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sample-01.vcf
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178 lines (178 loc) · 52.4 KB
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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/066/348/66348156/tmp/lofreq2_call_parallelrkr10tb5/0.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_72,Description="Minimum SNV Quality (Phred) 72">
##FILTER=<ID=min_indelqual_55,Description="Minimum Indel Quality (Phred) 55">
##FILTER=<ID=min_snvqual_79,Description="Minimum SNV Quality (Phred) 79">
##FILTER=<ID=min_indelqual_63,Description="Minimum Indel Quality (Phred) 63">
##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 21:40:22 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 21:41:43 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/066/348/66348336/outputs/dataset_cb0da566-f404-406c-8750-a0188611194c.dat NC_045512.2 /data/dnb09/galaxy_db/files/4/6/1/dataset_46129f47-0e63-4f5e-91c9-d735e0b3c0be.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'">
##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000">
##SnpSiftVersion="SnpSift 4.3t (build 2017-11-24 10:18), by Pablo Cingolani"
##SnpSiftCmd="SnpSift Filter -f /data/dnb09/galaxy_db/files/b/c/0/dataset_bc06cf4c-aa70-4789-8c22-b48bbd13a818.dat -e /data/jwd02f/main/066/348/66348991/configs/tmpurq0al3z"
##FILTER=<ID=SnpSift,Description="SnpSift 4.3t (build 2017-11-24 10:18), by Pablo Cingolani, Expression used: DP >= 1">
##SnpSiftCmd="SnpSift Filter -f /data/dnb09/galaxy_db/files/2/0/8/dataset_208f366a-bd21-41f6-988d-1c2caf4f46fc.dat -e /data/jwd02f/main/066/349/66349010/configs/tmpy2zr42h8 --addFilter min_af_0.05Xmin_dp_1Xmin_dp_alt_10"
##FILTER=<ID=SnpSift,Description="SnpSift 4.3t (build 2017-11-24 10:18), by Pablo Cingolani, Expression used: ( ( DP4[2] + DP4[3] ) < ( 0.05 * DP ) ) | ( DP < 1 ) | ( ( AF * DP ) < ( 10 - 0.5 ) )">
#CHROM POS ID REF ALT QUAL FILTER INFO
NC_045512.2 241 . C T 49314.0 PASS DP=2586;AF=0.939288;SB=0;DP4=2,2,1277,1302
NC_045512.2 443 . GT G 146.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=3080;AF=0.003247;SB=0;DP4=1580,1487,5,5;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 657.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=3703;AF=0.009182;SB=0;DP4=1830,1839,16,18;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 920.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=3697;AF=0.012443;SB=0;DP4=1816,1829,23,23;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 96.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=3697;AF=0.002164;SB=0;DP4=1816,1829,4,4;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 103.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=3697;AF=0.002164;SB=0;DP4=1816,1829,4,4;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 261.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=3689;AF=0.004337;SB=0;DP4=1828,1845,8,8;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 157.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=3684;AF=0.002986;SB=0;DP4=1835,1851,5,6;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 255.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=3653;AF=0.00438;SB=0;DP4=1810,1828,8,8;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_045512.2 517 . TA T 73.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=3653;AF=0.001642;SB=0;DP4=1810,1828,3,3;INDEL;HRUN=1;EFF=FRAME_SHIFT(HIGH||atg/|M85|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),FRAME_SHIFT(HIGH||atg/|M85|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON),FRAME_SHIFT(HIGH||atg/|M85|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON),FRAME_SHIFT(HIGH||atg/|M85|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 518 . ATGGTT A 215.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=3597;AF=0.003892;SB=0;DP4=1811,1830,7,7;INDEL;HRUN=1;EFF=FRAME_SHIFT(HIGH||atggtt/|MV85|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),FRAME_SHIFT(HIGH||atggtt/|MV85|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON),FRAME_SHIFT(HIGH||atggtt/|MV85|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON),FRAME_SHIFT(HIGH||atggtt/|MV85|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 683 . CTA C 67.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2886;AF=0.001733;SB=1;DP4=1426,1491,3,2;INDEL;HRUN=1;EFF=FRAME_SHIFT(HIGH||cta/|L140|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),FRAME_SHIFT(HIGH||cta/|L140|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|C|WARNING_TRANSCRIPT_NO_STOP_CODON),FRAME_SHIFT(HIGH||cta/|L140|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|C|WARNING_TRANSCRIPT_NO_STOP_CODON),FRAME_SHIFT(HIGH||cta/|L140|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 831 . A C 90.0 sb_fdr;min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2479;AF=0.00363;SB=177;DP4=1249,1162,0,57;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aCc|N189T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aCc|N189T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aCc|N9T|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aCc|N9T|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 2164 . G C 49314.0 PASS DP=3347;AF=0.668061;SB=1;DP4=393,462,1157,1322;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E633D|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E633D|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E453D|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E453D|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 2330 . T A 301.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=810;AF=0.023457;SB=5;DP4=304,456,13,12;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 7707.0 PASS DP=1876;AF=0.160981;SB=6;DP4=711,835,138,189;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 49314.0 PASS DP=2001;AF=0.913043;SB=0;DP4=0,1,949,1037;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 3545 . AATG A 151.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2384;AF=0.004195;SB=0;DP4=1192,1186,5,5;INDEL;HRUN=2;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aatgga/aga|NG1094R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aatgga/aga|NG1094R|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aatgga/aga|NG276R|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aatgga/aga|NG276R|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 4148 . GT G 79.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1215;AF=0.004115;SB=0;DP4=605,605,3,2;INDEL;HRUN=4;EFF=FRAME_SHIFT(HIGH||tta/|L1296|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tta/|L1296|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tta/|L478|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tta/|L478|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 4758 . A T 93.0 sb_fdr;min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2275;AF=0.003956;SB=105;DP4=1097,1134,40,1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gTa|E1498V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gTa|E1498V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gTa|E680V|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gTa|E680V|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 4890 . C A 81.0 sb_fdr;min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2254;AF=0.003549;SB=59;DP4=1073,1134,1,25;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aAc|T1542N|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aAc|T1542N|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aAc|T724N|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aAc|T724N|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 5386 . T G 5780.0 PASS DP=2544;AF=0.096305;SB=0;DP4=1111,1133,142,147;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 1702.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2671;AF=0.037439;SB=4;DP4=1280,1252,59,69;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 1921.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2668;AF=0.041229;SB=3;DP4=1262,1265,71,61;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 5816 . GCTTTA G 90.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2309;AF=0.002599;SB=0;DP4=1160,1147,3,3;INDEL;HRUN=1;EFF=FRAME_SHIFT(HIGH||ttactt/|LL1852|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttactt/|LL1852|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttactt/|LL1034|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttactt/|LL1034|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 6027 . C T 45861.0 PASS DP=1941;AF=0.68882;SB=1;DP4=243,242,734,708;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCa/cTa|P1921L|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCa/cTa|P1921L|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCa/cTa|P1103L|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCa/cTa|P1103L|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 6512 . AGTT A 4047.0 PASS DP=2170;AF=0.071429;SB=0;DP4=1038,977,80,75;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 6696 . C CT 66.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2254;AF=0.002218;SB=1;DP4=1145,1154,3,2;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 7432 . ATT A 88.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1865;AF=0.003217;SB=0;DP4=906,963,3,3;INDEL;HRUN=4;EFF=FRAME_SHIFT(HIGH||ttttat/|FY2390|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttttat/|FY2390|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttttat/|FY1572|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttttat/|FY1572|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14)
NC_045512.2 8376 . CA C 180.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1683;AF=0.006536;SB=0;DP4=921,751,6,5;INDEL;HRUN=5;EFF=FRAME_SHIFT(HIGH||agt/|S2706|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||agt/|S2706|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||agt/|S1888|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||agt/|S1888|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 8393 . G A 5071.0 PASS DP=2008;AF=0.106076;SB=2;DP4=978,795,124,109;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 8620 . T C 7394.0 PASS DP=2556;AF=0.119327;SB=3;DP4=1028,1183,163,172;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A2785|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A2785|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A22|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A22|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 9498 . T C 47065.0 PASS DP=1981;AF=0.705199;SB=0;DP4=203,182,828,755;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gCt|V3078A|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gCt|V3078A|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gCt|V315A|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gCt|V315A|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 9621 . A T 87.0 sb_fdr;min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2834;AF=0.003176;SB=97;DP4=1354,1410,51,6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gTt|D3119V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gTt|D3119V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gTt|D356V|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gTt|D356V|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 10029 . C T 3418.0 PASS DP=2616;AF=0.063838;SB=0;DP4=1207,1211,98,97;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 6386.0 PASS DP=2901;AF=0.096863;SB=3;DP4=1275,1287,154,170;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 89.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2282;AF=0.003944;SB=2;DP4=1221,1041,9,5;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 11083 . G T 102.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2731;AF=0.004028;SB=37;DP4=1377,1307,35,9;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttT|L3606F|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttT|L3606F|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttT|L37F|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttT|L37F|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 11282 . AGTTTGTCTG A 6418.0 PASS DP=3007;AF=0.077486;SB=0;DP4=1309,1464,110,123;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 11537 . A G 7226.0 PASS DP=3602;AF=0.089395;SB=2;DP4=1588,1634,174,192;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 11625 . G T 79.0 sb_fdr;min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2400;AF=0.003333;SB=124;DP4=1055,1300,40,1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGc/gTc|G3787V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGc/gTc|G3787V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGc/gTc|G218V|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGc/gTc|G218V|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 13195 . T C 10130.0 PASS DP=4311;AF=0.101833;SB=8;DP4=2013,1803,275,213;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 13728 . TGCTA T 125.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2026;AF=0.003949;SB=0;DP4=1039,1031,4,4;INDEL;HRUN=1;EFF=FRAME_SHIFT(HIGH||gctaaa/|AK4489|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),FRAME_SHIFT(HIGH||gctaaa/|AK97|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 13914 . TA T 103.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2937;AF=0.002724;SB=0;DP4=1472,1457,4,4;INDEL;HRUN=5;EFF=FRAME_SHIFT(HIGH||aag/|K4552|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aag/|K160|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 14407 . CCTACAAG C 129.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1836;AF=0.004357;SB=0;DP4=963,910,4,4;INDEL;HRUN=2;EFF=FRAME_SHIFT(HIGH||cctacaagt/|PTS4715|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),FRAME_SHIFT(HIGH||cctacaagt/|PTS323|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|C|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 14408 . C T 49314.0 PASS DP=1836;AF=0.915033;SB=0;DP4=0,0,940,883;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 14852 . TTGTA T 77.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1755;AF=0.002849;SB=1;DP4=875,878,3,2;INDEL;HRUN=3;EFF=FRAME_SHIFT(HIGH||tttgta/|FV4863|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),FRAME_SHIFT(HIGH||tttgta/|FV471|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 14854 . GTA G 95.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1727;AF=0.003474;SB=0;DP4=864,867,3,3;INDEL;HRUN=1;EFF=FRAME_SHIFT(HIGH||gta/|V4864|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),FRAME_SHIFT(HIGH||gta/|V472|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|G|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 15021 . TTTCGCATATACAAAACGTA T 93.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2043;AF=0.002937;SB=0;DP4=1073,974,3,3;INDEL;HRUN=4;EFF=FRAME_SHIFT(HIGH||ttcgcatatacaaaacgtaat/|FAYTKRN4920|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),FRAME_SHIFT(HIGH||ttcgcatatacaaaacgtaat/|FAYTKRN528|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 15157 . C A 189.0 sb_fdr DP=2238;AF=0.006702;SB=941;DP4=1154,811,0,271;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Aaa|Q4965K|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Aaa|Q573K|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 15173 . C A 100.0 sb_fdr;min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2293;AF=0.003925;SB=611;DP4=1167,919,2,196;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 3970.0 PASS DP=2493;AF=0.074208;SB=0;DP4=1086,1199,94,102;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 15455 . C T 85.0 sb_fdr;min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1166;AF=0.006003;SB=362;DP4=450,602,106,0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S5064L|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S672L|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 15479 . C A 90.0 sb_fdr;min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1113;AF=0.006289;SB=245;DP4=422,592,90,6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aAc|T5072N|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aAc|T680N|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 15781 . A T 89.0 sb_fdr;min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2559;AF=0.003517;SB=94;DP4=1210,1289,47,5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aac/Tac|N5173Y|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aac/Tac|N781Y|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 16154 . T C 17668.0 PASS DP=5623;AF=0.129646;SB=6;DP4=2347,2447,411,391;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gCt|V5297A|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gCt|V905A|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 16946 . C T 49314.0 PASS DP=3389;AF=0.712305;SB=1;DP4=388,383,1295,1316;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A5561V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A237V|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 17766 . CT C 81.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=3045;AF=0.00197;SB=0;DP4=1532,1511,3,3;INDEL;HRUN=3;EFF=FRAME_SHIFT(HIGH||ttt/|F5835|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F511|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 17938 . G A 5468.0 PASS DP=1729;AF=0.127241;SB=1;DP4=707,785,107,126;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A5892T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A568T|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 18149 . G T 174.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1490;AF=0.008725;SB=3;DP4=722,740,9,6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G5962V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G37V|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 18163 . A G 3446.0 PASS DP=1464;AF=0.099727;SB=0;DP4=638,656,82,83;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 18742 . TACGTCTA T 86.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2353;AF=0.00255;SB=0;DP4=1179,1172,3,3;INDEL;HRUN=1;EFF=FRAME_SHIFT(HIGH||tacgtctat/|YVY6160|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),FRAME_SHIFT(HIGH||tacgtctat/|YVY235|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 19517 . TGTA T 71.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2081;AF=0.002403;SB=1;DP4=1081,1044,2,3;INDEL;HRUN=1;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ttgtat/ttt|LY6418F|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ttgtat/ttt|LY493F|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 20117 . C A 97.0 sb_fdr;min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1514;AF=0.005284;SB=134;DP4=741,705,4,60;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aAa|T6618K|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aAa|T166K|345|ORF1ab|protein_coding|CODING|YP_009725310.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 20268 . A G 49314.0 PASS DP=2298;AF=0.827241;SB=0;DP4=110,109,1034,1038;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttA/ttG|L6668|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),SYNONYMOUS_CODING(LOW|SILENT|ttA/ttG|L216|345|ORF1ab|protein_coding|CODING|YP_009725310.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 21575 . C T 145.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2936;AF=0.005109;SB=38;DP4=1406,1477,31,8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L5F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 21735 . TC T 1172.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2410;AF=0.023651;SB=0;DP4=1172,1181,29,28;INDEL;HRUN=1;EFF=FRAME_SHIFT(HIGH||ttc/|F58|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 21736 . C CT 138.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2412;AF=0.01534;SB=3;DP4=1181,1193,21,16;INDEL;HRUN=4;EFF=FRAME_SHIFT(HIGH||tcc/tTcc|S60F?|1273|S|protein_coding|CODING|GU280_gp02|1|CT|INFO_REALIGN_3_PRIME)
NC_045512.2 21736 . C T 49314.0 PASS DP=2412;AF=0.659619;SB=0;DP4=309,315,861,865;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F58|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 21740 . TCCAATGTTACTTGGTTCCATGCTATACATGTCTCTGGGA T 127.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2378;AF=0.003364;SB=0;DP4=1188,1200,4,4;INDEL;HRUN=2;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gttacttggttccatgctatacatgtctctgggaccaatggt/ggt|VTWFHAIHVSGTNG62G|1273|S|protein_coding|CODING|GU280_gp02|1|T|INFO_REALIGN_3_PRIME)
NC_045512.2 21762 . C T 3568.0 PASS DP=2536;AF=0.067429;SB=1;DP4=1156,1179,92,99;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A67V|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 21764 . ATACATG A 4746.0 PASS DP=2467;AF=0.072558;SB=1;DP4=1135,1153,86,93;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 7112.0 PASS DP=1795;AF=0.154318;SB=1;DP4=708,785,147,154;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T95I|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 21890 . TTA T 77.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1489;AF=0.003358;SB=0;DP4=716,783,2,3;INDEL;HRUN=3;EFF=FRAME_SHIFT(HIGH||tta/|L110|1273|S|protein_coding|CODING|GU280_gp02|1|T);LOF=(S|GU280_gp02|1|1.00)
NC_045512.2 21986 . GGTGTTTATT G 3906.0 PASS DP=1232;AF=0.119318;SB=1;DP4=562,525,73,74;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 2168.0 PASS DP=1551;AF=0.055448;SB=3;DP4=744,863,44,42;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 1932.0 PASS DP=1279;AF=0.059421;SB=3;DP4=578,622,40,36;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 22578 . G A 6222.0 PASS DP=2755;AF=0.098004;SB=6;DP4=1247,1208,140,158;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G339D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 22583 . GT G 74.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2721;AF=0.002205;SB=0;DP4=1374,1357,3,3;INDEL;HRUN=5;EFF=FRAME_SHIFT(HIGH||ttt/|F342|1273|S|protein_coding|CODING|GU280_gp02|1|G|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00)
NC_045512.2 22583 . GTT G 90.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2721;AF=0.002573;SB=0;DP4=1374,1357,4,3;INDEL;HRUN=5;EFF=FRAME_SHIFT(HIGH||ttt/|F342|1273|S|protein_coding|CODING|GU280_gp02|1|G|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00)
NC_045512.2 22673 . T C 2644.0 PASS DP=1786;AF=0.069429;SB=11;DP4=791,849,55,82;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tcc/Ccc|S371P|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512.2 22674 . C T 2569.0 PASS DP=1617;AF=0.074212;SB=2;DP4=607,850,63,79;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S371F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 22679 . T C 3086.0 PASS DP=1585;AF=0.085804;SB=0;DP4=608,820,61,86;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Cca|S373P|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512.2 22686 . C T 3049.0 PASS DP=1584;AF=0.084596;SB=0;DP4=595,844,58,86;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S375F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 22992 . G A 4087.0 PASS DP=1827;AF=0.103448;SB=13;DP4=803,809,121,90;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S477N|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 22995 . C A 4203.0 PASS DP=1785;AF=0.103641;SB=13;DP4=781,785,122,91;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aAa|T478K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 23013 . A C 8000.0 PASS DP=1827;AF=0.16913;SB=5;DP4=785,695,191,148;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gCa|E484A|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512.2 23040 . A G 7782.0 PASS DP=1831;AF=0.162206;SB=0;DP4=795,705,173,150;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q493R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512.2 23048 . G A 8816.0 PASS DP=1974;AF=0.168693;SB=0;DP4=850,760,189,164;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G496S|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 23055 . A G 8046.0 PASS DP=2039;AF=0.155468;SB=0;DP4=869,784,196,177;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q498R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512.2 23063 . A T 10122.0 PASS DP=2415;AF=0.163561;SB=0;DP4=1064,941,220,189;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Tat|N501Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 23075 . T C 8442.0 PASS DP=2408;AF=0.142442;SB=0;DP4=1059,940,217,190;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y505H|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512.2 23202 . C A 11348.0 PASS DP=3160;AF=0.143038;SB=0;DP4=1319,1338,242,251;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=4080;AF=0.888235;SB=2;DP4=6,4,2017,2036;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D614G|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512.2 23525 . C T 12646.0 PASS DP=3508;AF=0.147092;SB=0;DP4=1395,1546,266,292;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H655Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 23554 . ACCCATTGGTGCAGGTATATGCGCTAGTT A 102.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2819;AF=0.002483;SB=3;DP4=1312,1532,2,5;INDEL;HRUN=3;EFF=FRAME_SHIFT(HIGH||cccattggtgcaggtatatgcgctagttat/|PIGAGICASY665|1273|S|protein_coding|CODING|GU280_gp02|1|A);LOF=(S|GU280_gp02|1|1.00)
NC_045512.2 23563 . T G 85.0 sb_fdr;min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2470;AF=0.003644;SB=179;DP4=1056,1306,67,4;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggT/ggG|G667|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512.2 23568 . GTA G 183.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2419;AF=0.004547;SB=0;DP4=1112,1303,5,6;INDEL;HRUN=1;EFF=FRAME_SHIFT(HIGH||atatgc/|IC670|1273|S|protein_coding|CODING|GU280_gp02|1|G|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00)
NC_045512.2 23599 . T G 11508.0 PASS DP=2113;AF=0.207761;SB=3;DP4=755,850,226,276;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N679K|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512.2 23604 . C A 6944.0 PASS DP=1776;AF=0.156532;SB=4;DP4=682,782,131,169;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cAt|P681H|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 23948 . G T 3413.0 PASS DP=1381;AF=0.1021;SB=0;DP4=644,566,82,72;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Tat|D796Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 24025 . ACTT A 111.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1760;AF=0.003977;SB=0;DP4=877,876,4,3;INDEL;HRUN=1;EFF=CODON_DELETION(MODERATE||ctt/|L822|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 24130 . C A 4441.0 PASS DP=1541;AF=0.121999;SB=4;DP4=608,716,89,120;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaC/aaA|N856K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 24195 . TA T 89.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1980;AF=0.00303;SB=0;DP4=1017,957,3,3;INDEL;HRUN=1;EFF=FRAME_SHIFT(HIGH||tta/|L878|1273|S|protein_coding|CODING|GU280_gp02|1|T);LOF=(S|GU280_gp02|1|1.00)
NC_045512.2 24424 . A T 9980.0 PASS DP=2405;AF=0.166736;SB=4;DP4=976,990,226,209;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caA/caT|Q954H|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 24469 . T A 7685.0 PASS DP=3251;AF=0.101507;SB=1;DP4=1430,1456,180,177;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaA|N969K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 24503 . C T 8963.0 PASS DP=3365;AF=0.111738;SB=1;DP4=1422,1533,190,213;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L981F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 24942 . A T 126.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1776;AF=0.006757;SB=2;DP4=879,876,10,7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gTt|D1127V|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 25000 . C T 5496.0 PASS DP=1468;AF=0.155995;SB=0;DP4=597,600,130,128;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D1146|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 25584 . C T 10776.0 PASS DP=2554;AF=0.164056;SB=0;DP4=1042,1054,222,227;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T64|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
NC_045512.2 26144 . G A 5571.0 PASS DP=2938;AF=0.085092;SB=1;DP4=1267,1329,145,146;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G251D|275|ORF3a|protein_coding|CODING|GU280_gp03|1|A)
NC_045512.2 26194 . A T 98.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2862;AF=0.003843;SB=0;DP4=1395,1420,8,8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acg/Tcg|T268S|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
NC_045512.2 26270 . C T 8205.0 PASS DP=2423;AF=0.135782;SB=1;DP4=950,1103,162,199;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T9I|75|E|protein_coding|CODING|GU280_gp04|1|T)
NC_045512.2 26283 . AGTT A 63.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=3361;AF=0.001488;SB=1;DP4=1647,1709,3,2;INDEL;HRUN=1;EFF=CODON_DELETION(MODERATE||gtt/|V14|75|E|protein_coding|CODING|GU280_gp04|1|A)
NC_045512.2 26493 . G GT 66.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1929;AF=0.002592;SB=0;DP4=944,997,2,3;INDEL;HRUN=5
NC_045512.2 26530 . A G 260.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1814;AF=0.010474;SB=3;DP4=850,922,14,10;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D3G|222|M|protein_coding|CODING|GU280_gp05|1|G)
NC_045512.2 26649 . A T 82.0 sb_fdr;min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2050;AF=0.003902;SB=135;DP4=1040,954,49,0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Tat|N43Y|222|M|protein_coding|CODING|GU280_gp05|1|T)
NC_045512.2 26709 . G A 99.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2598;AF=0.003849;SB=0;DP4=1244,1294,6,7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A63T|222|M|protein_coding|CODING|GU280_gp05|1|A)
NC_045512.2 26779 . GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT G 807.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2783;AF=0.013654;SB=1;DP4=1290,1455,19,19;INDEL;HRUN=1;EFF=FRAME_SHIFT(HIGH||gtaggcttgatgtggctcagctacttcattgcttctttc/|VGLMWLSYFIASF88|222|M|protein_coding|CODING|GU280_gp05|1|G|INFO_REALIGN_3_PRIME);LOF=(M|GU280_gp05|1|1.00)
NC_045512.2 26784 . GTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT G 105.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2641;AF=0.002651;SB=3;DP4=1235,1405,2,5;INDEL;HRUN=1;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gtaggcttgatgtggctcagctacttcattgcttctttc/gtc|VGLMWLSYFIASF88V|222|M|protein_coding|CODING|GU280_gp05|1|G|INFO_REALIGN_3_PRIME)
NC_045512.2 26786 . AGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT A 162.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2629;AF=0.003804;SB=0;DP4=1224,1401,5,5;INDEL;HRUN=2;EFF=FRAME_SHIFT(HIGH||ggcttgatgtggctcagctacttcattgcttctttc/|GLMWLSYFIASF89|222|M|protein_coding|CODING|GU280_gp05|1|A);LOF=(M|GU280_gp05|1|1.00)
NC_045512.2 27131 . CTA C 82.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2815;AF=0.002131;SB=0;DP4=1382,1429,3,3;INDEL;HRUN=1;EFF=FRAME_SHIFT(HIGH||tataaa/|YK204|222|M|protein_coding|CODING|GU280_gp05|1|C|INFO_REALIGN_3_PRIME);LOF=(M|GU280_gp05|1|1.00)
NC_045512.2 27131 . CTATAAAT C 66.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2879;AF=0.001737;SB=1;DP4=1441,1434,2,3;INDEL;HRUN=1;EFF=FRAME_SHIFT(HIGH||tataaatta/|YKL204|222|M|protein_coding|CODING|GU280_gp05|1|C|INFO_REALIGN_3_PRIME);LOF=(M|GU280_gp05|1|1.00)
NC_045512.2 27133 . ATAAATT A 83.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2813;AF=0.002133;SB=1;DP4=1382,1429,2,4;INDEL;HRUN=1;EFF=STOP_GAINED+CODON_CHANGE_PLUS_CODON_DELETION(HIGH||tataaatta/taa|YKL204*|222|M|protein_coding|CODING|GU280_gp05|1|A)
NC_045512.2 27190 . AAGTGACAACAGATGTTTCATCTCGTTGACTT A 78.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=3646;AF=0.001646;SB=0;DP4=1860,1794,3,3;INDEL;HRUN=2;EFF=GENE_FUSION(HIGH|||||M+ORF6||CODING|||A),FRAME_SHIFT+STOP_LOST+SPLICE_SITE_REGION(HIGH||taa/|*223|222|M|protein_coding|CODING|GU280_gp05|1|A),FRAME_SHIFT+START_LOST(HIGH||atgtttcatctcgttgacttt/|MFHLVDF1|61|ORF6|protein_coding|CODING|GU280_gp06|1|A);LOF=(ORF6|GU280_gp06|1|1.00)
NC_045512.2 27213 . C T 696.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=3568;AF=0.013453;SB=2;DP4=1776,1708,27,31;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L4|61|ORF6|protein_coding|CODING|GU280_gp06|1|T)
NC_045512.2 27259 . A C 4789.0 PASS DP=2095;AF=0.09642;SB=1;DP4=991,861,123,114;EFF=SYNONYMOUS_CODING(LOW|SILENT|Agg/Cgg|R20|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
NC_045512.2 27382 . G C 5593.0 PASS DP=3415;AF=0.073499;SB=0;DP4=1558,1566,137,142;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Cat|D61H|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
NC_045512.2 27383 . A T 5412.0 PASS DP=3410;AF=0.071554;SB=0;DP4=1558,1555,138,139;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gTt|D61V|61|ORF6|protein_coding|CODING|GU280_gp06|1|T)
NC_045512.2 27384 . T C 5537.0 PASS DP=3424;AF=0.073598;SB=0;DP4=1562,1567,142,145;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D61|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
NC_045512.2 27753 . A C 49314.0 PASS DP=2359;AF=0.690123;SB=0;DP4=279,274,914,887;EFF=SYNONYMOUS_CODING(LOW|SILENT|acA/acC|T120|121|ORF7a|protein_coding|CODING|GU280_gp07|1|C)
NC_045512.2 27807 . C T 8827.0 PASS DP=2560;AF=0.141406;SB=0;DP4=1058,1099,196,201;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L18|43|ORF7b|protein_coding|CODING|GU280_gp08|1|T)
NC_045512.2 28271 . A T 11174.0 PASS DP=3057;AF=0.145895;SB=0;DP4=1261,1299,236,243
NC_045512.2 28311 . C T 10614.0 PASS DP=3165;AF=0.138073;SB=1;DP4=1261,1370,246,259;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cTc|P13L|419|N|protein_coding|CODING|GU280_gp10|1|T)
NC_045512.2 28361 . GGAGAACGCA G 6660.0 PASS DP=3198;AF=0.080363;SB=1;DP4=1401,1547,126,131;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 28370 . A G 397.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2962;AF=0.012829;SB=7;DP4=1264,1378,31,23;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agt/Ggt|S33G|419|N|protein_coding|CODING|GU280_gp10|1|G)
NC_045512.2 28854 . C T 49314.0 PASS DP=5231;AF=0.630663;SB=2;DP4=773,886,1694,1864;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S194L|419|N|protein_coding|CODING|GU280_gp10|1|T)
NC_045512.2 28881 . G A 1190.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=4804;AF=0.016861;SB=1;DP4=2192,2513,48,50;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aAg|R203K|419|N|protein_coding|CODING|GU280_gp10|1|A)
NC_045512.2 28882 . G A 1089.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=4764;AF=0.015953;SB=3;DP4=2163,2494,47,45;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R203|419|N|protein_coding|CODING|GU280_gp10|1|A)
NC_045512.2 28883 . G C 1049.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=4749;AF=0.016214;SB=1;DP4=2173,2445,43,53;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gga/Cga|G204R|419|N|protein_coding|CODING|GU280_gp10|1|C)
NC_045512.2 28981 . T G 97.0 sb_fdr DP=2932;AF=0.003411;SB=811;DP4=1186,1466,256,1;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggT/ggG|G236|419|N|protein_coding|CODING|GU280_gp10|1|G)
NC_045512.2 28987 . CCAA C 100.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2935;AF=0.002385;SB=0;DP4=1469,1494,3,4;INDEL;HRUN=2;EFF=CODON_DELETION(MODERATE||caa/|Q242|419|N|protein_coding|CODING|GU280_gp10|1|C|INFO_REALIGN_3_PRIME)
NC_045512.2 29623 . T C 14384.0 PASS DP=978;AF=0.473415;SB=0;DP4=233,236,255,249;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaT/aaC|N22|38|ORF10|protein_coding|CODING|GU280_gp11|1|C)
NC_045512.2 29719 . C T 979.0 PASS DP=984;AF=0.049797;SB=0;DP4=459,470,25,27
NC_045512.2 29736 . G T 13283.0 PASS DP=951;AF=0.453207;SB=0;DP4=238,241,230,241