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sample-06.vcf
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sample-06.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/066/348/66348161/tmp/lofreq2_call_parallelyg27hph0/0.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_71,Description="Minimum SNV Quality (Phred) 71">
##FILTER=<ID=min_indelqual_55,Description="Minimum Indel Quality (Phred) 55">
##FILTER=<ID=min_snvqual_77,Description="Minimum SNV Quality (Phred) 77">
##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 21:36:29 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 21:37:31 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/066/348/66348341/outputs/dataset_02ce699b-43e1-4510-83c8-9eba98cb6aa4.dat NC_045512.2 /data/dnb09/galaxy_db/files/f/5/5/dataset_f55c6fe0-c69e-4d2f-8951-0548b6f6bb8c.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 30837.0 PASS DP=885;AF=0.946893;SB=3;DP4=1,0,438,445
NC_045512.2 443 . GT G 124.0 PASS DP=3300;AF=0.002727;SB=0;DP4=1685,1608,5,4;INDEL;HRUN=4;EFF=FRAME_SHIFT(HIGH||ttg/|L61|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L61|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L61|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L61|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 507 . ATGGTCATGTTATGGT A 341.0 PASS DP=3799;AF=0.005265;SB=0;DP4=1885,1894,10,10;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 779.0 PASS DP=3772;AF=0.010604;SB=0;DP4=1852,1862,20,20;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 276.0 PASS DP=3772;AF=0.004772;SB=0;DP4=1852,1862,9,9;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_045512.2 509 . GGTCATGTTA G 110.0 PASS DP=3772;AF=0.002121;SB=0;DP4=1852,1862,4,4;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_045512.2 514 . TGTTATG T 183.0 PASS DP=3791;AF=0.003165;SB=0;DP4=1882,1897,6,6;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_045512.2 517 . TATG T 162.0 PASS DP=3751;AF=0.002933;SB=0;DP4=1866,1880,5,6;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 . ATGGTT A 75.0 PASS DP=3684;AF=0.001629;SB=0;DP4=1867,1879,3,3;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_045512.2 685 . AAAGTCATTT A 162.0 PASS DP=2587;AF=0.003865;SB=0;DP4=1268,1341,5,5;INDEL;HRUN=3;EFF=CODON_DELETION(MODERATE||aagtcattt/|KSF141|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),CODON_DELETION(MODERATE||aagtcattt/|KSF141|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON),CODON_DELETION(MODERATE||aagtcattt/|KSF141|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON),CODON_DELETION(MODERATE||aagtcattt/|KSF141|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A)
NC_045512.2 1026 . C CT 236.0 PASS DP=1686;AF=0.007711;SB=0;DP4=885,788,7,6;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 1218 . C T 78.0 PASS DP=1653;AF=0.004235;SB=1;DP4=782,860,5,4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S318L|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S318L|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S138L|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S138L|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 1495 . G GT 99.0 PASS DP=1163;AF=0.005159;SB=0;DP4=582,587,3,3;INDEL;HRUN=2;EFF=FRAME_SHIFT(HIGH||ttc/ttTc|F411F?|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|GT|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttc/ttTc|F411F?|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|GT|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttc/ttTc|F231F?|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|GT|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttc/ttTc|F231F?|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|GT|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14)
NC_045512.2 1957 . G T 49314.0 PASS DP=2748;AF=0.92067;SB=4;DP4=1,3,1389,1349;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaG/aaT|K564N|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaG/aaT|K564N|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaG/aaT|K384N|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaG/aaT|K384N|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 2330 . T A 126.0 PASS DP=2123;AF=0.005181;SB=8;DP4=982,1067,12,6;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 49314.0 PASS DP=1451;AF=0.93315;SB=0;DP4=0,0,677,773;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 34025.0 PASS DP=970;AF=0.928866;SB=0;DP4=0,0,465,496;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 3319 . A G 49314.0 PASS DP=1990;AF=0.91206;SB=1;DP4=4,5,999,981;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P1018|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P1018|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P200|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P200|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 3545 . AATG A 227.0 PASS DP=2360;AF=0.005508;SB=0;DP4=1169,1180,6,7;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 123.0 PASS DP=159;AF=0.037736;SB=1;DP4=75,76,5,3;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 4528 . ATT A 61.0 PASS DP=1231;AF=0.003249;SB=0;DP4=612,611,2,2;INDEL;HRUN=4;EFF=FRAME_SHIFT(HIGH||ttttac/|FY1422|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttttac/|FY1422|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttttac/|FY604|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttttac/|FY604|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 4579 . TAACGATCTA T 66.0 PASS DP=1170;AF=0.003419;SB=0;DP4=568,598,2,2;INDEL;HRUN=2;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aacgatctaaat/aat|NDLN1439N|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aacgatctaaat/aat|NDLN1439N|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aacgatctaaat/aat|NDLN621N|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aacgatctaaat/aat|NDLN621N|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME)
NC_045512.2 5183 . C A 91.0 PASS DP=2387;AF=0.00377;SB=66;DP4=1190,1147,6,39;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Act|P1640T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Act|P1640T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Act|P822T|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Act|P822T|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=2396;AF=0.890234;SB=0;DP4=4,5,1183,1193;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 1003.0 PASS DP=2014;AF=0.030288;SB=0;DP4=980,962,33,34;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 976.0 PASS DP=2014;AF=0.029791;SB=0;DP4=974,961,37,34;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 36682.0 PASS DP=1048;AF=0.996183;SB=0;DP4=3,3,556,488;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 252.0 PASS DP=1842;AF=0.008143;SB=0;DP4=926,930,8,7;INDEL;HRUN=4;EFF=FRAME_SHIFT(HIGH||ctt/Tctt|L2146S?|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|CT|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ctt/Tctt|L2146S?|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|CT|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ctt/Tctt|L1328S?|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|CT|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ctt/Tctt|L1328S?|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|CT|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14)
NC_045512.2 7196 . AT A 76.0 PASS DP=1890;AF=0.002646;SB=0;DP4=993,894,3,2;INDEL;HRUN=3;EFF=FRAME_SHIFT(HIGH||tca/|S2312|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tca/|S2312|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tca/|S1494|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tca/|S1494|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 7246 . GTT G 82.0 PASS DP=1992;AF=0.003012;SB=0;DP4=994,1006,3,3;INDEL;HRUN=5;EFF=FRAME_SHIFT(HIGH||ttg/|L2329|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L2329|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L1511|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L1511|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 8393 . G A 49314.0 PASS DP=1851;AF=0.942193;SB=0;DP4=1,1,1021,826;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 9135 . T C 81.0 PASS DP=2070;AF=0.003865;SB=1;DP4=1023,1035,5,4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M2957T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M2957T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M194T|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M194T|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 9621 . A T 77.0 PASS DP=2630;AF=0.003042;SB=157;DP4=1249,1321,51,0;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 9859 . ATT A 67.0 PASS DP=1043;AF=0.003835;SB=0;DP4=548,493,2,2;INDEL;HRUN=2;EFF=FRAME_SHIFT(HIGH||tta/|L3199|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),FRAME_SHIFT(HIGH||tta/|L3199|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),FRAME_SHIFT(HIGH||tta/|L436|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),FRAME_SHIFT(HIGH||tta/|L436|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.14)
NC_045512.2 10029 . C T 49314.0 PASS DP=1721;AF=0.872748;SB=4;DP4=8,4,850,848;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 10046 . GTT G 73.0 PASS DP=1638;AF=0.003053;SB=0;DP4=815,845,2,3;INDEL;HRUN=4;EFF=FRAME_SHIFT(HIGH||ttg/|L3262|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L3262|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L499|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L499|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 10408 . C T 150.0 PASS DP=1933;AF=0.006208;SB=8;DP4=886,1024,11,6;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y3381|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y3381|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y118|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y118|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 10449 . C A 49314.0 PASS DP=2214;AF=0.900181;SB=2;DP4=1,3,1060,1145;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 179.0 PASS DP=1291;AF=0.01007;SB=0;DP4=669,606,7,7;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 217.0 PASS DP=1502;AF=0.010652;SB=4;DP4=734,736,8,13;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 11095 . C CT 266.0 PASS DP=1566;AF=0.009579;SB=0;DP4=815,736,8,7;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 11268 . ATATGGTTGATACTAGTTTGTCTGGTTTTAAGC A 90.0 PASS DP=2312;AF=0.002595;SB=0;DP4=1113,1195,3,3;INDEL;HRUN=1;EFF=FRAME_SHIFT(HIGH||atggttgatactagtttgtctggttttaagcta/|MVDTSLSGFKL3669|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||atggttgatactagtttgtctggttttaagcta/|MVDTSLSGFKL3669|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||atggttgatactagtttgtctggttttaagcta/|MVDTSLSGFKL100|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||atggttgatactagtttgtctggttttaagcta/|MVDTSLSGFKL100|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14)
NC_045512.2 11282 . AGTTTGTCTG A 49314.0 PASS DP=2094;AF=0.920726;SB=13;DP4=89,73,903,1025;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 11485 . TA T 118.0 PASS DP=4016;AF=0.002241;SB=0;DP4=1998,2016,4,5;INDEL;HRUN=1;EFF=FRAME_SHIFT(HIGH||act/|T3741|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),FRAME_SHIFT(HIGH||act/|T3741|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),FRAME_SHIFT(HIGH||act/|T172|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),FRAME_SHIFT(HIGH||act/|T172|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.14)
NC_045512.2 11537 . A G 49314.0 PASS DP=3821;AF=0.897671;SB=0;DP4=2,2,1882,1928;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 12132 . CTTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTG C 65.0 PASS DP=2508;AF=0.001994;SB=1;DP4=1266,1259,2,3;INDEL;HRUN=4;EFF=FRAME_SHIFT(HIGH||tttgctactgctcaagaagcttatgagcaggctgtt/|FATAQEAYEQAV3957|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tttgctactgctcaagaagcttatgagcaggctgtt/|FATAQEAYEQAV3957|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tttgctactgctcaagaagcttatgagcaggctgtt/|FATAQEAYEQAV15|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tttgctactgctcaagaagcttatgagcaggctgtt/|FATAQEAYEQAV15|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14)
NC_045512.2 12503 . T C 101.0 PASS DP=1240;AF=0.006452;SB=1;DP4=603,624,6,5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tat/Cat|Y4080H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tat/Cat|Y4080H|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tat/Cat|Y138H|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tat/Cat|Y138H|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 13195 . T C 49314.0 PASS DP=3874;AF=0.920754;SB=1;DP4=4,2,2055,1805;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 14408 . C T 49314.0 PASS DP=1988;AF=0.934608;SB=2;DP4=1,2,1024,952;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 14900 . GTAT G 66.0 PASS DP=1052;AF=0.003802;SB=0;DP4=524,526,2,2;INDEL;HRUN=1;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||attaat/aat|IN4880N|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||attaat/aat|IN488N|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME)
NC_045512.2 15157 . C A 355.0 PASS DP=2011;AF=0.011934;SB=834;DP4=1036,716,3,255;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 224.0 PASS DP=2059;AF=0.007771;SB=621;DP4=1049,811,1,192;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=1936;AF=0.928719;SB=0;DP4=1,1,922,1004;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 15672 . GT G 64.0 PASS DP=2535;AF=0.001972;SB=1;DP4=1319,1221,2,3;INDEL;HRUN=4;EFF=FRAME_SHIFT(HIGH||tac/|Y5138|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tac/|Y746|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 17144 . G A 79.0 PASS DP=1360;AF=0.005147;SB=0;DP4=686,665,4,4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R5627H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R303H|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 18163 . A G 15785.0 PASS DP=465;AF=0.931183;SB=0;DP4=0,0,231,232;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 18877 . C T 77.0 PASS DP=1379;AF=0.005076;SB=1;DP4=641,723,5,7;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L6205|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L280|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 19983 . C T 203.0 PASS DP=2894;AF=0.007256;SB=6;DP4=1447,1399,13,20;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 20091 . C CA 70.0 PASS DP=2054;AF=0.002434;SB=0;DP4=1038,1022,3,2;INDEL;HRUN=3;EFF=FRAME_SHIFT(HIGH||caa/Acaa|Q6611T?|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|CA|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||caa/Acaa|Q159T?|345|ORF1ab|protein_coding|CODING|YP_009725310.1|1|CA|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 20114 . T A 105.0 PASS DP=1611;AF=0.005587;SB=88;DP4=793,778,0,30;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 20117 . C A 79.0 PASS DP=1586;AF=0.004414;SB=145;DP4=775,740,4,64;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 21740 . TCCAATGTTACTTGGTTCCATGCTATACATGTCTCTGGGA T 192.0 PASS DP=1864;AF=0.005901;SB=0;DP4=928,925,6,5;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=1599;AF=0.923702;SB=0;DP4=0,1,771,803;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=1510;AF=0.990066;SB=0;DP4=8,7,737,758;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=1577;AF=0.954344;SB=0;DP4=0,1,764,812;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T95I|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 21974 . GATCCATTTT G 66.0 PASS DP=926;AF=0.00432;SB=0;DP4=475,447,2,2;INDEL;HRUN=1;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gatccatttttg/gtg|DPFL138V|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512.2 21986 . GGTGTTTATT G 28101.0 PASS DP=874;AF=0.981693;SB=3;DP4=29,22,436,422;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 22158 . GTTAT G 63.0 PASS DP=1370;AF=0.00292;SB=0;DP4=683,692,2,2;INDEL;HRUN=2;EFF=FRAME_SHIFT(HIGH||tatttt/|YF200|1273|S|protein_coding|CODING|GU280_gp02|1|G|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00)
NC_045512.2 22193 . AATT A 27599.0 PASS DP=910;AF=0.934066;SB=45;DP4=143,236,431,419;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 19057.0 PASS DP=778;AF=0.727506;SB=7;DP4=83,109,278,288;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 69.0 PASS DP=778;AF=0.005141;SB=8;DP4=83,109,0,4;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 TGAGCCAGTA 92.0 PASS DP=778;AF=0.007712;SB=21;DP4=83,109,6,0;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 22207 . T G 154.0 PASS DP=1321;AF=0.01514;SB=3;DP4=654,640,11,15;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaT/gaG|D215E|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512.2 22218 . GT G 213.0 PASS DP=1342;AF=0.008942;SB=0;DP4=682,683,6,6;INDEL;HRUN=5;EFF=FRAME_SHIFT(HIGH||tcg/|S221|1273|S|protein_coding|CODING|GU280_gp02|1|G|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00)
NC_045512.2 22578 . G A 49314.0 PASS DP=1793;AF=0.96319;SB=0;DP4=0,0,901,891;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G339D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 22673 . T C 33537.0 PASS DP=996;AF=0.906627;SB=11;DP4=3,0,409,584;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tcc/Ccc|S371P|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512.2 22674 . C T 31816.0 PASS DP=991;AF=0.866801;SB=0;DP4=0,1,402,579;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S371F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 22679 . T C 34707.0 PASS DP=1045;AF=0.889952;SB=15;DP4=4,0,431,609;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Cca|S373P|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512.2 22685 . TC T 110.0 PASS DP=1054;AF=0.005693;SB=0;DP4=435,613,2,4;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 37081.0 PASS DP=1054;AF=0.93074;SB=0;DP4=0,0,434,613;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S375F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 22992 . G A 13361.0 PASS DP=407;AF=0.911548;SB=0;DP4=1,1,219,186;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S477N|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 22995 . C A 13617.0 PASS DP=411;AF=0.902676;SB=3;DP4=0,1,221,189;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aAa|T478K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 23013 . A C 20810.0 PASS DP=600;AF=0.916667;SB=0;DP4=2,1,320,276;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gCa|E484A|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512.2 23040 . A G 24349.0 PASS DP=725;AF=0.902069;SB=0;DP4=2,1,370,349;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q493R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512.2 23048 . G A 30741.0 PASS DP=850;AF=0.955294;SB=0;DP4=0,0,442,408;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G496S|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 23055 . A G 27514.0 PASS DP=877;AF=0.851767;SB=0;DP4=0,0,452,417;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q498R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512.2 23063 . A T 36959.0 PASS DP=1033;AF=0.957406;SB=0;DP4=0,0,546,487;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Tat|N501Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 23075 . T C 34146.0 PASS DP=1050;AF=0.893333;SB=19;DP4=10,1,539,497;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=1562;AF=0.930218;SB=0;DP4=0,0,763,790;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=3830;AF=0.888512;SB=6;DP4=4,1,1892,1919;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D614G|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512.2 23458 . T C 78.0 PASS DP=3959;AF=0.002526;SB=3;DP4=1966,1962,7,11;EFF=SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T632|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512.2 23525 . C T 49314.0 PASS DP=3361;AF=0.934543;SB=3;DP4=1,0,1603,1753;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=1705;AF=0.937243;SB=6;DP4=2,0,765,937;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=1475;AF=0.947119;SB=0;DP4=0,1,657,812;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cAt|P681H|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 23948 . G T 38892.0 PASS DP=1143;AF=0.898513;SB=2;DP4=1,2,599,531;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Tat|D796Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 24025 . ACTTT A 61.0 PASS DP=1396;AF=0.002865;SB=0;DP4=699,694,2,2;INDEL;HRUN=1;EFF=FRAME_SHIFT(HIGH||cttttc/|LF822|1273|S|protein_coding|CODING|GU280_gp02|1|A);LOF=(S|GU280_gp02|1|1.00)
NC_045512.2 24130 . C A 39806.0 PASS DP=1191;AF=0.889169;SB=11;DP4=0,5,551,625;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=1687;AF=0.947244;SB=0;DP4=1,2,840,844;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=2702;AF=0.941155;SB=0;DP4=2,2,1371,1322;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=2777;AF=0.940223;SB=4;DP4=3,1,1365,1401;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L981F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 25000 . C T 28223.0 PASS DP=873;AF=0.907216;SB=9;DP4=0,3,439,430;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D1146|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 25195 . A G 89.0 PASS DP=1810;AF=0.00442;SB=1;DP4=903,891,6,4;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K1211|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512.2 25584 . C T 49314.0 PASS DP=1783;AF=0.91419;SB=3;DP4=1,0,884,897;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=1942;AF=0.925335;SB=6;DP4=2,0,893,1035;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T9I|75|E|protein_coding|CODING|GU280_gp04|1|T)
NC_045512.2 26530 . A G 6751.0 PASS DP=211;AF=0.886256;SB=0;DP4=0,0,102,108;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D3G|222|M|protein_coding|CODING|GU280_gp05|1|G)
NC_045512.2 26577 . C G 2561.0 PASS DP=72;AF=0.944444;SB=0;DP4=0,0,37,35;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q19E|222|M|protein_coding|CODING|GU280_gp05|1|G)
NC_045512.2 26709 . G A 3601.0 PASS DP=105;AF=0.914286;SB=0;DP4=0,0,50,55;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A63T|222|M|protein_coding|CODING|GU280_gp05|1|A)
NC_045512.2 26786 . AGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT A 105.0 PASS DP=125;AF=0.032;SB=0;DP4=58,63,2,2;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 27133 . ATAAATT A 65.0 PASS DP=5;AF=0.4;SB=0;DP4=1,2,1,1;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 27259 . A C 49314.0 PASS DP=1633;AF=0.914881;SB=6;DP4=0,2,863,764;EFF=SYNONYMOUS_CODING(LOW|SILENT|Agg/Cgg|R20|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
NC_045512.2 27384 . T C 96.0 PASS DP=2252;AF=0.00444;SB=0;DP4=1116,1121,5,5;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D61|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
NC_045512.2 27481 . C T 79.0 PASS DP=2285;AF=0.003501;SB=1;DP4=1117,1155,5,4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L30F|121|ORF7a|protein_coding|CODING|GU280_gp07|1|T)
NC_045512.2 27512 . A G 127.0 PASS DP=2297;AF=0.005224;SB=13;DP4=1140,1126,5,14;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tAc/tGc|Y40C|121|ORF7a|protein_coding|CODING|GU280_gp07|1|G)
NC_045512.2 27578 . AATT A 65.0 PASS DP=1221;AF=0.003276;SB=0;DP4=635,582,2,2;INDEL;HRUN=2;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||caattt/cat|QF62H|121|ORF7a|protein_coding|CODING|GU280_gp07|1|A)
NC_045512.2 27686 . C T 1642.0 PASS DP=1382;AF=0.055716;SB=0;DP4=645,643,44,47;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tTt|S98F|121|ORF7a|protein_coding|CODING|GU280_gp07|1|T)
NC_045512.2 27807 . C T 49314.0 PASS DP=1836;AF=0.944444;SB=0;DP4=1,1,877,948;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L18|43|ORF7b|protein_coding|CODING|GU280_gp08|1|T)
NC_045512.2 28271 . A T 49314.0 PASS DP=2635;AF=0.936622;SB=0;DP4=1,2,1289,1333
NC_045512.2 28311 . C T 49314.0 PASS DP=2632;AF=0.841945;SB=14;DP4=2,10,1258,1344;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=2240;AF=0.805804;SB=1;DP4=211,232,847,958;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 168.0 PASS DP=1853;AF=0.008635;SB=20;DP4=868,972,13,3;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 43800.0 PASS DP=1232;AF=0.936688;SB=3;DP4=0,1,630,599;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aAg|R203K|419|N|protein_coding|CODING|GU280_gp10|1|A)
NC_045512.2 28882 . G A 41939.0 PASS DP=1230;AF=0.917886;SB=3;DP4=0,1,628,595;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R203|419|N|protein_coding|CODING|GU280_gp10|1|A)
NC_045512.2 28883 . G C 43631.0 PASS DP=1232;AF=0.948052;SB=0;DP4=0,0,629,601;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gga/Cga|G204R|419|N|protein_coding|CODING|GU280_gp10|1|C)
NC_045512.2 28987 . CCAA C 88.0 PASS DP=1025;AF=0.004878;SB=0;DP4=519,519,2,3;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 29311 . CA C 61.0 PASS DP=1548;AF=0.002584;SB=0;DP4=779,765,2,2;INDEL;HRUN=3;EFF=FRAME_SHIFT(HIGH||aaa/|K347|419|N|protein_coding|CODING|GU280_gp10|1|C|INFO_REALIGN_3_PRIME);LOF=(N|GU280_gp10|1|1.00)
NC_045512.2 29355 . A T 137.0 PASS DP=1688;AF=0.006517;SB=1;DP4=840,828,6,7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAa/aTa|K361I|419|N|protein_coding|CODING|GU280_gp10|1|T)
NC_045512.2 29555 . C T 80.0 PASS DP=1239;AF=0.00565;SB=1;DP4=638,591,4,5
NC_045512.2 29574 . TTTTCGC T 144.0 PASS DP=1250;AF=0.0064;SB=0;DP4=643,599,4,4;INDEL;HRUN=4;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ttcgctttt/ttt|FAF7F|38|ORF10|protein_coding|CODING|GU280_gp11|1|T|INFO_REALIGN_3_PRIME)
NC_045512.2 29580 . CT C 61.0 PASS DP=1252;AF=0.003195;SB=0;DP4=647,605,2,2;INDEL;HRUN=4;EFF=FRAME_SHIFT(HIGH||ttt/|F9|38|ORF10|protein_coding|CODING|GU280_gp11|1|C|INFO_REALIGN_3_PRIME);LOF=(ORF10|GU280_gp11|1|1.00)