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sample-12.vcf
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sample-12.vcf
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##fileformat=VCFv4.0
##FILTER=<ID=PASS,Description="All filters passed">
##fileDate=20240114
##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 5 --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 0.0005 --bonf dynamic --no-default-filter --no-default-filter -r NC_045512.2:1-7475 -o /data/jwd05e/main/066/348/66348167/tmp/lofreq2_call_parallel3xcmz_fx/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="Lofreq Allele Frequency; Fraction of variant-supporting bases with q > --min-bq among all bases at the site">
##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_47,Description="Minimum Indel Quality (Phred) 47">
##FILTER=<ID=min_snvqual_73,Description="Minimum SNV Quality (Phred) 73">
##FILTER=<ID=min_indelqual_55,Description="Minimum Indel Quality (Phred) 55">
##contig=<ID=NC_045512.2>
##INFO=<ID=AmpliconBias,Number=0,Type=Flag,Description="Indicates that the AF value of the variant could not be corrected for potential amplicon bias.">
##bcftools_annotateVersion=1.10.2+htslib-1.10.2
##bcftools_annotateCommand=annotate --columns QUAL,INFO --annotations annotations.vcf.gz --mark-sites -AmpliconBias --output-type v --threads 1 input.vcf.gz; Date=Sun Jan 14 22:16:41 2024
##bcftools_annotateCommand=annotate --columns QUAL,INFO --annotations annotations.vcf.gz --mark-sites +AmpliconBias --output-type v --threads 1 input.vcf.gz; Date=Sun Jan 14 22:17:41 2024
##SnpEffVersion="4.5covid19 (build 2020-04-15 22:26), by Pablo Cingolani"
##SnpEffCmd="SnpEff -i vcf -o vcf -formatEff -classic -no-downstream -no-intergenic -no-upstream -stats /data/jwd02f/main/066/348/66348347/outputs/dataset_65b7fc87-8025-44cf-8d33-7cf59de0b914.dat NC_045512.2 /data/dnb09/galaxy_db/files/7/6/4/dataset_76410c3b-51f4-49a0-87e0-50004fc168bd.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_045512.2 241 . C T 150.0 PASS DP=5;AF=0.8;SB=0;DP4=0,0,3,2
NC_045512.2 2556 . A G 6467.0 PASS DP=188;AF=0.925532;SB=0;DP4=0,0,97,91;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q764R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q764R|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q584R|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q584R|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 3037 . C T 225.0 PASS DP=8;AF=0.75;SB=0;DP4=0,0,4,4;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F106|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F106|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 4975 . G A 94.0 PASS DP=1911;AF=0.00471;SB=18;DP4=862,1036,1,10;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V1570|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V1570|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V752|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V752|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 5308 . A G 648.0 PASS DP=597;AF=0.051926;SB=0;DP4=299,264,17,16;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttA/ttG|L1681|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),SYNONYMOUS_CODING(LOW|SILENT|ttA/ttG|L1681|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),SYNONYMOUS_CODING(LOW|SILENT|ttA/ttG|L863|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ttA/ttG|L863|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 5386 . T G 28749.0 PASS DP=857;AF=0.907818;SB=6;DP4=0,3,427,424;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcG|A1707|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcG|A1707|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcG|A889|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcG|A889|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 5743 . G C 124.0 PASS DP=500;AF=0.016;SB=0;DP4=246,245,4,4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E1826D|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E1826D|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E1008D|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E1008D|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 5744 . T C 121.0 PASS DP=498;AF=0.016064;SB=0;DP4=244,245,4,4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y1827H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y1827H|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y1009H|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y1009H|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 5924 . G A 10749.0 PASS DP=322;AF=0.919255;SB=0;DP4=0,0,160,161;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V1887I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V1887I|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V1069I|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V1069I|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 6076 . T C 1414.0 PASS DP=226;AF=0.225664;SB=0;DP4=85,85,28,28;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F1937|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F1937|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F1119|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F1119|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 6512 . AGTT A 253.0 PASS DP=8;AF=0.875;SB=0;DP4=1,0,3,4;INDEL;HRUN=1;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||agttta/ata|SL2083I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||agttta/ata|SL2083I|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||agttta/ata|SL1265I|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||agttta/ata|SL1265I|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 8393 . G A 8417.0 PASS DP=238;AF=0.945378;SB=0;DP4=0,0,122,115;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A2710T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A2710T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A1892T|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A1892T|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 10029 . C T 9530.0 PASS DP=297;AF=0.875421;SB=0;DP4=0,0,148,147;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T3255I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T3255I|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T492I|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T492I|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 10449 . C A 443.0 PASS DP=12;AF=1;SB=0;DP4=0,0,7,5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cAc|P3395H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cAc|P3395H|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cAc|P132H|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cAc|P132H|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 10484 . T G 284.0 PASS DP=45;AF=0.222222;SB=0;DP4=19,16,5,5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Gca|S3407A|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Gca|S3407A|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Gca|S144A|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Gca|S144A|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 10541 . C A 148.0 PASS DP=63;AF=0.095238;SB=0;DP4=29,28,3,3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Aac|H3426N|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Aac|H3426N|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Aac|H163N|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Aac|H163N|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 12285 . A G 106.0 PASS DP=670;AF=0.010448;SB=0;DP4=310,352,3,4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q4007R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q4007R|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q65R|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q65R|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 13195 . T C 32498.0 PASS DP=944;AF=0.934322;SB=0;DP4=1,1,512,430;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtT/gtC|V4310|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|gtT/gtC|V4310|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|gtT/gtC|V57|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|gtT/gtC|V57|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 13791 . A C 114.0 PASS DP=29;AF=0.172414;SB=1;DP4=13,11,2,3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caA/caC|Q4509H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caA/caC|Q117H|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 14408 . C T 24591.0 PASS DP=691;AF=0.949349;SB=0;DP4=0,0,357,333;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P4715L|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P323L|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 15017 . C T 781.0 PASS DP=341;AF=0.096774;SB=0;DP4=162,140,19,18;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A4918V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A526V|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 15240 . C T 18594.0 PASS DP=529;AF=0.931947;SB=0;DP4=0,0,257,272;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N4992|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N600|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 15884 . A G 75.0 PASS DP=2661;AF=0.003006;SB=0;DP4=1241,1405,5,5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q5207R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q815R|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 17572 . G A 11316.0 PASS DP=5897;AF=0.084111;SB=0;DP4=2672,2667,271,275;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A5770T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A446T|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 18530 . TA T 57.0 PASS DP=45;AF=0.044444;SB=0;DP4=21,22,1,1;INDEL;HRUN=3;EFF=FRAME_SHIFT(HIGH||aag/|K6090|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aag/|K165|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 21762 . C T 24686.0 PASS DP=729;AF=0.961591;SB=0;DP4=0,0,365,362;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A67V|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 21764 . ATACATG A 24598.0 PASS DP=709;AF=0.997179;SB=6;DP4=0,2,355,352;INDEL;HRUN=1;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||atacatgtc/atc|IHV68I|1273|S|protein_coding|CODING|GU280_gp02|1|A|INFO_REALIGN_3_PRIME)
NC_045512.2 21846 . C T 20228.0 PASS DP=564;AF=0.948582;SB=0;DP4=0,1,275,288;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T95I|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 22193 . AATT A 364.0 PASS DP=10;AF=1;SB=0;DP4=0,0,6,4;INDEL;HRUN=2;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aattta/ata|NL211I|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 22204 . T TGAGCCAGAA 353.0 PASS DP=10;AF=1;SB=0;DP4=0,0,6,4;INDEL;HRUN=1;EFF=CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||gat/gaGCCAGAAGAt|D215EPED|1273|S|protein_coding|CODING|GU280_gp02|1|TGAGCCAGAA|INFO_REALIGN_3_PRIME)
NC_045512.2 22992 . G A 1673.0 PASS DP=48;AF=0.958333;SB=0;DP4=0,0,25,23;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S477N|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 22995 . C A 1512.0 PASS DP=48;AF=0.854167;SB=0;DP4=0,0,25,23;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aAa|T478K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 23013 . A C 2501.0 PASS DP=68;AF=0.970588;SB=0;DP4=0,0,38,30;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gCa|E484A|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512.2 23040 . A G 3890.0 PASS DP=111;AF=0.936937;SB=0;DP4=0,0,59,51;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q493R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512.2 23048 . G A 4778.0 PASS DP=132;AF=0.954545;SB=0;DP4=0,0,72,60;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G496S|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 23055 . A G 4712.0 PASS DP=135;AF=0.948148;SB=0;DP4=0,0,73,62;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q498R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512.2 23063 . A T 5465.0 PASS DP=152;AF=0.953947;SB=0;DP4=0,0,81,71;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Tat|N501Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 23075 . T C 5263.0 PASS DP=152;AF=0.940789;SB=0;DP4=0,0,80,72;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y505H|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512.2 23202 . C A 8294.0 PASS DP=233;AF=0.944206;SB=0;DP4=0,0,115,118;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aAa|T547K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 24424 . A T 4826.0 PASS DP=131;AF=0.969466;SB=0;DP4=0,0,65,66;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caA/caT|Q954H|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 24469 . T A 48621.0 PASS DP=1405;AF=0.932384;SB=0;DP4=2,1,740,660;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaA|N969K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 24503 . C T 28469.0 PASS DP=1943;AF=0.471951;SB=0;DP4=497,464,502,475;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L981F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 25000 . C T 158.0 PASS DP=6;AF=1;SB=0;DP4=0,0,3,3;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D1146|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 25584 . C T 17820.0 PASS DP=531;AF=0.898305;SB=0;DP4=0,0,266,261;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T64|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
NC_045512.2 26126 . A G 140.0 PASS DP=3705;AF=0.003779;SB=0;DP4=1843,1841,8,8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q245R|275|ORF3a|protein_coding|CODING|GU280_gp03|1|G)
NC_045512.2 26270 . C T 49314.0 PASS DP=3496;AF=0.884439;SB=0;DP4=103,113,1558,1714;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T9I|75|E|protein_coding|CODING|GU280_gp04|1|T)
NC_045512.2 26325 . G A 118.0 PASS DP=2367;AF=0.004647;SB=33;DP4=1061,1290,0,13;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttG/ttA|L27|75|E|protein_coding|CODING|GU280_gp04|1|A)
NC_045512.2 26530 . A G 338.0 PASS DP=10;AF=0.9;SB=0;DP4=0,0,5,5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D3G|222|M|protein_coding|CODING|GU280_gp05|1|G)
NC_045512.2 27259 . A C 1244.0 PASS DP=38;AF=0.894737;SB=0;DP4=0,0,20,18;EFF=SYNONYMOUS_CODING(LOW|SILENT|Agg/Cgg|R20|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
NC_045512.2 27807 . C T 40609.0 PASS DP=1139;AF=0.954346;SB=0;DP4=0,0,570,567;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L18|43|ORF7b|protein_coding|CODING|GU280_gp08|1|T)
NC_045512.2 28214 . CT C 56.0 PASS DP=5410;AF=0.001109;SB=0;DP4=2720,2730,3,3;INDEL;HRUN=5;EFF=FRAME_SHIFT(HIGH||tta/|L109|121|ORF8|protein_coding|CODING|GU280_gp09|1|C|INFO_REALIGN_3_PRIME);LOF=(ORF8|GU280_gp09|1|1.00)
NC_045512.2 28254 . A C 287.0 PASS DP=6112;AF=0.005072;SB=0;DP4=3029,3036,19,20;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Ctc|I121L|121|ORF8|protein_coding|CODING|GU280_gp09|1|C)
NC_045512.2 28265 . C T 103.0 PASS DP=8103;AF=0.001975;SB=36;DP4=4026,4047,18,2
NC_045512.2 28271 . A T 49314.0 PASS DP=8604;AF=0.953045;SB=9;DP4=1,6,4293,4295
NC_045512.2 28311 . C T 49314.0 PASS DP=8554;AF=0.873977;SB=17;DP4=5,17,4156,4338;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cTc|P13L|419|N|protein_coding|CODING|GU280_gp10|1|T)
NC_045512.2 28361 . GGAGAACGCA G 49314.0 PASS DP=7473;AF=0.825238;SB=2;DP4=621,689,2977,3190;INDEL;HRUN=2;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggagaacgcagt/ggt|GERS30G|419|N|protein_coding|CODING|GU280_gp10|1|G|INFO_REALIGN_3_PRIME)
NC_045512.2 28363 . AGAACGCAGT A 431.0 PASS DP=6305;AF=0.006979;SB=120;DP4=3030,3257,43,1;INDEL;HRUN=1;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gaacgcagtggg/ggg|ERSG31G|419|N|protein_coding|CODING|GU280_gp10|1|A|INFO_REALIGN_3_PRIME)
NC_045512.2 28383 . CA C 81.0 PASS DP=7200;AF=0.001111;SB=0;DP4=3515,3698,4,4;INDEL;HRUN=4;EFF=FRAME_SHIFT(HIGH||aaa/|K38|419|N|protein_coding|CODING|GU280_gp10|1|C|INFO_REALIGN_3_PRIME);LOF=(N|GU280_gp10|1|1.00)
NC_045512.2 28388 . C T 82.0 PASS DP=7347;AF=0.001769;SB=24;DP4=3557,3766,15,3;EFF=STOP_GAINED(HIGH|NONSENSE|Caa/Taa|Q39*|419|N|protein_coding|CODING|GU280_gp10|1|T)
NC_045512.2 28776 . CA C 114.0 PASS DP=4033;AF=0.002232;SB=0;DP4=1981,2046,4,5;INDEL;HRUN=4;EFF=FRAME_SHIFT(HIGH||aaa/|K169|419|N|protein_coding|CODING|GU280_gp10|1|C|INFO_REALIGN_3_PRIME);LOF=(N|GU280_gp10|1|1.00)
NC_045512.2 28845 . G A 180.0 PASS DP=2283;AF=0.007008;SB=1;DP4=1084,1179,8,11;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R191H|419|N|protein_coding|CODING|GU280_gp10|1|A)
NC_045512.2 28881 . G A 49314.0 PASS DP=1608;AF=0.93408;SB=0;DP4=1,1,784,819;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aAg|R203K|419|N|protein_coding|CODING|GU280_gp10|1|A)
NC_045512.2 28882 . G A 49314.0 PASS DP=1601;AF=0.891318;SB=2;DP4=1,3,779,804;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R203|419|N|protein_coding|CODING|GU280_gp10|1|A)
NC_045512.2 28883 . G C 49314.0 PASS DP=1603;AF=0.928259;SB=0;DP4=1,2,780,819;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gga/Cga|G204R|419|N|protein_coding|CODING|GU280_gp10|1|C)
NC_045512.2 28969 . CA C 114.0 PASS DP=1371;AF=0.005106;SB=0;DP4=681,687,3,4;INDEL;HRUN=4;EFF=FRAME_SHIFT(HIGH||atg/|M234|419|N|protein_coding|CODING|GU280_gp10|1|C|INFO_REALIGN_3_PRIME);LOF=(N|GU280_gp10|1|1.00)
NC_045512.2 28981 . T G 109.0 PASS DP=1435;AF=0.006272;SB=450;DP4=570,721,137,0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggT/ggG|G236|419|N|protein_coding|CODING|GU280_gp10|1|G)
NC_045512.2 29053 . A G 112.0 PASS DP=1408;AF=0.007102;SB=1;DP4=688,703,7,6;EFF=SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q260|419|N|protein_coding|CODING|GU280_gp10|1|G)