputs>
+        <param name="sinputs" type="data_collection" format="vcf" label="Variant lists data" help="Select at least two datasets (or a dataset collection) with variant lists. Datasets are expected to represent individual samples and dataset names will be used as sample identifiers." multiple="true" collection_type="list" />
+        <conditional name="genome_data">
+            <param name="choice" type="select"
+                   label="Data for genomic annotation">
+                <option value="length">length of the genome</option>
+                <option value="gff3">gff3 file</option>
+            </param>
+            <when value="length">
+                <param name="genome_length" argument="-l" type="integer" min="0" label="Genome length"/>
+            </when>
+            <when value="gff3">
+                <param name="gff3_file" argument="-g" type="data" format="gff3" label="GFF3 file" help="GFF3 file contains annotations for the genome and allows to display genes harboring a mutation. Ensure that the file follows the GFF3 specification."/>
+            </when>
+        </conditional>
+        <param name="varfreq" argument="-t" type="float" min="0" max="1" value="0" optional="true" label="Variant Frequency Threshold" help="Only plot variants with an intrasample frequency above this threshold in at least one sample." />
+        <param argument="--delete" type="boolean" truevalue="--delete" falsevalue="--no-delete" checked="true" label="Delete mutations that are present in all samples and their maximum frequency divergence is smaller than 0.5"/>
+        <param name="delete_n" argument="-n" type="integer" min="0" value="0" label="Do not show mutations that occur n times or less"/>
+        <conditional name="zoom">
+            <param name="choice" type="select" label="Restrict the plot to a specific genomic region">
+                <option value="yes">Yes</option>
+                <option value="no">No</option>
+            </param>
+            <when value="yes">
+                <param name="zoom_start" type="integer" label="Start"/>
+                <param name="zoom_stop" type="integer" label="End"/>
+            </when>
+            <when value="no"/>
+        </conditional>
+        <param argument="--sort" type="boolean" truevalue="--sort" falsevalue="--no-sort" checked="false" label="Sort sample names alphanumerically"/>
+        <param argument="--min-cov" type="integer" min="1" max="1000" value="20" label="Display mutations covered at least x time"/>
+        <section name="advanced" title="Image Properties" expanded="true">
+            <param name="output_type" type="select" label="Plot output format" >
+                <option value="pdf" selected="true" >PDF</option>
+                <option value="png" >PNG</option>
+                <option value="svg">SVG</option>
+                <option value="tiff" >TIFF</option>
+                <option value="bmp" >BMP</option>
+                <option value="jpeg" >JPEG</option>
+            </param>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="outfile" format="pdf" from_work_dir="output_dir/tmp_output.*"
+            label="Variant-Frequency Plot on ${on_string}: ${advanced.output_type}">
+            <change_format>
+                <when input="advanced.output_type" value="svg" format="svg" />
+                <when input="advanced.output_type" value="png" format="png" />
+                <when input="advanced.output_type" value="tiff" format="tiff" />
+                <when input="advanced.output_type" value="bmp" format="bmp" />
+                <when input="advanced.output_type" value="jpeg" format="jpg" />
+            </change_format>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <!-- test1: gff3, pdf -->
+            <param name="sinputs" value="day_0.vcf,day_2.vcf,day_4.vcf,day_18.vcf,day_26.vcf,day_32.vcf,day_47.vcf,day_55.vcf,day_60.vcf,day_76.vcf,day_83.vcf,day_85.vcf,day_91.vcf,day_96.vcf,day_100.vcf,day_103.vcf,day_111.vcf"/>
+            <conditional name="genome_data">
+                <param name="choice" value="gff3"/>
+                <param name="gff3_file" value="SARS-CoV-2.gff3"/>
+            </conditional>
+            <conditional name="zoom">
+                <param name="choice" value="yes"/>
+                <param name="zoom_start" value="22599"/>
+                <param name="zoom_stop" value="23278"/>
+            </conditional>
+            <output name="outfile" ftype="pdf">
+                <assert_contents>
+                    <has_text text="day"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <!-- test2: length, svg -->
+            <param name="sinputs" value="day_76.vcf,day_83.vcf,day_91.vcf,day_103.vcf" ftype="vcf" />
+            <conditional name="genome_data">
+                <param name="choice" value="length"/>
+                <param name="genome_length" value="29903"/>
+            </conditional>
+            <conditional name="zoom">
+                <param name="choice" value="yes"/>
+                <param name="zoom_start" value="22599"/>
+                <param name="zoom_stop" value="23278"/>
+            </conditional>
+            <output name="outfile" ftype="svg">
+                <assert_contents>
+                    <has_text text="day"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <!-- test3: gff3, threshold, png, delete, delete-n -->
+            <param name="sinputs" value="day_76.vcf,day_83.vcf,day_91.vcf,day_103.vcf" ftype="vcf" />
+            <param name="varfreq" value="0.1"/>
+            <param name="delete" value="yes"/>
+            <param name="delete_n" value="1"/>
+            <conditional name="genome_data">
+                <param name="choice" value="gff3"/>
+                <param name="gff3_file" value="SARS-CoV-2.gff3"/>
+            </conditional>
+            <conditional name="zoom">
+                <param name="choice" value="no"/>
+            </conditional>
+            <output name="outfile" ftype="png">
+                <assert_contents>
+                    <has_text text="day"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <!-- test4: length, zoom, sort, tiff -->
+            <param name="sinputs" value="day_0.vcf,day_2.vcf,day_4.vcf,day_18.vcf,day_26.vcf,day_32.vcf,day_47.vcf,day_55.vcf,day_60.vcf,day_76.vcf,day_83.vcf,day_85.vcf,day_91.vcf,day_96.vcf,day_100.vcf,day_103.vcf,day_111.vcf"/>
+            <param name="varfreq" value="0.1"/>
+            <param name="delete" value="false"/>
+            <param name="delete_n" value="0"/>
+            <param name="sort" value="true"/>
+            <param name="min_cov" value="25"/>
+            <conditional name="zoom">
+                <param name="choice" value="yes"/>
+                <param name="zoom_start" value="22599"/>
+                <param name="zoom_stop" value="23278"/>
+            </conditional>
+            <section name="advanced">
+                <param name="output_type" value="tiff"/>
+            </section>
+            <conditional name="genome_data">
+                <param name="choice" value="length"/>
+                <param name="genome_length" value="29903"/>
+            </conditional>
+            <output name="outfile">
+                <assert_contents>
+                    <has_text text="day"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+@HELP_HEADER@
+    ]]></help>
+    <expand macro="citations"/>
+</tool>