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sample-05.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/jwd02f/main/066/348/66348160/tmp/lofreq2_call_parallelj76ljs3e/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_57,Description="Minimum Indel Quality (Phred) 57">
##FILTER=<ID=min_snvqual_79,Description="Minimum SNV Quality (Phred) 79">
##FILTER=<ID=min_indelqual_64,Description="Minimum Indel Quality (Phred) 64">
##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 20:42:25 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 20:43:28 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/066/348/66348340/outputs/dataset_e414f2b7-2b1b-4ea6-97a7-a1580144d8d2.dat NC_045512.2 /data/dnb09/galaxy_db/files/2/5/f/dataset_25f072f9-1bb7-4d2d-b4ab-585f015e71dc.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 49314.0 PASS DP=2246;AF=0.943455;SB=4;DP4=3,1,1113,1127
NC_045512.2 506 . CATGGTCATGTT C 98.0 PASS DP=5493;AF=0.001456;SB=0;DP4=2769,2770,4,4;INDEL;HRUN=1;EFF=FRAME_SHIFT(HIGH||catgttatggtt/|HVMV83|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||catgttatggtt/|HVMV83|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|C|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||catgttatggtt/|HVMV83|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|C|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||catgttatggtt/|HVMV83|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 507 . ATGGTCATGTTATGGT A 83.0 PASS DP=5498;AF=0.001273;SB=0;DP4=2746,2746,3,4;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 . GGTCATGTTA G 424.0 PASS DP=5467;AF=0.004756;SB=0;DP4=2708,2711,13,13;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 . GGTCATGTTATGGTT G 487.0 PASS DP=5467;AF=0.005305;SB=0;DP4=2708,2711,14,15;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 . GGTCATGTT G 66.0 PASS DP=5467;AF=0.001097;SB=0;DP4=2708,2711,3,3;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 271.0 PASS DP=5435;AF=0.003312;SB=0;DP4=2707,2715,9,9;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 . GTTA G 67.0 PASS DP=5431;AF=0.001105;SB=0;DP4=2709,2719,3,3;INDEL;HRUN=2;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gttatg/gtg|VM84V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gttatg/gtg|VM84V|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gttatg/gtg|VM84V|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gttatg/gtg|VM84V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME)
NC_045512.2 515 . GTTATGGTT G 97.0 PASS DP=5431;AF=0.001473;SB=0;DP4=2709,2719,4,4;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 97.0 PASS DP=5381;AF=0.001487;SB=0;DP4=2688,2697,4,4;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_045512.2 518 . ATGGTTG A 68.0 PASS DP=5289;AF=0.001134;SB=0;DP4=2688,2697,3,3;INDEL;HRUN=1;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||atggttgag/aag|MVE85K|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||atggttgag/aag|MVE85K|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||atggttgag/aag|MVE85K|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||atggttgag/aag|MVE85K|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A)
NC_045512.2 582 . T C 103.0 PASS DP=4894;AF=0.002656;SB=5;DP4=2379,2449,13,8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTc/gCc|V106A|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTc/gCc|V106A|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|C|WARNING_TRANSCRIPT_NO_STOP_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTc/gCc|V106A|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|C|WARNING_TRANSCRIPT_NO_STOP_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTc/gCc|V106A|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C)
NC_045512.2 593 . C T 150.0 PASS DP=4709;AF=0.003398;SB=8;DP4=2289,2383,18,10;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H110Y|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H110Y|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H110Y|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H110Y|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T)
NC_045512.2 683 . CTA C 75.0 PASS DP=3889;AF=0.001543;SB=0;DP4=1906,2022,3,3;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_045512.2 746 . TG T 72.0 PASS DP=2120;AF=0.002358;SB=0;DP4=1071,1044,3,2;INDEL;HRUN=2;EFF=FRAME_SHIFT(HIGH||tgg/|W161|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tgg/|W161|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tgg/|W161|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tgg/|W161|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 1026 . C CT 217.0 PASS DP=2290;AF=0.005677;SB=0;DP4=1198,1079,7,6;INDEL;HRUN=4;EFF=FRAME_SHIFT+STOP_GAINED(HIGH||gaa/Tgaa|E256*?|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|CT|INFO_REALIGN_3_PRIME),FRAME_SHIFT+STOP_GAINED(HIGH||gaa/Tgaa|E256*?|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|CT|INFO_REALIGN_3_PRIME),FRAME_SHIFT+STOP_GAINED(HIGH||gaa/Tgaa|E76*?|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|CT|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT+STOP_GAINED(HIGH||gaa/Tgaa|E76*?|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|CT|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14);NMD=(ORF1ab|GU280_gp01|28|0.04)
NC_045512.2 1135 . G GA 74.0 PASS DP=2780;AF=0.002158;SB=0;DP4=1399,1395,3,3;INDEL;HRUN=5;EFF=FRAME_SHIFT(HIGH||aag/aaAg|K292K?|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|GA|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aag/aaAg|K292K?|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|GA|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aag/aaAg|K112K?|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|GA|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aag/aaAg|K112K?|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|GA|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.11)
NC_045512.2 2330 . T A 419.0 PASS DP=2858;AF=0.010847;SB=0;DP4=1351,1414,19,18;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 2434 . CAG C 69.0 PASS DP=2617;AF=0.001911;SB=0;DP4=1197,1430,2,3;INDEL;HRUN=1;EFF=FRAME_SHIFT(HIGH||gaa/|E725|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||gaa/|E725|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||gaa/|E545|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||gaa/|E545|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14)
NC_045512.2 2832 . A G 49314.0 PASS DP=2369;AF=0.921064;SB=0;DP4=1,1,1108,1250;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=1855;AF=0.930997;SB=3;DP4=1,0,884,959;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 94.0 PASS DP=3388;AF=0.002066;SB=1;DP4=1689,1697,4,3;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 3862 . T A 178.0 PASS DP=451;AF=0.022173;SB=1;DP4=220,219,7,5;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 4160 . G T 182.0 PASS DP=1906;AF=0.00787;SB=2;DP4=936,937,13,9;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Ttg|V1299L|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Ttg|V1299L|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Ttg|V481L|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Ttg|V481L|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 5386 . T G 49314.0 PASS DP=3743;AF=0.878707;SB=5;DP4=9,5,1850,1865;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 1108.0 PASS DP=3233;AF=0.022889;SB=1;DP4=1573,1551,46,50;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 1101.0 PASS DP=3230;AF=0.02291;SB=2;DP4=1569,1566,49,43;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 49314.0 PASS DP=2353;AF=0.99575;SB=6;DP4=8,3,1201,1142;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 99.0 PASS DP=3142;AF=0.002228;SB=1;DP4=1561,1581,4,3;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 7019 . G GT 146.0 PASS DP=2956;AF=0.003383;SB=0;DP4=1436,1530,5,5;INDEL;HRUN=4;EFF=FRAME_SHIFT(HIGH||tta/ttTa|L2253F?|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|GT|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tta/ttTa|L2253F?|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|GT|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tta/ttTa|L1435F?|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|GT|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tta/ttTa|L1435F?|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|GT|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14)
NC_045512.2 8393 . G A 49314.0 PASS DP=2771;AF=0.926019;SB=4;DP4=1,3,1529,1230;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A2710T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A2710T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A1892T|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A1892T|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 10029 . C T 49314.0 PASS DP=3230;AF=0.878019;SB=1;DP4=5,3,1606,1592;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 10069 . A G 1516.0 PASS DP=2739;AF=0.029938;SB=1;DP4=1275,1369,40,47;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K3268|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K3268|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K5|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K5|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 10449 . C A 49314.0 PASS DP=3662;AF=0.895958;SB=2;DP4=4,7,1770,1856;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 265.0 PASS DP=2480;AF=0.008871;SB=2;DP4=1285,1165,13,15;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Gca|S3407A|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Gca|S3407A|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Gca|S144A|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Gca|S144A|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 10541 . C A 96.0 PASS DP=2752;AF=0.00436;SB=18;DP4=1356,1344,9,24;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Aac|H3426N|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Aac|H3426N|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Aac|H163N|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Aac|H163N|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 10660 . TA T 117.0 PASS DP=3002;AF=0.002665;SB=0;DP4=1469,1534,4,4;INDEL;HRUN=2;EFF=FRAME_SHIFT(HIGH||aat/|N3466|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aat/|N3466|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aat/|N203|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aat/|N203|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14)
NC_045512.2 11088 . A T 103.0 PASS DP=3622;AF=0.003037;SB=98;DP4=1811,1759,42,2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gTa|E3608V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gTa|E3608V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gTa|E39V|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gTa|E39V|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 11095 . C T 118.0 PASS DP=2741;AF=0.004743;SB=0;DP4=1422,1293,10,8;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A3610|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A3610|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A41|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A41|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 11270 . ATGGTT A 73.0 PASS DP=3921;AF=0.00153;SB=0;DP4=1907,2044,3,3;INDEL;HRUN=1;EFF=FRAME_SHIFT(HIGH||atggtt/|MV3669|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),FRAME_SHIFT(HIGH||atggtt/|MV3669|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),FRAME_SHIFT(HIGH||atggtt/|MV100|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),FRAME_SHIFT(HIGH||atggtt/|MV100|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.14)
NC_045512.2 11279 . ACTAGTTTGT A 74.0 PASS DP=3660;AF=0.002732;SB=32;DP4=1732,1921,10,0;INDEL;HRUN=1;EFF=CODON_DELETION(MODERATE||agtttgtct/|SLS3673|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A|INFO_REALIGN_3_PRIME),CODON_DELETION(MODERATE||agtttgtct/|SLS3673|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A|INFO_REALIGN_3_PRIME),CODON_DELETION(MODERATE||agtttgtct/|SLS104|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),CODON_DELETION(MODERATE||agtttgtct/|SLS104|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME)
NC_045512.2 11282 . AGTTTGTCTG A 49314.0 PASS DP=3563;AF=0.920011;SB=11;DP4=149,134,1543,1735;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 49314.0 PASS DP=4961;AF=0.903044;SB=1;DP4=3,2,2442,2504;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 11847 . A C 89.0 PASS DP=2709;AF=0.003691;SB=1;DP4=1339,1350,6,5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAa/aCa|K3861T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAa/aCa|K3861T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAa/aCa|K2T|82|ORF1ab|protein_coding|CODING|YP_009725303.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAa/aCa|K2T|82|ORF1ab|protein_coding|CODING|YP_009742614.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 12004 . A G 80.0 PASS DP=3213;AF=0.002801;SB=0;DP4=1646,1544,5,5;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S3913|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S3913|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S54|82|ORF1ab|protein_coding|CODING|YP_009725303.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S54|82|ORF1ab|protein_coding|CODING|YP_009742614.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 12427 . TG T 85.0 PASS DP=2764;AF=0.002171;SB=0;DP4=1385,1375,3,3;INDEL;HRUN=2;EFF=FRAME_SHIFT(HIGH||ggt/|G4055|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ggt/|G4055|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ggt/|G113|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ggt/|G113|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14)
NC_045512.2 12484 . C T 82.0 PASS DP=2486;AF=0.00362;SB=1;DP4=1243,1231,6,4;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtC/gtT|V4073|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|gtC/gtT|V4073|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|gtC/gtT|V131|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|gtC/gtT|V131|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 12661 . G T 88.0 PASS DP=3466;AF=0.002885;SB=0;DP4=1705,1719,14,14;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agG/agT|R4132S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agG/agT|R4132S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agG/agT|R190S|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agG/agT|R190S|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 13195 . T C 49314.0 PASS DP=5323;AF=0.904565;SB=1;DP4=4,2,2815,2486;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 13571 . G T 87.0 PASS DP=1237;AF=0.005659;SB=0;DP4=655,567,5,4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G4436V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G44V|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 14407 . CCTACAAG C 77.0 PASS DP=2853;AF=0.002103;SB=0;DP4=1504,1419,3,3;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=2853;AF=0.930249;SB=0;DP4=1,1,1461,1374;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 14848 . CTATTTG C 97.0 PASS DP=1729;AF=0.00347;SB=0;DP4=870,869,3,3;INDEL;HRUN=1;EFF=CODON_DELETION(MODERATE||tttgta/|FV4863|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C|INFO_REALIGN_3_PRIME),CODON_DELETION(MODERATE||tttgta/|FV471|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME)
NC_045512.2 15157 . C A 288.0 PASS DP=2851;AF=0.007717;SB=1237;DP4=1472,1023,0,355;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 229.0 PASS DP=2922;AF=0.00616;SB=813;DP4=1497,1176,0,244;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 49314.0 PASS DP=2750;AF=0.937091;SB=2;DP4=2,1,1307,1433;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 15906 . G A 158.0 PASS DP=4133;AF=0.003871;SB=0;DP4=2055,2051,9,9;EFF=SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q5214|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q822|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 15983 . TA T 68.0 PASS DP=3442;AF=0.001743;SB=0;DP4=1791,1646,3,3;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 16022 . CT C 75.0 PASS DP=3898;AF=0.001539;SB=0;DP4=2037,2056,3,3;INDEL;HRUN=3;EFF=FRAME_SHIFT(HIGH||tta/|L5254|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tta/|L862|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 16597 . AT A 85.0 PASS DP=2158;AF=0.00278;SB=0;DP4=1073,1079,3,3;INDEL;HRUN=4;EFF=FRAME_SHIFT(HIGH||tta/|L5446|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tta/|L122|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 17200 . TTAAAA T 82.0 PASS DP=3004;AF=0.001997;SB=0;DP4=1501,1497,3,3;INDEL;HRUN=2;EFF=FRAME_SHIFT(HIGH||aaatat/|KY5647|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaatat/|KY323|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 18163 . A G 49314.0 PASS DP=1502;AF=0.91478;SB=0;DP4=0,1,746,747;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 18659 . GTT G 77.0 PASS DP=3278;AF=0.00183;SB=0;DP4=1692,1598,3,3;INDEL;HRUN=2;EFF=FRAME_SHIFT(HIGH||tgttgt/|CC6132|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),FRAME_SHIFT(HIGH||tgttgt/|CC207|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 18739 . GATTA G 79.0 PASS DP=3391;AF=0.001769;SB=0;DP4=1694,1689,3,3;INDEL;HRUN=1;EFF=FRAME_SHIFT(HIGH||gattac/|DY6159|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),FRAME_SHIFT(HIGH||gattac/|DY234|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 18742 . TACGTCTA T 79.0 PASS DP=3345;AF=0.001794;SB=0;DP4=1673,1670,3,3;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 19983 . C T 81.0 PASS DP=3938;AF=0.003047;SB=3;DP4=1972,1923,11,15;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtC/gtT|V6573|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),SYNONYMOUS_CODING(LOW|SILENT|gtC/gtT|V121|345|ORF1ab|protein_coding|CODING|YP_009725310.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 20114 . T A 98.0 PASS DP=2158;AF=0.004171;SB=109;DP4=1058,1039,2,45;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTc/gAc|V6617D|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTc/gAc|V165D|345|ORF1ab|protein_coding|CODING|YP_009725310.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 20296 . AAATT A 114.0 PASS DP=3199;AF=0.002501;SB=0;DP4=1599,1596,4,4;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 20483 . C T 173.0 PASS DP=1904;AF=0.007353;SB=0;DP4=1009,869,9,7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tTt|S6740F|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tTt|S288F|345|ORF1ab|protein_coding|CODING|YP_009725310.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 21233 . C A 79.0 PASS DP=2467;AF=0.003648;SB=64;DP4=1226,1207,1,26;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gAc|A6990D|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gAc|A192D|297|ORF1ab|protein_coding|CODING|YP_009725311.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 21622 . C A 80.0 PASS DP=3836;AF=0.002868;SB=4;DP4=1888,1920,6,11;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acA|T20|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 21740 . TCCAATGTTACTTGGTTCCATGCTATACATGTCTCTGGGA T 223.0 PASS DP=2522;AF=0.005155;SB=0;DP4=1249,1260,6,7;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 49314.0 PASS DP=2214;AF=0.923216;SB=3;DP4=0,2,1066,1119;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A67V|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 21764 . ATACATG A 49314.0 PASS DP=2068;AF=0.98501;SB=3;DP4=13,18,1000,1037;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 49314.0 PASS DP=2082;AF=0.942363;SB=0;DP4=0,1,1003,1076;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T95I|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 21985 . GGGTGTTTAT G 84.0 PASS DP=1570;AF=0.004459;SB=9;DP4=787,774,6,1;INDEL;HRUN=3;EFF=CODON_DELETION(MODERATE||ggtgtttat/|GVY142|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512.2 21986 . GGTGTTTATT G 49272.0 PASS DP=1525;AF=0.987541;SB=2;DP4=35,29,759,747;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 41683.0 PASS DP=1422;AF=0.909986;SB=68;DP4=244,400,654,640;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 28146.0 PASS DP=1180;AF=0.713559;SB=6;DP4=136,161,421,421;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 TGAGACAGAA 199.0 PASS DP=1180;AF=0.009322;SB=15;DP4=136,161,1,10;INDEL;HRUN=1;EFF=CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||gat/gaGACAGAAGAt|D215ETED|1273|S|protein_coding|CODING|GU280_gp02|1|TGAGACAGAA|INFO_REALIGN_3_PRIME)
NC_045512.2 22204 . T TGATCCAGAA 161.0 PASS DP=1180;AF=0.007627;SB=10;DP4=136,161,7,2;INDEL;HRUN=1;EFF=CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||ctc/cCAGAAGATCtc|L216PEDL|1273|S|protein_coding|CODING|GU280_gp02|1|TGATCCAGAA|INFO_REALIGN_3_PRIME)
NC_045512.2 22578 . G A 49314.0 PASS DP=3304;AF=0.95793;SB=3;DP4=0,1,1662,1636;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G339D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 22583 . GTTT G 100.0 PASS DP=3268;AF=0.002448;SB=0;DP4=1640,1622,4,4;INDEL;HRUN=5;EFF=CODON_DELETION(MODERATE||ttt/|F342|1273|S|protein_coding|CODING|GU280_gp02|1|G|INFO_REALIGN_3_PRIME)
NC_045512.2 22673 . T C 49314.0 PASS DP=1718;AF=0.903376;SB=15;DP4=4,0,700,1001;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tcc/Ccc|S371P|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512.2 22674 . C T 49314.0 PASS DP=1711;AF=0.863238;SB=0;DP4=1,1,702,984;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S371F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 22679 . T C 49314.0 PASS DP=1811;AF=0.890116;SB=32;DP4=11,1,747,1041;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Cca|S373P|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512.2 22685 . TC T 88.0 PASS DP=1830;AF=0.003279;SB=1;DP4=764,1060,3,3;INDEL;HRUN=2;EFF=FRAME_SHIFT(HIGH||tcc/|S375|1273|S|protein_coding|CODING|GU280_gp02|1|T|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00)
NC_045512.2 22686 . C T 49314.0 PASS DP=1830;AF=0.930601;SB=0;DP4=2,3,762,1055;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S375F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 22992 . G A 24970.0 PASS DP=754;AF=0.928382;SB=0;DP4=0,0,402,349;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S477N|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 22995 . C A 26297.0 PASS DP=773;AF=0.934023;SB=0;DP4=0,0,412,361;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aAa|T478K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 23013 . A C 37973.0 PASS DP=1083;AF=0.928901;SB=0;DP4=2,1,571,508;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gCa|E484A|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512.2 23040 . A G 41466.0 PASS DP=1242;AF=0.896135;SB=0;DP4=3,2,636,598;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q493R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512.2 23048 . G A 49314.0 PASS DP=1461;AF=0.960986;SB=0;DP4=1,1,757,701;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G496S|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 23055 . A G 48277.0 PASS DP=1505;AF=0.869767;SB=0;DP4=0,0,774,721;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q498R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512.2 23063 . A T 49314.0 PASS DP=1811;AF=0.967973;SB=0;DP4=1,0,943,865;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Tat|N501Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 23075 . T C 49314.0 PASS DP=1836;AF=0.90305;SB=17;DP4=7,0,948,879;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y505H|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512.2 23202 . C A 49314.0 PASS DP=2798;AF=0.931022;SB=0;DP4=0,1,1383,1400;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=5180;AF=0.897104;SB=19;DP4=15,4,2546,2597;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=4496;AF=0.93105;SB=3;DP4=1,0,2148,2341;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H655Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 23599 . T G 49314.0 PASS DP=2390;AF=0.932218;SB=1;DP4=3,2,1101,1280;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N679K|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512.2 23604 . C A 49314.0 PASS DP=2025;AF=0.937284;SB=0;DP4=1,2,920,1095;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cAt|P681H|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 23854 . C A 643.0 PASS DP=17;AF=1;SB=0;DP4=0,0,8,9;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaC/aaA|N764K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 23948 . G T 28897.0 PASS DP=890;AF=0.859551;SB=0;DP4=0,0,434,441;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Tat|D796Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 24025 . ACTT A 97.0 PASS DP=1549;AF=0.003873;SB=0;DP4=724,825,3,3;INDEL;HRUN=1;EFF=CODON_DELETION(MODERATE||ctt/|L822|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 24130 . C A 49314.0 PASS DP=1674;AF=0.916368;SB=0;DP4=1,2,765,886;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaC/aaA|N856K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 24424 . A T 49314.0 PASS DP=2734;AF=0.940746;SB=14;DP4=1,7,1367,1358;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caA/caT|Q954H|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 24469 . T A 49314.0 PASS DP=4027;AF=0.939409;SB=0;DP4=1,1,2016,1999;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaA|N969K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 24503 . C T 49314.0 PASS DP=4060;AF=0.932512;SB=0;DP4=1,2,1971,2069;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L981F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 24858 . G A 112.0 PASS DP=2435;AF=0.004517;SB=38;DP4=1240,1162,4,23;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGc/gAc|G1099D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 24866 . TG T 86.0 PASS DP=2511;AF=0.002389;SB=0;DP4=1291,1226,3,3;INDEL;HRUN=2;EFF=FRAME_SHIFT(HIGH||tgg/|W1102|1273|S|protein_coding|CODING|GU280_gp02|1|T|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00)
NC_045512.2 24942 . A T 131.0 PASS DP=2150;AF=0.006047;SB=0;DP4=1068,1064,8,7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gTt|D1127V|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 25000 . C T 49314.0 PASS DP=1739;AF=0.890742;SB=5;DP4=2,5,867,860;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D1146|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 25584 . C T 49314.0 PASS DP=3424;AF=0.922313;SB=3;DP4=1,0,1702,1719;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T64|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
NC_045512.2 26194 . A T 106.0 PASS DP=3464;AF=0.003753;SB=2;DP4=1692,1715,14,11;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acg/Tcg|T268S|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
NC_045512.2 26270 . C T 49314.0 PASS DP=3121;AF=0.93784;SB=0;DP4=3,3,1458,1645;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T9I|75|E|protein_coding|CODING|GU280_gp04|1|T)
NC_045512.2 26530 . A G 33497.0 PASS DP=1009;AF=0.908821;SB=1;DP4=2,4,484,514;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D3G|222|M|protein_coding|CODING|GU280_gp05|1|G)
NC_045512.2 26577 . C G 13027.0 PASS DP=416;AF=0.872596;SB=0;DP4=16,16,185,198;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q19E|222|M|protein_coding|CODING|GU280_gp05|1|G)
NC_045512.2 26709 . G A 33637.0 PASS DP=1057;AF=0.856197;SB=0;DP4=0,0,494,558;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A63T|222|M|protein_coding|CODING|GU280_gp05|1|A)
NC_045512.2 27259 . A C 49314.0 PASS DP=2596;AF=0.901387;SB=0;DP4=1,1,1368,1219;EFF=SYNONYMOUS_CODING(LOW|SILENT|Agg/Cgg|R20|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
NC_045512.2 27800 . C A 99.0 PASS DP=2812;AF=0.003912;SB=28;DP4=1323,1448,25,8;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcA|A15|43|ORF7b|protein_coding|CODING|GU280_gp08|1|A)
NC_045512.2 27807 . C T 49314.0 PASS DP=2789;AF=0.933668;SB=0;DP4=1,1,1347,1432;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L18|43|ORF7b|protein_coding|CODING|GU280_gp08|1|T)
NC_045512.2 28214 . C CT 173.0 PASS DP=2046;AF=0.005376;SB=1;DP4=1013,1034,6,5;INDEL;HRUN=5;EFF=FRAME_SHIFT(HIGH||tta/ttTa|L109F?|121|ORF8|protein_coding|CODING|GU280_gp09|1|CT|INFO_REALIGN_3_PRIME);LOF=(ORF8|GU280_gp09|1|1.00)
NC_045512.2 28253 . CA C 80.0 PASS DP=3148;AF=0.001906;SB=0;DP4=1576,1571,3,3;INDEL;HRUN=1;EFF=FRAME_SHIFT(HIGH||atc/|I121|121|ORF8|protein_coding|CODING|GU280_gp09|1|C)
NC_045512.2 28271 . A T 49314.0 PASS DP=3633;AF=0.944674;SB=0;DP4=2,3,1796,1824
NC_045512.2 28311 . C T 49314.0 PASS DP=3776;AF=0.851165;SB=27;DP4=4,20,1810,1914;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cTc|P13L|419|N|protein_coding|CODING|GU280_gp10|1|T)
NC_045512.2 28361 . GGAGAACGCA G 49314.0 PASS DP=3397;AF=0.815131;SB=3;DP4=315,323,1319,1450;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 375.0 PASS DP=2825;AF=0.010265;SB=76;DP4=1341,1463,28,1;INDEL;HRUN=1;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gaacgcagtggg/ggg|ERSG31G|419|N|protein_coding|CODING|GU280_gp10|1|A|INFO_REALIGN_3_PRIME)
NC_045512.2 28541 . G T 564.0 PASS DP=3086;AF=0.012962;SB=1;DP4=1561,1465,25,20;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A90S|419|N|protein_coding|CODING|GU280_gp10|1|T)
NC_045512.2 28881 . G A 49314.0 PASS DP=2000;AF=0.9365;SB=0;DP4=2,3,992,999;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aAg|R203K|419|N|protein_coding|CODING|GU280_gp10|1|A)
NC_045512.2 28882 . G A 49314.0 PASS DP=1993;AF=0.911691;SB=0;DP4=0,0,989,989;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R203|419|N|protein_coding|CODING|GU280_gp10|1|A)
NC_045512.2 28883 . G C 49314.0 PASS DP=1996;AF=0.943888;SB=6;DP4=2,0,988,1003;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gga/Cga|G204R|419|N|protein_coding|CODING|GU280_gp10|1|C)
NC_045512.2 28987 . CCAA C 216.0 PASS DP=1693;AF=0.007088;SB=0;DP4=856,868,6,6;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 29518 . C T 44476.0 PASS DP=1331;AF=0.909842;SB=3;DP4=0,1,700,622;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D415|419|N|protein_coding|CODING|GU280_gp10|1|T)