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sample-07.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/066/348/66348162/tmp/lofreq2_call_parallel78jkk747/0.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_54,Description="Minimum Indel Quality (Phred) 54">
##FILTER=<ID=min_snvqual_79,Description="Minimum SNV Quality (Phred) 79">
##FILTER=<ID=min_indelqual_61,Description="Minimum Indel Quality (Phred) 61">
##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 21:37:04 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 21:37:50 2024
##SnpEffVersion="4.5covid19 (build 2020-04-15 22:26), by Pablo Cingolani"
##SnpEffCmd="SnpEff -i vcf -o vcf -formatEff -classic -no-downstream -no-intergenic -no-upstream -stats /data/jwd05e/main/066/348/66348342/outputs/dataset_e4626423-1aa5-4f44-8512-7fa4819dae1e.dat NC_045512.2 /data/dnb09/galaxy_db/files/d/5/2/dataset_d52f9a88-3f77-488a-b6b2-d7e595058705.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 22488.0 PASS DP=695;AF=0.886331;SB=0;DP4=0,0,342,352
NC_045512.2 509 . GGTCATGTTATGGTT G 145.0 PASS DP=4068;AF=0.002704;SB=0;DP4=2009,2042,5,6;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 75.0 PASS DP=4068;AF=0.001475;SB=0;DP4=2009,2042,3,3;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 1026 . C CT 426.0 PASS DP=1827;AF=0.012042;SB=0;DP4=961,844,12,10;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 1628 . C CA 66.0 PASS DP=1901;AF=0.00263;SB=0;DP4=1019,877,3,2;INDEL;HRUN=5;EFF=FRAME_SHIFT(HIGH||gag/Agag|E457R?|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|CA|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||gag/Agag|E457R?|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|CA|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||gag/Agag|E277R?|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|CA|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||gag/Agag|E277R?|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|CA|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14)
NC_045512.2 2248 . T G 92.0 PASS DP=1328;AF=0.006024;SB=273;DP4=577,651,88,0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggT/ggG|G661|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),SYNONYMOUS_CODING(LOW|SILENT|ggT/ggG|G661|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),SYNONYMOUS_CODING(LOW|SILENT|ggT/ggG|G481|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ggT/ggG|G481|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 2330 . T A 218.0 PASS DP=1723;AF=0.009286;SB=2;DP4=780,868,12,10;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 32215.0 PASS DP=1033;AF=0.856728;SB=0;DP4=0,1,468,559;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 2952 . AT A 69.0 PASS DP=800;AF=0.005;SB=0;DP4=379,423,2,2;INDEL;HRUN=3;EFF=FRAME_SHIFT(HIGH||tta/|L897|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tta/|L897|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tta/|L79|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tta/|L79|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 3037 . C T 30661.0 PASS DP=958;AF=0.859081;SB=0;DP4=0,0,454,492;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F106|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F106|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 3862 . T A 111.0 PASS DP=84;AF=0.059524;SB=0;DP4=39,39,3,3;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 5386 . T G 49314.0 PASS DP=2607;AF=0.807825;SB=13;DP4=4,13,1277,1290;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 214.0 PASS DP=1631;AF=0.010423;SB=1;DP4=803,794,11,13;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E1826D|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E1826D|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E1008D|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E1008D|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 5744 . T C 261.0 PASS DP=1631;AF=0.012262;SB=4;DP4=795,797,18,12;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 6510 . ATAG A 109.0 PASS DP=1214;AF=0.00659;SB=7;DP4=635,570,2,6;INDEL;HRUN=1;EFF=CODON_DELETION(MODERATE||agt/|S2083|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A|INFO_REALIGN_3_PRIME),CODON_DELETION(MODERATE||agt/|S2083|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A|INFO_REALIGN_3_PRIME),CODON_DELETION(MODERATE||agt/|S1265|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),CODON_DELETION(MODERATE||agt/|S1265|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME)
NC_045512.2 6512 . AGTT A 40895.0 PASS DP=1213;AF=0.988458;SB=3;DP4=6,9,631,568;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 688.0 PASS DP=1748;AF=0.018879;SB=0;DP4=866,880,17,16;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 6961 . G GT 72.0 PASS DP=1341;AF=0.003729;SB=1;DP4=657,682,3,2;INDEL;HRUN=5;EFF=FRAME_SHIFT(HIGH||tta/ttTa|L2234F?|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|GT|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tta/ttTa|L2234F?|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|GT|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tta/ttTa|L1416F?|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|GT|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tta/ttTa|L1416F?|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 8376 . CA C 83.0 PASS DP=1706;AF=0.003517;SB=0;DP4=936,764,3,3;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 49314.0 PASS DP=1974;AF=0.890577;SB=0;DP4=5,4,1078,879;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 9078 . T C 49314.0 PASS DP=2034;AF=0.807768;SB=14;DP4=7,1,971,1026;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTa/gCa|V2938A|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTa/gCa|V2938A|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTa/gCa|V175A|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTa/gCa|V175A|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 9541 . CTGTTTAACACCAGTTTACTCATTCTTACCTGG C 73.0 PASS DP=2166;AF=0.002308;SB=0;DP4=1170,991,3,2;INDEL;HRUN=1;EFF=FRAME_SHIFT(HIGH||acaccagtttactcattcttacctggtgtttat/|TPVYSFLPGVY3095|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||acaccagtttactcattcttacctggtgtttat/|TPVYSFLPGVY3095|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||acaccagtttactcattcttacctggtgtttat/|TPVYSFLPGVY332|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||acaccagtttactcattcttacctggtgtttat/|TPVYSFLPGVY332|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14)
NC_045512.2 10029 . C T 45418.0 PASS DP=1524;AF=0.813648;SB=2;DP4=4,6,750,740;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 10148 . C T 105.0 PASS DP=2224;AF=0.004496;SB=12;DP4=1118,1067,19,8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L3295F|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L3295F|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L32F|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L32F|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 10326 . T G 113.0 PASS DP=2619;AF=0.0042;SB=343;DP4=1135,1332,124,4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gGt|V3354G|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gGt|V3354G|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gGt|V91G|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gGt|V91G|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=2050;AF=0.836098;SB=24;DP4=3,18,955,1057;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 300.0 PASS DP=865;AF=0.020809;SB=6;DP4=440,395,9,14;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 252.0 PASS DP=1008;AF=0.015873;SB=2;DP4=492,482,11,14;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 10763 . T G 82.0 PASS DP=1959;AF=0.004084;SB=86;DP4=943,959,37,2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Gac|Y3500D|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Gac|Y3500D|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Gac|Y237D|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Gac|Y237D|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 11095 . C CT 253.0 PASS DP=1184;AF=0.011824;SB=0;DP4=611,559,7,7;INDEL;HRUN=5;EFF=FRAME_SHIFT(HIGH||tta/ttTa|L3612F?|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|CT|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tta/ttTa|L3612F?|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|CT|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tta/ttTa|L43F?|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|CT|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tta/ttTa|L43F?|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|CT|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14)
NC_045512.2 11279 . ACTAGTTTGT A 67.0 PASS DP=1577;AF=0.005707;SB=10;DP4=728,844,7,2;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=1538;AF=0.894668;SB=19;DP4=91,72,621,755;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 11287 . GTCTGGTTTT G 64.0 PASS DP=1413;AF=0.004246;SB=20;DP4=642,768,6,0;INDEL;HRUN=1;EFF=CODON_DELETION(MODERATE||tctggtttt/|SGF3675|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),CODON_DELETION(MODERATE||tctggtttt/|SGF3675|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),CODON_DELETION(MODERATE||tctggtttt/|SGF106|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),CODON_DELETION(MODERATE||tctggtttt/|SGF106|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 11537 . A G 49314.0 PASS DP=3607;AF=0.821181;SB=2;DP4=6,4,1742,1831;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 11613 . A T 94.0 PASS DP=2508;AF=0.004386;SB=319;DP4=1038,1328,119,7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tAt/tTt|Y3783F|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tAt/tTt|Y3783F|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tAt/tTt|Y214F|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tAt/tTt|Y214F|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 13142 . AATTGTG A 62.0 PASS DP=1505;AF=0.002658;SB=0;DP4=688,814,2,2;INDEL;HRUN=2;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aattgtgtt/att|NCV4293I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aattgtgtt/att|NCV4293I|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aattgtgtt/att|NCV40I|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aattgtgtt/att|NCV40I|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 13195 . T C 49314.0 PASS DP=3608;AF=0.857539;SB=21;DP4=11,1,1915,1662;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 13442 . T G 96.0 PASS DP=3054;AF=0.003274;SB=315;DP4=1196,1682,144,21;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Gca|S4393A|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Gca|S4393A|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Gca|S1A|12|ORF1ab|protein_coding|CODING|YP_009725312.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Gca|S1A|931|ORF1ab|protein_coding|CODING|YP_009725307.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 14408 . C T 49314.0 PASS DP=1942;AF=0.883625;SB=3;DP4=0,1,982,950;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 14866 . G GT 70.0 PASS DP=809;AF=0.004944;SB=0;DP4=401,408,2,2;INDEL;HRUN=2;EFF=FRAME_SHIFT+STOP_GAINED(HIGH||gat/Tgat|D4869*?|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|GT|INFO_REALIGN_3_PRIME),FRAME_SHIFT+STOP_GAINED(HIGH||gat/Tgat|D477*?|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|GT|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 15157 . C A 335.0 PASS DP=1959;AF=0.011741;SB=679;DP4=1048,715,1,194;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 119.0 PASS DP=2033;AF=0.004919;SB=517;DP4=1063,810,0,151;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=1866;AF=0.88746;SB=0;DP4=0,0,878,976;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 15781 . A T 124.0 PASS DP=2895;AF=0.004145;SB=223;DP4=1325,1461,85,3;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 16251 . T G 124.0 PASS DP=2841;AF=0.004224;SB=377;DP4=1284,1431,120,0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tgT/tgG|C5329W|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tgT/tgG|C5W|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 16457 . C T 121.0 PASS DP=2109;AF=0.005216;SB=17;DP4=991,1087,19,7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S5398L|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S74L|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 16501 . G GT 61.0 PASS DP=935;AF=0.004278;SB=0;DP4=479,452,2,2;INDEL;HRUN=5;EFF=FRAME_SHIFT(HIGH||ggt/Tggt|G5415W?|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|GT|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ggt/Tggt|G91W?|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|GT|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 16837 . GA G 84.0 PASS DP=3165;AF=0.002212;SB=0;DP4=1659,1499,4,3;INDEL;HRUN=5;EFF=FRAME_SHIFT(HIGH||aaa/|K5526|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K202|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 17502 . C T 1416.0 PASS DP=2614;AF=0.029457;SB=1;DP4=1259,1257,50,45;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F5746|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F422|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 18163 . A G 13018.0 PASS DP=437;AF=0.82151;SB=0;DP4=1,0,218,216;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 19983 . C T 92.0 PASS DP=2801;AF=0.00357;SB=13;DP4=1408,1339,8,18;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 21740 . TCCAATGTTACTTGGTTCCATGCTATACATGTCTCTGGGA T 196.0 PASS DP=1825;AF=0.006027;SB=4;DP4=903,911,7,4;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 45113.0 PASS DP=1506;AF=0.87915;SB=0;DP4=2,2,706,769;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A67V|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 21764 . ATACATG A 46688.0 PASS DP=1423;AF=0.983837;SB=5;DP4=15,10,672,728;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 48800.0 PASS DP=1406;AF=0.921764;SB=6;DP4=0,3,666,729;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T95I|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 21985 . GGGTGTTTAT G 156.0 PASS DP=750;AF=0.013333;SB=9;DP4=371,373,8,2;INDEL;HRUN=3;EFF=CODON_DELETION(MODERATE||ggtgtttat/|GVY142|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512.2 21986 . GGTGTTTATT G 21812.0 PASS DP=729;AF=0.964335;SB=4;DP4=27,20,348,355;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 21016.0 PASS DP=727;AF=0.918845;SB=62;DP4=98,194,342,326;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 12438.0 PASS DP=597;AF=0.638191;SB=6;DP4=83,103,192,189;INDEL;HRUN=1;EFF=CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||gat/gaGCCAGAAGAt|D215EPED|1273|S|protein_coding|CODING|GU280_gp02|1|TGAGCCAGAA|INFO_REALIGN_3_PRIME)
NC_045512.2 22204 . T TGAGCCAGTA 70.0 PASS DP=597;AF=0.0067;SB=13;DP4=83,103,4,0;INDEL;HRUN=1;EFF=CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||gat/gaGCCAGTAGAt|D215EPVD|1273|S|protein_coding|CODING|GU280_gp02|1|TGAGCCAGTA|INFO_REALIGN_3_PRIME)
NC_045512.2 22204 . T TGAGACAGAA 80.0 PASS DP=597;AF=0.008375;SB=11;DP4=83,103,0,5;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 22578 . G A 49314.0 PASS DP=1514;AF=0.937913;SB=0;DP4=0,0,762,748;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G339D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 22673 . T C 22762.0 PASS DP=746;AF=0.83244;SB=0;DP4=2,2,309,427;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tcc/Ccc|S371P|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512.2 22674 . C T 21500.0 PASS DP=743;AF=0.79004;SB=0;DP4=0,1,307,417;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S371F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 22679 . T C 23838.0 PASS DP=783;AF=0.8212;SB=7;DP4=4,1,328,441;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Cca|S373P|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512.2 22686 . C T 25311.0 PASS DP=792;AF=0.853535;SB=1;DP4=1,3,331,452;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S375F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 22992 . G A 12027.0 PASS DP=387;AF=0.865633;SB=0;DP4=0,0,211,174;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S477N|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 22995 . C A 12825.0 PASS DP=398;AF=0.88191;SB=3;DP4=2,4,215,177;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aAa|T478K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 23013 . A C 18316.0 PASS DP=550;AF=0.883636;SB=1;DP4=2,3,296,249;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gCa|E484A|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512.2 23040 . A G 20062.0 PASS DP=629;AF=0.860095;SB=0;DP4=0,0,325,299;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q493R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512.2 23048 . G A 25705.0 PASS DP=729;AF=0.930041;SB=0;DP4=1,0,376,351;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G496S|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 23055 . A G 22128.0 PASS DP=753;AF=0.806109;SB=0;DP4=0,0,382,362;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q498R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512.2 23063 . A T 31095.0 PASS DP=899;AF=0.931035;SB=0;DP4=0,0,471,427;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Tat|N501Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 23075 . T C 26190.0 PASS DP=894;AF=0.815436;SB=13;DP4=8,1,462,417;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y505H|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512.2 23202 . C A 44604.0 PASS DP=1360;AF=0.873529;SB=4;DP4=3,1,659,685;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=3542;AF=0.806889;SB=14;DP4=14,5,1725,1762;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D614G|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512.2 23501 . G T 49314.0 PASS DP=3367;AF=0.810514;SB=6;DP4=9,16,1603,1712;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Tca|A647S|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 23525 . C T 49314.0 PASS DP=2954;AF=0.883886;SB=3;DP4=5,3,1391,1545;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=1584;AF=0.885732;SB=3;DP4=4,2,698,874;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N679K|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512.2 23604 . C A 45331.0 PASS DP=1354;AF=0.905465;SB=5;DP4=0,3,591,755;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cAt|P681H|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 23948 . G T 37979.0 PASS DP=1220;AF=0.82623;SB=0;DP4=3,3,647,541;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Tat|D796Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 24130 . C A 43955.0 PASS DP=1461;AF=0.80835;SB=3;DP4=6,11,656,777;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaC/aaA|N856K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 24424 . A T 44036.0 PASS DP=1376;AF=0.869913;SB=0;DP4=4,4,684,682;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=2552;AF=0.892633;SB=0;DP4=6,6,1306,1232;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=2676;AF=0.886771;SB=1;DP4=3,2,1315,1341;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L981F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 24858 . G A 160.0 PASS DP=1119;AF=0.010724;SB=15;DP4=563,524,6,16;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGc/gAc|G1099D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 25000 . C T 22907.0 PASS DP=794;AF=0.806045;SB=10;DP4=3,10,389,382;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D1146|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 25584 . C T 47011.0 PASS DP=1495;AF=0.854181;SB=0;DP4=1,2,722,759;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T64|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
NC_045512.2 26270 . C T 49314.0 PASS DP=1730;AF=0.858382;SB=1;DP4=2,4,800,912;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T9I|75|E|protein_coding|CODING|GU280_gp04|1|T)
NC_045512.2 26530 . A G 22206.0 PASS DP=735;AF=0.834014;SB=0;DP4=0,0,343,381;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D3G|222|M|protein_coding|CODING|GU280_gp05|1|G)
NC_045512.2 26574 . GAAC G 82.0 PASS DP=441;AF=0.00907;SB=0;DP4=214,225,2,2;INDEL;HRUN=2;EFF=CODON_DELETION(MODERATE||caa/|Q19|222|M|protein_coding|CODING|GU280_gp05|1|G|INFO_REALIGN_3_PRIME)
NC_045512.2 26577 . C G 7860.0 PASS DP=261;AF=0.83908;SB=0;DP4=4,4,121,129;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q19E|222|M|protein_coding|CODING|GU280_gp05|1|G)
NC_045512.2 26654 . G GT 67.0 PASS DP=197;AF=0.020305;SB=0;DP4=95,98,2,2;INDEL;HRUN=5;EFF=FRAME_SHIFT(HIGH||ttg/ttTg|L46F?|222|M|protein_coding|CODING|GU280_gp05|1|GT|INFO_REALIGN_3_PRIME);LOF=(M|GU280_gp05|1|1.00)
NC_045512.2 26709 . G A 8623.0 PASS DP=289;AF=0.806228;SB=0;DP4=0,0,141,144;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A63T|222|M|protein_coding|CODING|GU280_gp05|1|A)
NC_045512.2 27259 . A C 41901.0 PASS DP=1356;AF=0.84292;SB=0;DP4=1,0,714,632;EFF=SYNONYMOUS_CODING(LOW|SILENT|Agg/Cgg|R20|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
NC_045512.2 27373 . A ACTTTCGATCTCT 65.0 PASS DP=2067;AF=0.002903;SB=0;DP4=1030,1032,3,3;INDEL;HRUN=1;EFF=CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||atg/aCTTTCGATCTCTtg|M58TFDLL|61|ORF6|protein_coding|CODING|GU280_gp06|1|ACTTTCGATCTCT)
NC_045512.2 27637 . G GT 63.0 PASS DP=1363;AF=0.002935;SB=0;DP4=682,677,2,2;INDEL;HRUN=3;EFF=FRAME_SHIFT(HIGH||tca/tTca|S83F?|121|ORF7a|protein_coding|CODING|GU280_gp07|1|GT|INFO_REALIGN_3_PRIME);LOF=(ORF7a|GU280_gp07|1|1.00)
NC_045512.2 27807 . C T 49314.0 PASS DP=1765;AF=0.887819;SB=0;DP4=1,1,839,916;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L18|43|ORF7b|protein_coding|CODING|GU280_gp08|1|T)
NC_045512.2 28254 . A C 96.0 PASS DP=2153;AF=0.004645;SB=11;DP4=1049,1070,6,15;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Ctc|I121L|121|ORF8|protein_coding|CODING|GU280_gp09|1|C)
NC_045512.2 28271 . A T 49314.0 PASS DP=2451;AF=0.880865;SB=2;DP4=2,1,1180,1258
NC_045512.2 28311 . C T 49314.0 PASS DP=2470;AF=0.780972;SB=15;DP4=3,14,1130,1293;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=2093;AF=0.777353;SB=1;DP4=219,256,738,889;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 514.0 PASS DP=1691;AF=0.020698;SB=75;DP4=759,906,32,3;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 28881 . G A 43468.0 PASS DP=1275;AF=0.905098;SB=4;DP4=1,4,634,633;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aAg|R203K|419|N|protein_coding|CODING|GU280_gp10|1|A)
NC_045512.2 28882 . G A 40913.0 PASS DP=1274;AF=0.869702;SB=18;DP4=0,6,634,622;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R203|419|N|protein_coding|CODING|GU280_gp10|1|A)
NC_045512.2 28883 . G C 43420.0 PASS DP=1279;AF=0.915559;SB=0;DP4=0,0,637,640;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gga/Cga|G204R|419|N|protein_coding|CODING|GU280_gp10|1|C)
NC_045512.2 29377 . TA T 79.0 PASS DP=2170;AF=0.002765;SB=0;DP4=1087,1082,3,3;INDEL;HRUN=5;EFF=FRAME_SHIFT(HIGH||aag/|K370|419|N|protein_coding|CODING|GU280_gp10|1|T|INFO_REALIGN_3_PRIME);LOF=(N|GU280_gp10|1|1.00)
NC_045512.2 29562 . G A 102.0 PASS DP=1093;AF=0.007319;SB=0;DP4=555,514,7,8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGc/gAc|G2D|38|ORF10|protein_coding|CODING|GU280_gp11|1|A)
NC_045512.2 29750 . C T 38295.0 PASS DP=1281;AF=0.824356;SB=0;DP4=0,0,593,669