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sample-04.vcf
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sample-04.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/066/348/66348159/tmp/lofreq2_call_parallelg2b1i656/0.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_69,Description="Minimum SNV Quality (Phred) 69">
##FILTER=<ID=min_indelqual_53,Description="Minimum Indel Quality (Phred) 53">
##FILTER=<ID=min_snvqual_76,Description="Minimum SNV Quality (Phred) 76">
##FILTER=<ID=min_indelqual_59,Description="Minimum Indel Quality (Phred) 59">
##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 20:37:07 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 20:41:19 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/jwd05e/main/066/348/66348339/outputs/dataset_c9bf8f2a-6a14-417e-8a98-92ed8f219848.dat NC_045512.2 /data/dnb09/galaxy_db/files/4/2/c/dataset_42c6a953-bed7-4fa9-897a-0edfc4726561.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 16854.0 PASS DP=506;AF=0.913043;SB=0;DP4=1,1,250,252
NC_045512.2 443 . GT G 158.0 PASS DP=1275;AF=0.007059;SB=0;DP4=651,611,5,4;INDEL;HRUN=4;EFF=FRAME_SHIFT(HIGH||ttg/|L61|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L61|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L61|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L61|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 443 . GTT G 61.0 PASS DP=1275;AF=0.003137;SB=0;DP4=651,611,2,2;INDEL;HRUN=4;EFF=FRAME_SHIFT(HIGH||ttg/|L61|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L61|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L61|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L61|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 507 . ATGGTCATGTTATGGT A 159.0 PASS DP=1673;AF=0.00538;SB=0;DP4=831,834,4,5;INDEL;HRUN=1;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggtcatgttatggttgag/gag|GHVMVE82E|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggtcatgttatggttgag/gag|GHVMVE82E|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggtcatgttatggttgag/gag|GHVMVE82E|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggtcatgttatggttgag/gag|GHVMVE82E|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A|INFO_REALIGN_3_PRIME)
NC_045512.2 509 . GGTCATGTTATGGTT G 473.0 PASS DP=1661;AF=0.013847;SB=0;DP4=811,819,12,11;INDEL;HRUN=2;EFF=FRAME_SHIFT(HIGH||ggtcatgttatggttgag/|GHVMVE82|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ggtcatgttatggttgag/|GHVMVE82|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ggtcatgttatggttgag/|GHVMVE82|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ggtcatgttatggttgag/|GHVMVE82|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 509 . GGTCATGTTA G 136.0 PASS DP=1661;AF=0.004816;SB=0;DP4=811,819,4,4;INDEL;HRUN=2;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggtcatgttatg/gtg|GHVM82V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggtcatgttatg/gtg|GHVM82V|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggtcatgttatg/gtg|GHVM82V|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggtcatgttatg/gtg|GHVM82V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G)
NC_045512.2 509 . GGTCATGTT G 60.0 PASS DP=1661;AF=0.002408;SB=0;DP4=811,819,2,2;INDEL;HRUN=2;EFF=FRAME_SHIFT(HIGH||ggtcatgtt/|GHV82|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),FRAME_SHIFT(HIGH||ggtcatgtt/|GHV82|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON),FRAME_SHIFT(HIGH||ggtcatgtt/|GHV82|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON),FRAME_SHIFT(HIGH||ggtcatgtt/|GHV82|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 514 . TGTTATG T 60.0 PASS DP=1675;AF=0.002388;SB=0;DP4=832,839,2,2;INDEL;HRUN=1;EFF=CODON_DELETION(MODERATE||atggtt/|MV85|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),CODON_DELETION(MODERATE||atggtt/|MV85|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),CODON_DELETION(MODERATE||atggtt/|MV85|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),CODON_DELETION(MODERATE||atggtt/|MV85|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME)
NC_045512.2 515 . GTTATGGTT G 95.0 PASS DP=1669;AF=0.003595;SB=0;DP4=831,838,3,3;INDEL;HRUN=2;EFF=FRAME_SHIFT(HIGH||gttatggtt/|VMV84|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),FRAME_SHIFT(HIGH||gttatggtt/|VMV84|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON),FRAME_SHIFT(HIGH||gttatggtt/|VMV84|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON),FRAME_SHIFT(HIGH||gttatggtt/|VMV84|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 517 . TATG T 60.0 PASS DP=1657;AF=0.002414;SB=0;DP4=822,831,2,2;INDEL;HRUN=1;EFF=CODON_DELETION(MODERATE||atg/|M85|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),CODON_DELETION(MODERATE||atg/|M85|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON),CODON_DELETION(MODERATE||atg/|M85|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON),CODON_DELETION(MODERATE||atg/|M85|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T)
NC_045512.2 685 . AAAGTCATTT A 64.0 PASS DP=1263;AF=0.003167;SB=0;DP4=630,657,2,2;INDEL;HRUN=3;EFF=CODON_DELETION(MODERATE||aagtcattt/|KSF141|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),CODON_DELETION(MODERATE||aagtcattt/|KSF141|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON),CODON_DELETION(MODERATE||aagtcattt/|KSF141|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON),CODON_DELETION(MODERATE||aagtcattt/|KSF141|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A)
NC_045512.2 2113 . C T 79.0 PASS DP=1512;AF=0.00463;SB=0;DP4=726,772,5,5;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I616|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I616|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I436|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I436|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 2330 . T A 203.0 PASS DP=909;AF=0.014301;SB=2;DP4=426,451,6,9;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Agt|C689S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Agt|C689S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Agt|C509S|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Agt|C509S|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 2832 . A G 24107.0 PASS DP=716;AF=0.913408;SB=0;DP4=0,1,329,383;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K856R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K856R|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K38R|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K38R|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 3037 . C T 14627.0 PASS DP=425;AF=0.910588;SB=3;DP4=1,0,207,212;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 3862 . T A 79.0 PASS DP=132;AF=0.030303;SB=0;DP4=64,64,2,2;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtT/gtA|V1199|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),SYNONYMOUS_CODING(LOW|SILENT|gtT/gtA|V1199|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),SYNONYMOUS_CODING(LOW|SILENT|gtT/gtA|V381|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|gtT/gtA|V381|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 4440 . GTGTGGAAACTAAAGCCATAGTTTCAACTA G 78.0 PASS DP=593;AF=0.006745;SB=0;DP4=297,296,2,2;INDEL;HRUN=1;EFF=FRAME_SHIFT(HIGH||gtggaaactaaagccatagtttcaactata/|VETKAIVSTI1393|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||gtggaaactaaagccatagtttcaactata/|VETKAIVSTI1393|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||gtggaaactaaagccatagtttcaactata/|VETKAIVSTI575|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||gtggaaactaaagccatagtttcaactata/|VETKAIVSTI575|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14)
NC_045512.2 4794 . C A 92.0 PASS DP=1023;AF=0.006843;SB=28;DP4=500,491,5,22;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tAc|S1510Y|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tAc|S1510Y|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tAc|S692Y|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tAc|S692Y|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 5386 . T G 34494.0 PASS DP=1077;AF=0.862581;SB=6;DP4=0,3,530,540;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 227.0 PASS DP=1059;AF=0.015109;SB=1;DP4=520,513,11,13;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 230.0 PASS DP=1058;AF=0.015123;SB=3;DP4=514,515,15,10;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 6512 . AGTT A 20035.0 PASS DP=569;AF=0.996485;SB=3;DP4=0,1,297,270;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 6653 . GTTAATAGTGTCCCTTGGGATACTATAGCTA G 71.0 PASS DP=910;AF=0.004396;SB=0;DP4=458,450,2,2;INDEL;HRUN=2;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gttaatagtgtcccttgggatactatagctaat/gat|VNSVPWDTIAN2130D|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gttaatagtgtcccttgggatactatagctaat/gat|VNSVPWDTIAN2130D|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gttaatagtgtcccttgggatactatagctaat/gat|VNSVPWDTIAN1312D|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gttaatagtgtcccttgggatactatagctaat/gat|VNSVPWDTIAN1312D|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 6655 . TAATAGTGTCCCTTGGGATACTATAGCTA T 92.0 PASS DP=909;AF=0.005501;SB=1;DP4=457,449,2,3;INDEL;HRUN=2;EFF=FRAME_SHIFT(HIGH||aatagtgtcccttgggatactatagctaat/|NSVPWDTIAN2131|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aatagtgtcccttgggatactatagctaat/|NSVPWDTIAN2131|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aatagtgtcccttgggatactatagctaat/|NSVPWDTIAN1313|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aatagtgtcccttgggatactatagctaat/|NSVPWDTIAN1313|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14)
NC_045512.2 6696 . C CT 281.0 PASS DP=839;AF=0.016687;SB=0;DP4=416,415,7,7;INDEL;HRUN=4;EFF=FRAME_SHIFT(HIGH||ctt/Tctt|L2146S?|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|CT|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ctt/Tctt|L2146S?|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|CT|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ctt/Tctt|L1328S?|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|CT|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ctt/Tctt|L1328S?|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|CT|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14)
NC_045512.2 8393 . G A 27333.0 PASS DP=787;AF=0.928844;SB=5;DP4=3,0,436,347;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 9125 . TA T 71.0 PASS DP=857;AF=0.004667;SB=0;DP4=426,427,2,2;INDEL;HRUN=1;EFF=FRAME_SHIFT(HIGH||tat/|Y2954|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),FRAME_SHIFT(HIGH||tat/|Y2954|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),FRAME_SHIFT(HIGH||tat/|Y191|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),FRAME_SHIFT(HIGH||tat/|Y191|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.14)
NC_045512.2 10029 . C T 29085.0 PASS DP=924;AF=0.856061;SB=0;DP4=3,2,456,456;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 33519.0 PASS DP=1046;AF=0.868069;SB=1;DP4=2,4,494,539;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 115.0 PASS DP=734;AF=0.010899;SB=0;DP4=384,338,6,5;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 11282 . AGTTTGTCTG A 35550.0 PASS DP=1018;AF=0.920432;SB=11;DP4=46,35,430,507;INDEL;HRUN=1;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ttgtctggtttt/ttt|LSGF3674F|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ttgtctggtttt/ttt|LSGF3674F|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ttgtctggtttt/ttt|LSGF105F|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ttgtctggtttt/ttt|LSGF105F|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME)
NC_045512.2 11481 . CTGTTACTTCTAACTACTCAGGTGTAGTTACAACTGTCATGTTTTTGGCCAGAGGTAT C 59.0 PASS DP=1718;AF=0.002328;SB=0;DP4=857,867,2,2;INDEL;HRUN=1;EFF=CODON_DELETION(MODERATE||acttctaactactcaggtgtagttacaactgtcatgtttttggccagaggtattgtt/|TSNYSGVVTTVMFLARGIV3741|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),CODON_DELETION(MODERATE||acttctaactactcaggtgtagttacaactgtcatgtttttggccagaggtattgtt/|TSNYSGVVTTVMFLARGIV3741|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),CODON_DELETION(MODERATE||acttctaactactcaggtgtagttacaactgtcatgtttttggccagaggtattgtt/|TSNYSGVVTTVMFLARGIV172|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),CODON_DELETION(MODERATE||acttctaactactcaggtgtagttacaactgtcatgtttttggccagaggtattgtt/|TSNYSGVVTTVMFLARGIV172|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME)
NC_045512.2 11537 . A G 49314.0 PASS DP=1665;AF=0.878078;SB=0;DP4=1,1,813,840;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Gtt|I3758V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Gtt|I3758V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Gtt|I189V|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Gtt|I189V|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 11636 . ACTT A 64.0 PASS DP=954;AF=0.004193;SB=0;DP4=428,526,2,2;INDEL;HRUN=1;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||acttgt/agt|TC3791S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||acttgt/agt|TC3791S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||acttgt/agt|TC222S|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||acttgt/agt|TC222S|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 13195 . T C 49314.0 PASS DP=1565;AF=0.89393;SB=1;DP4=4,2,831,720;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 13459 . GT G 67.0 PASS DP=1271;AF=0.003934;SB=0;DP4=572,715,2,3;INDEL;HRUN=5;EFF=FRAME_SHIFT(HIGH||tta/|L4400|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tta/|L4400|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tta/|L8|12|ORF1ab|protein_coding|CODING|YP_009725312.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tta/|L8|931|ORF1ab|protein_coding|CODING|YP_009725307.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 13461 . TTTTA T 64.0 PASS DP=1271;AF=0.003147;SB=0;DP4=563,704,2,2;INDEL;HRUN=5;EFF=FRAME_SHIFT(HIGH||ttttta/|FL4399|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),FRAME_SHIFT(HIGH||ttttta/|FL4399|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),FRAME_SHIFT(HIGH||ttttta/|FL7|12|ORF1ab|protein_coding|CODING|YP_009725312.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),FRAME_SHIFT(HIGH||ttttta/|FL7|931|ORF1ab|protein_coding|CODING|YP_009725307.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 14408 . C T 28174.0 PASS DP=847;AF=0.910272;SB=6;DP4=0,2,426,411;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 15173 . C A 102.0 PASS DP=815;AF=0.008589;SB=272;DP4=423,309,0,79;EFF=STOP_GAINED(HIGH|NONSENSE|tCa/tAa|S4970*|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),STOP_GAINED(HIGH|NONSENSE|tCa/tAa|S578*|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 15240 . C T 27849.0 PASS DP=797;AF=0.927227;SB=3;DP4=1,0,371,423;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 15983 . TA T 59.0 PASS DP=1133;AF=0.00353;SB=0;DP4=588,541,2,2;INDEL;HRUN=5;EFF=FRAME_SHIFT(HIGH||aca/|T5242|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aca/|T850|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 16935 . G T 77.0 PASS DP=1613;AF=0.00434;SB=1;DP4=799,801,6,4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atG/atT|M5557I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atG/atT|M233I|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 17825 . C T 26141.0 PASS DP=763;AF=0.906946;SB=0;DP4=1,1,380,374;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T5854I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T530I|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 18163 . A G 7301.0 PASS DP=226;AF=0.893805;SB=0;DP4=0,1,113,112;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I5967V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I42V|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 20296 . AAATT A 67.0 PASS DP=988;AF=0.004049;SB=0;DP4=492,495,2,2;INDEL;HRUN=3;EFF=FRAME_SHIFT(HIGH||aaatta/|KL6678|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaatta/|KL226|345|ORF1ab|protein_coding|CODING|YP_009725310.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 20445 . TA T 60.0 PASS DP=995;AF=0.00402;SB=0;DP4=489,500,2,2;INDEL;HRUN=5;EFF=FRAME_SHIFT(HIGH||aac/|N6729|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aac/|N277|345|ORF1ab|protein_coding|CODING|YP_009725310.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 21034 . C T 26508.0 PASS DP=790;AF=0.888608;SB=0;DP4=0,0,396,384;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctc/Ttc|L6924F|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctc/Ttc|L126F|297|ORF1ab|protein_coding|CODING|YP_009725311.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 21101 . G GT 155.0 PASS DP=729;AF=0.015089;SB=1;DP4=371,347,5,6;INDEL;HRUN=6;EFF=FRAME_SHIFT(HIGH||ttc/ttTc|F6948F?|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|GT|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttc/ttTc|F150F?|297|ORF1ab|protein_coding|CODING|YP_009725311.1|1|GT|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.04)
NC_045512.2 21137 . A G 82.0 PASS DP=741;AF=0.008097;SB=0;DP4=362,366,3,3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K6958R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K160R|297|ORF1ab|protein_coding|CODING|YP_009725311.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 21762 . C T 20845.0 PASS DP=648;AF=0.91821;SB=0;DP4=0,1,321,325;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A67V|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 21764 . ATACATG A 21400.0 PASS DP=626;AF=0.995208;SB=0;DP4=1,2,312,311;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 22408.0 PASS DP=621;AF=0.951691;SB=0;DP4=0,1,299,321;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T95I|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 21986 . GGTGTTTATT G 13943.0 PASS DP=439;AF=0.986333;SB=0;DP4=11,12,222,211;INDEL;HRUN=3;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggtgtttattac/gac|GVYY142D|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512.2 22193 . AATT A 13617.0 PASS DP=458;AF=0.923581;SB=24;DP4=78,133,208,215;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 9573.0 PASS DP=385;AF=0.72987;SB=0;DP4=38,45,128,153;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 22204 . T TGAGCCAGTA 71.0 PASS DP=385;AF=0.01039;SB=12;DP4=38,45,4,0;INDEL;HRUN=1;EFF=CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||gat/gaGCCAGTAGAt|D215EPVD|1273|S|protein_coding|CODING|GU280_gp02|1|TGAGCCAGTA|INFO_REALIGN_3_PRIME)
NC_045512.2 22578 . G A 32390.0 PASS DP=920;AF=0.944565;SB=0;DP4=0,0,463,452;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G339D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 22673 . T C 16172.0 PASS DP=483;AF=0.900621;SB=7;DP4=2,0,193,283;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tcc/Ccc|S371P|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512.2 22674 . C T 15572.0 PASS DP=483;AF=0.873706;SB=0;DP4=0,0,196,280;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S371F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 22679 . T C 16856.0 PASS DP=511;AF=0.886497;SB=11;DP4=3,0,208,297;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Cca|S373P|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512.2 22686 . C T 17918.0 PASS DP=515;AF=0.920388;SB=3;DP4=1,0,210,304;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S375F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 22992 . G A 6583.0 PASS DP=203;AF=0.901478;SB=0;DP4=0,0,105,97;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S477N|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 22995 . C A 7019.0 PASS DP=213;AF=0.910798;SB=0;DP4=0,0,110,103;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aAa|T478K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 23013 . A C 10718.0 PASS DP=313;AF=0.910543;SB=0;DP4=0,0,168,145;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gCa|E484A|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512.2 23040 . A G 12315.0 PASS DP=376;AF=0.880319;SB=0;DP4=2,1,191,182;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q493R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512.2 23048 . G A 15700.0 PASS DP=440;AF=0.945455;SB=0;DP4=0,0,225,214;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G496S|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 23055 . A G 13956.0 PASS DP=452;AF=0.845133;SB=0;DP4=0,0,228,218;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q498R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512.2 23063 . A T 19708.0 PASS DP=556;AF=0.953237;SB=0;DP4=0,0,293,263;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Tat|N501Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 23075 . T C 17361.0 PASS DP=563;AF=0.845471;SB=12;DP4=5,0,286,271;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y505H|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512.2 23202 . C A 29018.0 PASS DP=831;AF=0.922984;SB=0;DP4=0,1,402,421;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aAa|T547K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 23403 . A G 49314.0 PASS DP=1784;AF=0.867713;SB=3;DP4=4,2,875,895;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D614G|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512.2 23525 . C T 49314.0 PASS DP=1502;AF=0.913449;SB=0;DP4=1,1,706,790;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H655Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 23540 . T C 80.0 PASS DP=1413;AF=0.004954;SB=2;DP4=647,753,6,4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tat/Cat|Y660H|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512.2 23599 . T G 24616.0 PASS DP=734;AF=0.916894;SB=1;DP4=3,2,326,403;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N679K|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512.2 23604 . C A 20646.0 PASS DP=595;AF=0.934454;SB=3;DP4=1,0,258,335;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cAt|P681H|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 23948 . G T 15732.0 PASS DP=478;AF=0.868201;SB=0;DP4=0,0,251,214;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Tat|D796Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 24130 . C A 16664.0 PASS DP=506;AF=0.87747;SB=2;DP4=0,2,231,270;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaC/aaA|N856K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 24424 . A T 27727.0 PASS DP=818;AF=0.914425;SB=0;DP4=1,2,407,406;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caA/caT|Q954H|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 24469 . T A 43387.0 PASS DP=1249;AF=0.928743;SB=0;DP4=3,3,628,611;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaA|N969K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 24503 . C T 44381.0 PASS DP=1280;AF=0.923437;SB=0;DP4=1,1,623,650;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L981F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 25000 . C T 15366.0 PASS DP=496;AF=0.836694;SB=11;DP4=1,6,247,238;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D1146|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 25584 . C T 34503.0 PASS DP=1032;AF=0.891473;SB=3;DP4=1,0,503,521;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T64|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
NC_045512.2 26215 . T C 146.0 PASS DP=979;AF=0.010215;SB=0;DP4=470,494,6,6;EFF=SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L275|275|ORF3a|protein_coding|CODING|GU280_gp03|1|C)
NC_045512.2 26270 . C T 29169.0 PASS DP=860;AF=0.898837;SB=0;DP4=0,0,393,465;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T9I|75|E|protein_coding|CODING|GU280_gp04|1|T)
NC_045512.2 26530 . A G 3877.0 PASS DP=126;AF=0.84127;SB=0;DP4=0,0,60,66;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D3G|222|M|protein_coding|CODING|GU280_gp05|1|G)
NC_045512.2 26577 . C G 1326.0 PASS DP=41;AF=0.878049;SB=0;DP4=1,1,19,20;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q19E|222|M|protein_coding|CODING|GU280_gp05|1|G)
NC_045512.2 26709 . G A 3475.0 PASS DP=110;AF=0.854545;SB=0;DP4=0,0,50,60;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A63T|222|M|protein_coding|CODING|GU280_gp05|1|A)
NC_045512.2 27259 . A C 26760.0 PASS DP=818;AF=0.887531;SB=3;DP4=0,1,430,383;EFF=SYNONYMOUS_CODING(LOW|SILENT|Agg/Cgg|R20|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
NC_045512.2 27263 . CTTTTAAAGTTTCCATTTGGAATCTTGA C 67.0 PASS DP=909;AF=0.0044;SB=0;DP4=484,421,2,2;INDEL;HRUN=4;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||tttaaagtttccatttggaatcttgattac/tac|FKVSIWNLDY22Y|61|ORF6|protein_coding|CODING|GU280_gp06|1|C|INFO_REALIGN_3_PRIME)
NC_045512.2 27807 . C T 28196.0 PASS DP=816;AF=0.935049;SB=0;DP4=0,0,395,420;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L18|43|ORF7b|protein_coding|CODING|GU280_gp08|1|T)
NC_045512.2 28271 . A T 37938.0 PASS DP=1087;AF=0.930083;SB=0;DP4=0,1,530,552
NC_045512.2 28311 . C T 34465.0 PASS DP=1148;AF=0.818815;SB=2;DP4=3,6,535,588;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cTc|P13L|419|N|protein_coding|CODING|GU280_gp10|1|T)
NC_045512.2 28361 . GGAGAACGCA G 28153.0 PASS DP=1041;AF=0.813641;SB=0;DP4=94,104,398,449;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 126.0 PASS DP=870;AF=0.010345;SB=29;DP4=406,460,9,0;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 28754 . C T 31727.0 PASS DP=931;AF=0.90333;SB=0;DP4=1,1,471,454;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L161F|419|N|protein_coding|CODING|GU280_gp10|1|T)
NC_045512.2 28881 . G A 18291.0 PASS DP=529;AF=0.922495;SB=0;DP4=0,0,265,264;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aAg|R203K|419|N|protein_coding|CODING|GU280_gp10|1|A)
NC_045512.2 28882 . G A 16928.0 PASS DP=523;AF=0.869981;SB=3;DP4=0,1,259,254;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R203|419|N|protein_coding|CODING|GU280_gp10|1|A)
NC_045512.2 28883 . G C 18465.0 PASS DP=524;AF=0.946565;SB=3;DP4=2,0,260,262;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gga/Cga|G204R|419|N|protein_coding|CODING|GU280_gp10|1|C)