Mercurial > repos > iuc > snpfreqplot
view test-data/1085841.vcf @ 0:1062d6ad6503 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
| author | iuc |
|---|---|
| date | Wed, 02 Dec 2020 21:23:06 +0000 |
| parents | |
| children |
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##fileformat=VCFv4.0 ##fileDate=20201106 ##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_045512.2:1-14951 -o /data/dnb03/galaxy_db/job_working_directory/012/246/12246264/tmp/lofreq2_call_parallelozwg3m_j/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="Allele Frequency"> ##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_77,Description="Minimum SNV Quality (Phred) 77"> ##FILTER=<ID=min_indelqual_63,Description="Minimum Indel Quality (Phred) 63"> ##FILTER=<ID=min_snvqual_81,Description="Minimum SNV Quality (Phred) 81"> ##FILTER=<ID=min_indelqual_67,Description="Minimum Indel Quality (Phred) 67"> ##FILTER=<ID=min_af_0.050000,Description="Minimum allele frequency 0.050000"> ##FILTER=<ID=min_dp_5,Description="Minimum Coverage 5"> ##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000"> ##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/dnb03/galaxy_db/job_working_directory/012/246/12246344/outputs/galaxy_dataset_bf9af93e-df97-4905-9528-e5733fd0f335.dat NC_045512.2 /data/dnb03/galaxy_db/files/9/7/0/dataset_970a100a-939e-4af8-9511-ce9ea0a545ea.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 40 . CT C 98.0 min_af_0.050000 AF=0.003612;DP=1661;DP4=9,1646,0,6;HRUN=3;SB=0;INDEL NC_045512.2 186 . C T 86.0 min_af_0.050000 AF=0.001217;DP=13143;DP4=8948,4173,14,5;SB=0 NC_045512.2 241 . C T 49314.0 PASS AF=0.994071;DP=7084;DP4=0,1,3410,3672;SB=0 NC_045512.2 323 . GT G 77.0 min_af_0.050000 AF=0.000621;DP=16109;DP4=3862,12282,3,7;HRUN=4;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||tta/|L21|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tta/|L21|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tta/|L21|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tta/|L21|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07) NC_045512.2 361 . A G 134.0 min_af_0.050000 AF=0.001169;DP=19673;DP4=7430,12213,13,12;SB=8;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G32|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G32|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G32|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G32|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G) NC_045512.2 443 . GT G 91.0 min_af_0.050000 AF=0.001118;DP=8048;DP4=5853,2241,5,4;HRUN=4;SB=5;INDEL;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_045512.2 517 . TATG T 177.0 min_af_0.050000 AF=0.002808;DP=4274;DP4=2289,2025,5,7;HRUN=1;SB=2;INDEL;EFF=CODON_DELETION(MODERATE||atg/|M85|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),CODON_DELETION(MODERATE||atg/|M85|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON),CODON_DELETION(MODERATE||atg/|M85|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON),CODON_DELETION(MODERATE||atg/|M85|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T) NC_045512.2 685 . AAAGTCATTT A 94.0 min_af_0.050000 AF=0.000962;DP=9354;DP4=3244,6121,5,4;HRUN=3;SB=5;INDEL;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 1027 . T C 145.0 min_af_0.050000 AF=0.001334;DP=17235;DP4=13669,3528,24,4;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P254|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P254|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P74|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P74|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 1115 . A T 221.0 min_af_0.050000 AF=0.003510;DP=6267;DP4=2472,3771,2,21;SB=26;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Ttt|I284F|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Ttt|I284F|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Ttt|I104F|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Ttt|I104F|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 1330 . T A 202.0 min_af_0.050000 AF=0.003426;DP=5838;DP4=4195,1622,16,4;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|acT/acA|T355|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),SYNONYMOUS_CODING(LOW|SILENT|acT/acA|T355|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),SYNONYMOUS_CODING(LOW|SILENT|acT/acA|T175|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|acT/acA|T175|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 1559 . G A 86.0 min_af_0.050000 AF=0.002454;DP=4482;DP4=1543,2924,7,6;SB=8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G432S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G432S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G252S|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G252S|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 1644 . A C 264.0 min_af_0.050000 AF=0.002193;DP=14589;DP4=11414,3133,13,20;SB=58;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aCc|N460T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aCc|N460T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aCc|N280T|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aCc|N280T|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 1647 . T A 276.0 min_af_0.050000 AF=0.002255;DP=14635;DP4=11359,3236,13,20;SB=56;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTc/aAc|I461N|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTc/aAc|I461N|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTc/aAc|I281N|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTc/aAc|I281N|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 1656 . T A 298.0 min_af_0.050000 AF=0.002383;DP=14686;DP4=11280,3363,15,20;SB=48;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gAt|V464D|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gAt|V464D|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gAt|V284D|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gAt|V284D|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 1659 . G T 244.0 min_af_0.050000 AF=0.002100;DP=14761;DP4=11364,3356,16,17;SB=33;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G465V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G465V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G285V|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G285V|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 1702 . T C 340.0 min_af_0.050000 AF=0.002752;DP=14898;DP4=11421,3413,31,15;SB=8;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S479|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S479|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S299|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S299|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 1710 . C T 138.0 min_af_0.050000 AF=0.001415;DP=14840;DP4=11402,3411,14,10;SB=13;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A482V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A482V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A302V|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A302V|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 1886 . G A 84.0 min_af_0.050000 AF=0.001060;DP=16031;DP4=3181,12824,3,17;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A541T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A541T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A361T|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A361T|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 1914 . G A 136.0 min_af_0.050000 AF=0.001451;DP=14469;DP4=2859,11584,2,19;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R550H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R550H|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R370H|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R370H|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 1928 . G A 104.0 min_af_0.050000 AF=0.001217;DP=13965;DP4=2465,11480,5,13;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A555T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A555T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A375T|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A375T|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 2240 . A T 322.0 min_af_0.050000 AF=0.014104;DP=1418;DP4=289,1109,4,16;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Ttt|I659F|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Ttt|I659F|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Ttt|I479F|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Ttt|I479F|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 3037 . C T 49314.0 PASS AF=0.992931;DP=2122;DP4=0,1,1017,1102;SB=0;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 3290 . C G 280.0 min_af_0.050000 AF=0.003124;DP=9284;DP4=7465,1786,19,10;SB=12;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q1009E|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q1009E|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q191E|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q191E|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 4054 . T C 94.0 min_af_0.050000 AF=0.002820;DP=3546;DP4=864,2667,2,9;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctT/ctC|L1263|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|ctT/ctC|L1263|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|ctT/ctC|L445|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ctT/ctC|L445|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 4057 . T C 103.0 min_af_0.050000 AF=0.003482;DP=3734;DP4=849,2869,1,15;SB=8;EFF=SYNONYMOUS_CODING(LOW|SILENT|caT/caC|H1264|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|caT/caC|H1264|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|caT/caC|H446|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|caT/caC|H446|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 4142 . G A 107.0 min_af_0.050000 AF=0.001079;DP=18533;DP4=13023,5480,6,15;SB=40;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E1293K|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E1293K|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E475K|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E475K|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 4185 . G T 89.0 min_af_0.050000 AF=0.001094;DP=18280;DP4=13359,4896,11,11;SB=15;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G1307V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G1307V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G489V|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G489V|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 4216 . G A 856.0 min_af_0.050000 AF=0.007749;DP=8775;DP4=4191,4511,28,42;SB=7;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttG/ttA|L1317|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),SYNONYMOUS_CODING(LOW|SILENT|ttG/ttA|L1317|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),SYNONYMOUS_CODING(LOW|SILENT|ttG/ttA|L499|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ttG/ttA|L499|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 4425 . A G 97.0 min_af_0.050000 AF=0.002182;DP=5499;DP4=2348,3137,3,9;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAa/aGa|K1387R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAa/aGa|K1387R|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAa/aGa|K569R|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAa/aGa|K569R|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 4428 . T C 501.0 min_af_0.050000 AF=0.007099;DP=5494;DP4=2341,3113,9,31;SB=20;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTa/tCa|L1388S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTa/tCa|L1388S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTa/tCa|L570S|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTa/tCa|L570S|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 5118 . T A 201.0 min_af_0.050000 AF=0.037037;DP=270;DP4=132,128,5,5;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTt/tAt|F1618Y|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTt/tAt|F1618Y|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTt/tAt|F800Y|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTt/tAt|F800Y|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 5119 . T A 201.0 min_af_0.050000 AF=0.036900;DP=271;DP4=133,128,5,5;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttT/ttA|F1618L|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttT/ttA|F1618L|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttT/ttA|F800L|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttT/ttA|F800L|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 5120 . T A 202.0 min_af_0.050000 AF=0.037175;DP=269;DP4=132,127,5,5;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tat/Aat|Y1619N|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tat/Aat|Y1619N|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tat/Aat|Y801N|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tat/Aat|Y801N|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 5284 . C T 151.0 min_af_0.050000 AF=0.002708;DP=5908;DP4=4194,1696,5,11;SB=29;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N1673|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N1673|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N855|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N855|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 5691 . C T 105.0 min_af_0.050000 AF=0.001564;DP=10869;DP4=8349,2502,13,5;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A1809V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A1809V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A991V|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A991V|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 5743 . G C 536.0 min_af_0.050000;sb_fdr AF=0.007752;DP=5289;DP4=2762,2483,3,40;SB=95;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 787.0 min_af_0.050000 AF=0.010650;DP=5258;DP4=2767,2432,13,45;SB=54;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 5765 . G A 141.0 min_af_0.050000 AF=0.003029;DP=5282;DP4=2966,2298,3,15;SB=29;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G1834S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G1834S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G1016S|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G1016S|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 5805 . G A 81.0 min_af_0.050000 AF=0.001745;DP=6302;DP4=2918,3370,6,6;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C1847Y|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C1847Y|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C1029Y|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C1029Y|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 5832 . C T 830.0 min_af_0.050000 AF=0.006126;DP=11754;DP4=2930,8741,13,63;SB=9;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S1856F|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S1856F|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S1038F|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S1038F|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 6173 . AT A 89.0 min_af_0.050000 AF=0.000682;DP=14653;DP4=2727,11919,2,8;HRUN=2;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||att/|I1970|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||att/|I1970|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||att/|I1152|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||att/|I1152|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 6177 . AT A 96.0 min_af_0.050000 AF=0.000678;DP=16234;DP4=2638,13599,1,10;HRUN=2;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||tat/|Y1972|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tat/|Y1972|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tat/|Y1154|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tat/|Y1154|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 6242 . C T 150.0 min_af_0.050000 AF=0.000760;DP=48682;DP4=31997,16628,29,16;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H1993Y|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H1993Y|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H1175Y|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H1175Y|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 6245 . G A 107.0 min_af_0.050000 AF=0.000637;DP=48677;DP4=31963,16654,26,10;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V1994I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V1994I|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V1176I|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V1176I|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 6254 . G A 103.0 min_af_0.050000 AF=0.000673;DP=40125;DP4=32119,7966,28,5;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A1997T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A1997T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A1179T|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A1179T|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 6255 . C T 95.0 min_af_0.050000 AF=0.000647;DP=40215;DP4=32152,8018,23,5;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A1997V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A1997V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A1179V|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A1179V|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 6271 . G A 206.0 min_af_0.050000 AF=0.001157;DP=40638;DP4=31649,8914,37,22;SB=21;EFF=SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T2002|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T2002|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T1184|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T1184|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 6310 . C T 134.0 min_af_0.050000 AF=0.000782;DP=40919;DP4=31782,9083,30,7;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S2015|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S2015|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S1197|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S1197|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 6312 . CA C 272.0 min_af_0.050000 AF=0.000811;DP=40674;DP4=31822,9010,27,6;HRUN=4;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||aaa/|K2017|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K2017|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K1199|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K1199|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) NC_045512.2 6503 . G A 159.0 min_af_0.050000 AF=0.000902;DP=36594;DP4=6191,30357,6,32;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A2080T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A2080T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A1262T|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A1262T|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 6525 . C T 93.0 min_af_0.050000 AF=0.000746;DP=34836;DP4=4904,29889,2,27;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T2087I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T2087I|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T1269I|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T1269I|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 7614 . G C 249.0 min_af_0.050000;sb_fdr AF=0.015337;DP=978;DP4=360,601,14,1;SB=49;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGg/tCg|W2450S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGg/tCg|W2450S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGg/tCg|W1632S|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGg/tCg|W1632S|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 7615 . G C 249.0 min_af_0.050000;sb_fdr AF=0.015306;DP=980;DP4=362,601,14,1;SB=48;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tgG/tgC|W2450C|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tgG/tgC|W2450C|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tgG/tgC|W1632C|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tgG/tgC|W1632C|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 7813 . TTC T 116.0 min_af_0.050000 AF=0.002437;DP=3283;DP4=1512,1777,6,2;HRUN=2;SB=8;INDEL;EFF=FRAME_SHIFT(HIGH||tctcat/|SH2519|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tctcat/|SH2519|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tctcat/|SH1701|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tctcat/|SH1701|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) NC_045512.2 8084 . GA G 68.0 min_af_0.050000 AF=0.001201;DP=5829;DP4=4545,1301,5,2;HRUN=5;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||aaa/|K2608|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K2608|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K1790|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K1790|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 8927 . GT G 154.0 min_af_0.050000 AF=0.001826;DP=7669;DP4=5767,1892,6,8;HRUN=5;SB=20;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/|F2889|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F2889|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F126|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F126|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) NC_045512.2 8964 . CA C 94.0 min_af_0.050000 AF=0.001206;DP=7460;DP4=5950,1508,7,2;HRUN=4;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||aaa/|K2901|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K2901|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K138|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K138|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 10448 . C A 49314.0 PASS AF=0.941326;DP=7465;DP4=269,49,5438,1700;SB=33;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ccc/Acc|P3395T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ccc/Acc|P3395T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ccc/Acc|P132T|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ccc/Acc|P132T|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 10527 . CT C 78.0 min_af_0.050000 AF=0.001718;DP=4074;DP4=1930,2159,3,4;HRUN=5;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||tgt/|C3423|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tgt/|C3423|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tgt/|C160|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tgt/|C160|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) NC_045512.2 10641 . C T 127.0 min_af_0.050000 AF=0.002277;DP=7027;DP4=2613,4397,6,10;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T3459M|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T3459M|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T196M|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T196M|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 10679 . T C 886.0 min_af_0.050000 AF=0.009916;DP=6656;DP4=2234,4351,11,58;SB=29;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y3472H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y3472H|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y209H|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y209H|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 10790 . C T 90.0 min_af_0.050000 AF=0.003128;DP=2877;DP4=1592,1275,6,3;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H3509Y|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H3509Y|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H246Y|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H246Y|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 11071 . G GTTC 49314.0 PASS AF=0.906657;DP=17109;DP4=1189,441,11887,3625;HRUN=2;SB=29;INDEL;EFF=CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||ttt/ttCTTt|F3604FF|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|GTTC|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||ttt/ttCTTt|F3604FF|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|GTTC|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||ttt/ttCTTt|F35FF|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|GTTC|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||ttt/ttCTTt|F35FF|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|GTTC|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME) NC_045512.2 11074 . C CTTCT 5009.0 min_af_0.050000 AF=0.026098;DP=17511;DP4=12777,4287,354,103;HRUN=8;SB=6;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/ttCTTTt|F3604FF?|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|CTTCT|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/ttCTTTt|F3604FF?|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|CTTCT|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/ttCTTTt|F35FF?|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|CTTCT|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/ttCTTTt|F35FF?|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|CTTCT|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) NC_045512.2 11075 . T TTC 9644.0 min_af_0.050000 AF=0.025227;DP=17521;DP4=12767,4323,346,96;HRUN=8;SB=10;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/ttCTt|F3604F?|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|TTC|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/ttCTt|F3604F?|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|TTC|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/ttCTt|F35F?|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|TTC|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/ttCTt|F35F?|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|TTC|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) NC_045512.2 11075 . T TTCC 386.0 min_af_0.050000 AF=0.001826;DP=17521;DP4=12767,4323,24,8;HRUN=8;SB=0;INDEL;EFF=CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||ttt/ttCCTt|F3604FL|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|TTCC|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||ttt/ttCCTt|F3604FL|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|TTCC|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||ttt/ttCCTt|F35FL|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|TTCC|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||ttt/ttCCTt|F35FL|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|TTCC|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME) NC_045512.2 11076 . T TC 389.0 min_af_0.050000 AF=0.003118;DP=17637;DP4=13102,4493,37,18;HRUN=8;SB=6;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/ttCt|F3604F?|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|TC),FRAME_SHIFT(HIGH||ttt/ttCt|F3604F?|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|TC),FRAME_SHIFT(HIGH||ttt/ttCt|F35F?|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|TC|WARNING_TRANSCRIPT_NO_START_CODON),FRAME_SHIFT(HIGH||ttt/ttCt|F35F?|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|TC|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.14) NC_045512.2 11077 . T C 724.0 min_af_0.050000 AF=0.014504;DP=17650;DP4=13007,4376,127,139;SB=199;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F3604|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F3604|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F35|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F35|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 11083 . G T 2124.0 min_af_0.050000 AF=0.013410;DP=17673;DP4=12902,4511,165,85;SB=23;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttT|L3606F|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttT|L3606F|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttT|L37F|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttT|L37F|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 11103 . CT C 118.0 min_af_0.050000 AF=0.000779;DP=17972;DP4=13160,4835,11,3;HRUN=4;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/|F3614|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F3614|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F45|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F45|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) NC_045512.2 11750 . C T 1094.0 min_af_0.050000 AF=0.010133;DP=7895;DP4=4176,3636,40,42;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctc/Ttc|L3829F|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctc/Ttc|L3829F|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctc/Ttc|L260F|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctc/Ttc|L260F|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 11917 . A G 90.0 min_af_0.050000 AF=0.000781;DP=25595;DP4=14208,11360,10,11;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S3884|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S3884|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S25|82|ORF1ab|protein_coding|CODING|YP_009725303.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S25|82|ORF1ab|protein_coding|CODING|YP_009742614.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 12138 . C T 89.0 min_af_0.050000 AF=0.000859;DP=22110;DP4=5911,16177,6,13;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A3958V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A3958V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A16V|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A16V|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 12152 . G A 99.0 min_af_0.050000 AF=0.000914;DP=21891;DP4=5746,16113,8,17;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A3963T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A3963T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A21T|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A21T|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 12458 . A G 2756.0 min_af_0.050000;sb_fdr AF=0.011478;DP=15944;DP4=12445,3309,173,13;SB=65;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Gca|T4065A|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Gca|T4065A|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Gca|T123A|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Gca|T123A|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 12708 . C T 111.0 min_af_0.050000 AF=0.001289;DP=14745;DP4=3477,11246,5,15;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A4148V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A4148V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A8V|112|ORF1ab|protein_coding|CODING|YP_009725305.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A8V|112|ORF1ab|protein_coding|CODING|YP_009742616.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 13006 . T C 101.0 min_af_0.050000 AF=0.001060;DP=17925;DP4=4485,13411,8,13;SB=6;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A4247|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A4247|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A107|112|ORF1ab|protein_coding|CODING|YP_009725305.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A107|112|ORF1ab|protein_coding|CODING|YP_009742616.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 13011 . C T 98.0 min_af_0.050000 AF=0.000962;DP=19745;DP4=4418,15301,7,13;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T4249I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T4249I|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T109I|112|ORF1ab|protein_coding|CODING|YP_009725305.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T109I|112|ORF1ab|protein_coding|CODING|YP_009742616.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 13034 . G A 121.0 min_af_0.050000 AF=0.000738;DP=40648;DP4=24125,16482,22,13;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4257T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4257T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4T|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4T|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 13050 . C T 85.0 min_af_0.050000 AF=0.000605;DP=41322;DP4=24182,17103,17,12;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A4262V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A4262V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A9V|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A9V|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 13073 . T C 82.0 min_af_0.050000 AF=0.000603;DP=41477;DP4=24012,17430,21,6;SB=13;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C4270R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C4270R|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C17R|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C17R|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 13094 . G A 200.0 min_af_0.050000 AF=0.001158;DP=31086;DP4=23605,7439,25,14;SB=10;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A4277T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A4277T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A24T|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A24T|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 13123 . TG T 164.0 min_af_0.050000 AF=0.000748;DP=30768;DP4=22959,7835,17,6;HRUN=5;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||gga/|G4288|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||gga/|G4288|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||gga/|G35|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||gga/|G35|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.11) NC_045512.2 13129 . A G 142.0 min_af_0.050000 AF=0.001058;DP=31184;DP4=23121,8007,32,10;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G4288|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G4288|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G35|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G35|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 13235 . G A 137.0 min_af_0.050000 AF=0.001127;DP=28406;DP4=8123,20243,5,29;SB=10;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4324T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4324T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A71T|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A71T|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 13240 . G A 150.0 min_af_0.050000 AF=0.001122;DP=28523;DP4=8126,20358,10,25;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S4325|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S4325|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S72|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S72|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 13260 . G A 143.0 min_af_0.050000 AF=0.000976;DP=31774;DP4=8264,23460,9,25;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C4332Y|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C4332Y|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C79Y|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C79Y|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 13299 . TA T 128.0 min_af_0.050000 AF=0.000587;DP=30690;DP4=7825,22976,5,13;HRUN=4;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||aaa/|K4346|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K4346|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K93|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K93|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.11) NC_045512.2 13345 . T C 171.0 min_af_0.050000 AF=0.001096;DP=32859;DP4=10582,22225,23,18;SB=26;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P4360|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P4360|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P107|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P107|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 13346 . G A 110.0 min_af_0.050000 AF=0.000849;DP=32974;DP4=10653,22282,18,12;SB=25;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V4361M|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V4361M|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V108M|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V108M|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 13350 . GT G 190.0 min_af_0.050000 AF=0.000733;DP=32739;DP4=10556,22222,8,16;HRUN=4;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/|F4363|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F4363|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F110|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F110|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.11) NC_045512.2 13385 . G A 159.0 min_af_0.050000 AF=0.002573;DP=10105;DP4=7996,2074,27,4;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G4374S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G4374S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G121S|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G121S|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 13436 . C T 101.0 min_af_0.050000 AF=0.001858;DP=9150;DP4=6864,2269,10,7;SB=8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L4391F|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L4391F|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L138F|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L138F|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 13541 . CT C 181.0 min_af_0.050000 AF=0.001621;DP=9872;DP4=2602,7324,2,14;HRUN=4;SB=5;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/|F4427|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F35|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.04) NC_045512.2 13565 . T G 125.0 min_af_0.050000 AF=0.001695;DP=10031;DP4=2520,7488,9,8;SB=16;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTa/gGa|V4434G|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTa/gGa|V42G|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|G|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 13914 . TA T 229.0 min_af_0.050000 AF=0.001064;DP=25367;DP4=5262,20193,5,22;HRUN=5;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||aag/|K4552|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aag/|K160|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07) NC_045512.2 13924 . TG T 67.0 min_af_0.050000 AF=0.000391;DP=25562;DP4=4889,20711,5,5;HRUN=2;SB=15;INDEL;EFF=FRAME_SHIFT(HIGH||tgg/|W4554|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tgg/|W162|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 13966 . G A 142.0 min_af_0.050000 AF=0.001330;DP=18048;DP4=14913,3101,28,2;SB=8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A4568T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A176T|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 13982 . G A 333.0 min_af_0.050000 AF=0.002735;DP=16821;DP4=13274,3494,26,21;SB=36;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R4573H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R181H|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 14061 . A G 95.0 min_af_0.050000 AF=0.001054;DP=17076;DP4=12760,4296,16,4;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttA/ttG|L4599|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),SYNONYMOUS_CODING(LOW|SILENT|ttA/ttG|L207|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|G|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 14408 . C T 49314.0 PASS AF=0.993302;DP=1941;DP4=0,0,964,976;SB=0;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 14581 . C T 149.0 min_af_0.050000 AF=0.001747;DP=13165;DP4=10634,2505,19,6;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Tac|H4773Y|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Tac|H381Y|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 15324 . C T 49314.0 PASS AF=0.991877;DP=9972;DP4=5,3,7254,2709;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N5020|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N628|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 15481 . T C 752.0 min_af_0.050000 AF=0.005927;DP=10967;DP4=2564,8293,51,45;SB=91;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Cca|S5073P|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Cca|S681P|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|C|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 15556 . G A 135.0 min_af_0.050000 AF=0.001203;DP=22441;DP4=17610,4794,25,6;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A5098T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A706T|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 15682 . T A 2121.0 min_af_0.050000 AF=0.014388;DP=9730;DP4=4861,4725,78,64;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tat/Aat|Y5140N|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tat/Aat|Y748N|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 15685 . T A 2159.0 min_af_0.050000 AF=0.014534;DP=9770;DP4=4870,4756,79,64;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttg/Atg|L5141M|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttg/Atg|L749M|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 15723 . T C 118.0 min_af_0.050000 AF=0.001985;DP=9572;DP4=5143,4404,11,9;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D5153|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D761|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|C|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 15873 . AT A 114.0 min_af_0.050000 AF=0.000652;DP=23004;DP4=18635,4358,13,2;HRUN=4;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||tgc/|C5205|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tgc/|C813|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07) NC_045512.2 15878 . G A 148.0 min_af_0.050000;sb_fdr AF=0.001155;DP=23368;DP4=18628,4643,86,4;SB=43;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C5205Y|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C813Y|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 15890 . C T 95.0 min_af_0.050000 AF=0.000866;DP=21937;DP4=16930,4986,15,4;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T5209I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T817I|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 15962 . G A 120.0 min_af_0.050000 AF=0.001077;DP=23209;DP4=17206,5975,18,9;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGc/gAc|G5233D|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGc/gAc|G841D|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 16073 . C T 96.0 min_af_0.050000 AF=0.000886;DP=22579;DP4=5112,17438,7,16;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A5270V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A878V|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 18687 . CT C 108.0 min_af_0.050000 AF=0.000886;DP=13539;DP4=10518,3030,9,3;HRUN=4;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||tcc/|S6143|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tcc/|S218|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07) NC_045512.2 18744 . C T 102.0 min_af_0.050000 AF=0.001253;DP=13571;DP4=10434,3113,14,6;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y6160|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y235|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 18941 . A T 84.0 min_af_0.050000 AF=0.000782;DP=26854;DP4=15021,11802,3,18;SB=37;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gTt|D6226V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gTt|D301V|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 18959 . C T 144.0 min_af_0.050000 AF=0.001301;DP=18445;DP4=14957,3457,18,7;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A6232V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A307V|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 18998 . C T 103.0 min_af_0.050000 AF=0.001038;DP=18304;DP4=14106,4171,15,5;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A6245V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A320V|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 19029 . C T 93.0 min_af_0.050000 AF=0.001027;DP=18494;DP4=14228,4239,16,6;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H6255|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H330|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 19263 . C T 137.0 min_af_0.050000 AF=0.001291;DP=17047;DP4=2815,14204,4,21;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N6333|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N408|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 19610 . C T 203.0 min_af_0.050000 AF=0.001549;DP=18718;DP4=15146,3539,29,1;SB=14;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T6449I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T524I|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 19802 . G A 101.0 min_af_0.050000 AF=0.001022;DP=19577;DP4=4269,15277,7,16;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R6513H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R61H|345|ORF1ab|protein_coding|CODING|YP_009725310.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 20791 . G A 95.0 min_af_0.050000 AF=0.001279;DP=13295;DP4=2630,10646,5,12;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A6843T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A45T|297|ORF1ab|protein_coding|CODING|YP_009725311.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 20839 . G A 121.0 min_af_0.050000 AF=0.000944;DP=25429;DP4=14138,11258,14,13;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gta/Ata|V6859I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gta/Ata|V61I|297|ORF1ab|protein_coding|CODING|YP_009725311.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 20868 . TG T 93.0 min_af_0.050000 AF=0.000630;DP=17449;DP4=13993,3501,10,1;HRUN=2;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||ggt/|G6869|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ggt/|G71|297|ORF1ab|protein_coding|CODING|YP_009725311.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.04) NC_045512.2 20872 . G A 91.0 min_af_0.050000 AF=0.001077;DP=17635;DP4=13978,3635,14,5;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A6870T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A72T|297|ORF1ab|protein_coding|CODING|YP_009725311.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 20937 . G A 83.0 min_af_0.050000 AF=0.001049;DP=17166;DP4=12997,4144,14,5;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T6891|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T93|297|ORF1ab|protein_coding|CODING|YP_009725311.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 21054 . C T 145.0 min_af_0.050000 AF=0.001517;DP=15825;DP4=3477,12313,7,19;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y6930|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y132|297|ORF1ab|protein_coding|CODING|YP_009725311.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 21164 . T A 117.0 min_af_0.050000 AF=0.005592;DP=2861;DP4=2184,652,14,2;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTa/aAa|I6967K|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTa/aAa|I169K|297|ORF1ab|protein_coding|CODING|YP_009725311.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 21417 . A T 140.0 min_af_0.050000 AF=0.002057;DP=8266;DP4=6203,2043,9,8;SB=13;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaA/aaT|K7051N|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaA/aaT|K253N|297|ORF1ab|protein_coding|CODING|YP_009725311.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 21600 . GTCAGTGTGTTAATCT G 82.0 min_af_0.050000 AF=0.000897;DP=8916;DP4=2343,6600,4,4;HRUN=1;SB=6;INDEL;EFF=CODON_DELETION(MODERATE||cagtgtgttaatctt/|QCVNL14|1273|S|protein_coding|CODING|GU280_gp02|1|G|INFO_REALIGN_3_PRIME) NC_045512.2 21634 . A AC 203.0 min_af_0.050000 AF=0.002013;DP=8943;DP4=2367,6561,6,12;HRUN=5;SB=2;INDEL;EFF=FRAME_SHIFT(HIGH||cct/ccCt|P26P?|1273|S|protein_coding|CODING|GU280_gp02|1|AC|INFO_REALIGN_3_PRIME) NC_045512.2 21650 . A C 287.0 min_af_0.050000 AF=0.003285;DP=8827;DP4=2290,6504,4,26;SB=8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Cat|N30H|1273|S|protein_coding|CODING|GU280_gp02|1|C) NC_045512.2 21656 . TTCAC T 110.0 min_af_0.050000 AF=0.001142;DP=8756;DP4=2272,6523,2,8;HRUN=3;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||ttcaca/|FT32|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512.2 21714 . CT C 125.0 min_af_0.050000 AF=0.000856;DP=15185;DP4=7852,7357,12,1;HRUN=1;SB=24;INDEL;EFF=FRAME_SHIFT(HIGH||act/|T51|1273|S|protein_coding|CODING|GU280_gp02|1|C) NC_045512.2 21781 . C T 708.0 min_af_0.050000 AF=0.006219;DP=9809;DP4=7177,2567,44,20;SB=4;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T73|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512.2 21875 . AT A 91.0 min_af_0.050000 AF=0.001868;DP=4283;DP4=2040,2238,3,5;HRUN=5;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/|F106|1273|S|protein_coding|CODING|GU280_gp02|1|A|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00) NC_045512.2 22000 . CA C 220.0 min_af_0.050000 AF=0.001903;DP=10510;DP4=4000,6529,5,15;HRUN=5;SB=5;INDEL;EFF=FRAME_SHIFT(HIGH||aac/|N148|1273|S|protein_coding|CODING|GU280_gp02|1|C|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00) NC_045512.2 22591 . C T 100.0 min_af_0.050000 AF=0.001016;DP=18694;DP4=14731,3931,20,5;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N343|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512.2 22643 . T A 829.0 min_af_0.050000 AF=0.004008;DP=19462;DP4=14955,4414,61,17;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Agt|C361S|1273|S|protein_coding|CODING|GU280_gp02|1|A) NC_045512.2 22644 . G C 795.0 min_af_0.050000 AF=0.003931;DP=19588;DP4=14973,4528,60,17;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tCt|C361S|1273|S|protein_coding|CODING|GU280_gp02|1|C) NC_045512.2 22645 . T A 799.0 min_af_0.050000 AF=0.003933;DP=19578;DP4=14947,4530,66,17;SB=2;EFF=STOP_GAINED(HIGH|NONSENSE|tgT/tgA|C361*|1273|S|protein_coding|CODING|GU280_gp02|1|A) NC_045512.2 22858 . C T 109.0 min_af_0.050000 AF=0.001319;DP=15163;DP4=3803,11332,6,15;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C432|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512.2 23132 . GT G 317.0 min_af_0.050000 AF=0.003693;DP=5687;DP4=1851,3852,7,14;HRUN=3;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||tgt/|C525|1273|S|protein_coding|CODING|GU280_gp02|1|G|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00) NC_045512.2 23143 . TA T 83.0 min_af_0.050000 AF=0.001452;DP=5508;DP4=1682,3843,2,6;HRUN=5;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||aag/|K529|1273|S|protein_coding|CODING|GU280_gp02|1|T|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00) NC_045512.2 23334 . CT C 89.0 min_af_0.050000 AF=0.001077;DP=8358;DP4=4251,4134,6,3;HRUN=4;SB=2;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/|F592|1273|S|protein_coding|CODING|GU280_gp02|1|C|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00) NC_045512.2 23403 . A G 49314.0 PASS AF=0.991572;DP=17205;DP4=2,5,4395,12795;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D614G|1273|S|protein_coding|CODING|GU280_gp02|1|G) NC_045512.2 23412 . G A 108.0 min_af_0.050000 AF=0.001113;DP=17071;DP4=4291,12756,5,17;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C617Y|1273|S|protein_coding|CODING|GU280_gp02|1|A) NC_045512.2 24672 . CA C 86.0 min_af_0.050000 AF=0.003731;DP=1608;DP4=428,1183,3,3;HRUN=5;SB=7;INDEL;EFF=FRAME_SHIFT(HIGH||aga/|R1039|1273|S|protein_coding|CODING|GU280_gp02|1|C|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00) NC_045512.2 24729 . C T 192.0 min_af_0.050000 AF=0.001379;DP=21760;DP4=17349,4370,24,9;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A1056V|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512.2 24770 . G A 105.0 min_af_0.050000 AF=0.000925;DP=22693;DP4=17909,4759,16,5;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A1070T|1273|S|protein_coding|CODING|GU280_gp02|1|A) NC_045512.2 24942 . A T 299.0 min_af_0.050000 AF=0.001816;DP=22578;DP4=5252,17272,8,35;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gTt|D1127V|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512.2 24966 . A T 199.0 min_af_0.050000 AF=0.001429;DP=22394;DP4=5267,17072,19,16;SB=40;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aTc|N1135I|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512.2 25047 . C T 528.0 min_af_0.050000 AF=0.002900;DP=20688;DP4=4536,16083,13,51;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCa/cTa|P1162L|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512.2 25607 . C T 94.0 min_af_0.050000 AF=0.001450;DP=9658;DP4=1996,7642,6,11;SB=8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A72V|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T) NC_045512.2 25646 . T G 198.0 min_af_0.050000;sb_fdr AF=0.002768;DP=9032;DP4=2052,6950,24,1;SB=140;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTg/tGg|L85W|275|ORF3a|protein_coding|CODING|GU280_gp03|1|G) NC_045512.2 25797 . CA C 71.0 min_af_0.050000 AF=0.003369;DP=1484;DP4=700,794,2,3;HRUN=5;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||aac/|N137|275|ORF3a|protein_coding|CODING|GU280_gp03|1|C|INFO_REALIGN_3_PRIME);LOF=(ORF3a|GU280_gp03|1|1.00) NC_045512.2 25986 . A G 91.0 min_af_0.050000 AF=0.001282;DP=14817;DP4=11479,3318,14,6;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K198|275|ORF3a|protein_coding|CODING|GU280_gp03|1|G) NC_045512.2 26042 . C T 987.0 min_af_0.050000 AF=0.005497;DP=15281;DP4=11400,3796,56,29;SB=12;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T217I|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T) NC_045512.2 26044 . C G 956.0 min_af_0.050000 AF=0.005347;DP=15148;DP4=11320,3738,53,28;SB=12;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q218E|275|ORF3a|protein_coding|CODING|GU280_gp03|1|G) NC_045512.2 26046 . A G 977.0 min_af_0.050000 AF=0.005456;DP=15213;DP4=11325,3797,56,29;SB=12;EFF=SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q218|275|ORF3a|protein_coding|CODING|GU280_gp03|1|G) NC_045512.2 26057 . A C 216.0 min_af_0.050000 AF=0.003379;DP=9469;DP4=5738,3692,20,16;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAc/gCc|D222A|275|ORF3a|protein_coding|CODING|GU280_gp03|1|C) NC_045512.2 26103 . T A 273.0 min_af_0.050000;sb_fdr AF=0.004015;DP=6475;DP4=3141,3308,24,2;SB=54;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtT/gtA|V237|275|ORF3a|protein_coding|CODING|GU280_gp03|1|A) NC_045512.2 26120 . A G 249.0 min_af_0.050000 AF=0.003769;DP=6368;DP4=3269,3073,11,13;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cGt|H243R|275|ORF3a|protein_coding|CODING|GU280_gp03|1|G) NC_045512.2 26271 . A G 91.0 min_af_0.050000 AF=0.001094;DP=14624;DP4=3502,11102,5,11;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T9|75|E|protein_coding|CODING|GU280_gp04|1|G) NC_045512.2 26542 . C A 757.0 min_af_0.050000 AF=0.013404;DP=3581;DP4=374,3154,5,44;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aAt|T7N|222|M|protein_coding|CODING|GU280_gp05|1|A) NC_045512.2 26545 . T G 796.0 min_af_0.050000 AF=0.003886;DP=21356;DP4=18019,3242,44,43;SB=130;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTt/aGt|I8S|222|M|protein_coding|CODING|GU280_gp05|1|G) NC_045512.2 26554 . A G 214.0 min_af_0.050000 AF=0.001557;DP=21840;DP4=18203,3602,20,15;SB=36;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gGa|E11G|222|M|protein_coding|CODING|GU280_gp05|1|G) NC_045512.2 26561 . TA T 71.0 min_af_0.050000 AF=0.000541;DP=22195;DP4=18331,3864,10,2;HRUN=5;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||aag/|K15|222|M|protein_coding|CODING|GU280_gp05|1|T|INFO_REALIGN_3_PRIME);LOF=(M|GU280_gp05|1|1.00) NC_045512.2 26635 . C T 99.0 min_af_0.050000 AF=0.000866;DP=24240;DP4=19220,4993,16,7;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A38V|222|M|protein_coding|CODING|GU280_gp05|1|T) NC_045512.2 26640 . G A 93.0 min_af_0.050000 AF=0.000829;DP=24139;DP4=19141,4967,15,6;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A40T|222|M|protein_coding|CODING|GU280_gp05|1|A) NC_045512.2 26695 . G C 115.0 min_af_0.050000;sb_fdr AF=0.001784;DP=8971;DP4=4073,4876,0,17;SB=41;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGg/tCg|W58S|222|M|protein_coding|CODING|GU280_gp05|1|C) NC_045512.2 26713 . GT G 113.0 min_af_0.050000 AF=0.001199;DP=9176;DP4=4368,4832,4,7;HRUN=4;SB=2;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/|F65|222|M|protein_coding|CODING|GU280_gp05|1|G|INFO_REALIGN_3_PRIME);LOF=(M|GU280_gp05|1|1.00) NC_045512.2 26763 . G A 146.0 min_af_0.050000 AF=0.001152;DP=23441;DP4=5135,18267,7,21;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A81T|222|M|protein_coding|CODING|GU280_gp05|1|A) NC_045512.2 26779 . GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT G 177.0 min_af_0.050000 AF=0.000808;DP=23525;DP4=5243,18334,4,15;HRUN=1;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||gtaggcttgatgtggctcagctacttcattgcttctttc/|VGLMWLSYFIASF88|222|M|protein_coding|CODING|GU280_gp05|1|G|INFO_REALIGN_3_PRIME);LOF=(M|GU280_gp05|1|1.00) NC_045512.2 26889 . C T 117.0 min_af_0.050000 AF=0.000870;DP=34472;DP4=15378,19050,13,22;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cca/Tca|P123S|222|M|protein_coding|CODING|GU280_gp05|1|T) NC_045512.2 27335 . C T 287.0 min_af_0.050000 AF=0.003501;DP=8284;DP4=4742,3509,19,12;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T45I|61|ORF6|protein_coding|CODING|GU280_gp06|1|T) NC_045512.2 27344 . A T 384.0 min_af_0.050000 AF=0.004501;DP=8220;DP4=4741,3441,25,12;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAa/aTa|K48I|61|ORF6|protein_coding|CODING|GU280_gp06|1|T) NC_045512.2 27345 . A T 406.0 min_af_0.050000 AF=0.004619;DP=8226;DP4=4747,3439,27,12;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaA/aaT|K48N|61|ORF6|protein_coding|CODING|GU280_gp06|1|T) NC_045512.2 27354 . A G 302.0 min_af_0.050000 AF=0.003828;DP=7837;DP4=4560,3244,20,10;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q51|61|ORF6|protein_coding|CODING|GU280_gp06|1|G) NC_045512.2 27377 . A G 134.0 min_af_0.050000 AF=0.001660;DP=15056;DP4=4443,10575,10,23;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAg/gGg|E59G|61|ORF6|protein_coding|CODING|GU280_gp06|1|G) NC_045512.2 28147 . CT C 80.0 min_af_0.050000 AF=0.000570;DP=19282;DP4=16335,2941,9,2;HRUN=4;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/|F86|121|ORF8|protein_coding|CODING|GU280_gp09|1|C|INFO_REALIGN_3_PRIME);LOF=(ORF8|GU280_gp09|1|1.00) NC_045512.2 28148 . T C 104.0 min_af_0.050000 AF=0.000984;DP=19305;DP4=16333,2941,17,2;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P85|121|ORF8|protein_coding|CODING|GU280_gp09|1|C) NC_045512.2 28214 . CT C 129.0 min_af_0.050000 AF=0.000815;DP=20860;DP4=16749,4135,13,4;HRUN=5;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||tta/|L109|121|ORF8|protein_coding|CODING|GU280_gp09|1|C|INFO_REALIGN_3_PRIME);LOF=(ORF8|GU280_gp09|1|1.00) NC_045512.2 28292 . CA C 132.0 min_af_0.050000 AF=0.001453;DP=8257;DP4=4665,3660,7,5;HRUN=4;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||aat/|N8|419|N|protein_coding|CODING|GU280_gp10|1|C|INFO_REALIGN_3_PRIME) NC_045512.2 28333 . C A 206.0 min_af_0.050000 AF=0.001636;DP=22002;DP4=4970,16986,18,21;SB=28;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccC/ccA|P20|419|N|protein_coding|CODING|GU280_gp10|1|A) NC_045512.2 28346 . G T 310.0 min_af_0.050000 AF=0.001876;DP=21859;DP4=4946,16852,23,24;SB=41;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Tgc|G25C|419|N|protein_coding|CODING|GU280_gp10|1|T) NC_045512.2 28383 . CA C 77.0 min_af_0.050000 AF=0.000532;DP=20671;DP4=4000,16733,0,11;HRUN=4;SB=8;INDEL;EFF=FRAME_SHIFT(HIGH||aaa/|K38|419|N|protein_coding|CODING|GU280_gp10|1|C|INFO_REALIGN_3_PRIME);LOF=(N|GU280_gp10|1|1.00) NC_045512.2 28436 . G A 104.0 min_af_0.050000 AF=0.000961;DP=22898;DP4=6247,16623,4,20;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A55T|419|N|protein_coding|CODING|GU280_gp10|1|A) NC_045512.2 28754 . C T 81.0 min_af_0.050000 AF=0.000962;DP=16630;DP4=11578,5033,11,5;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L161F|419|N|protein_coding|CODING|GU280_gp10|1|T) NC_045512.2 28801 . C A 117.0 min_af_0.050000 AF=0.001334;DP=15738;DP4=11800,3891,9,16;SB=44;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agC/agA|S176R|419|N|protein_coding|CODING|GU280_gp10|1|A) NC_045512.2 28801 . C T 109.0 min_af_0.050000 AF=0.001271;DP=15738;DP4=11800,3891,14,8;SB=6;EFF=SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S176|419|N|protein_coding|CODING|GU280_gp10|1|T) NC_045512.2 28987 . CCAA C 913.0 min_af_0.050000 AF=0.003748;DP=15742;DP4=3519,12216,12,47;HRUN=2;SB=0;INDEL;EFF=CODON_DELETION(MODERATE||caa/|Q242|419|N|protein_coding|CODING|GU280_gp10|1|C|INFO_REALIGN_3_PRIME) NC_045512.2 29029 . T C 3848.0 min_af_0.050000 AF=0.009791;DP=27984;DP4=15396,12289,102,187;SB=111;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A252|419|N|protein_coding|CODING|GU280_gp10|1|C) NC_045512.2 29031 . A G 125.0 min_af_0.050000 AF=0.000927;DP=28044;DP4=15450,12550,11,25;SB=24;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAg/gGg|E253G|419|N|protein_coding|CODING|GU280_gp10|1|G) NC_045512.2 29035 . T C 147.0 min_af_0.050000 AF=0.001031;DP=28124;DP4=15520,12541,37,19;SB=9;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A254|419|N|protein_coding|CODING|GU280_gp10|1|C) NC_045512.2 29039 . A T 8605.0 min_af_0.050000 AF=0.018320;DP=28330;DP4=15395,12395,186,341;SB=193;EFF=STOP_GAINED(HIGH|NONSENSE|Aag/Tag|K256*|419|N|protein_coding|CODING|GU280_gp10|1|T) NC_045512.2 29049 . G A 832.0 min_af_0.050000 AF=0.004347;DP=19553;DP4=15587,3863,75,15;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R259Q|419|N|protein_coding|CODING|GU280_gp10|1|A) NC_045512.2 29077 . C T 81.0 min_af_0.050000 AF=0.000856;DP=19853;DP4=15391,4437,15,4;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y268|419|N|protein_coding|CODING|GU280_gp10|1|T) NC_045512.2 29127 . AT A 99.0 min_af_0.050000 AF=0.000637;DP=20411;DP4=15790,4632,10,3;HRUN=4;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/|F286|419|N|protein_coding|CODING|GU280_gp10|1|A|INFO_REALIGN_3_PRIME);LOF=(N|GU280_gp10|1|1.00) NC_045512.2 29187 . C T 217.0 min_af_0.050000 AF=0.002703;DP=9249;DP4=5107,4112,17,11;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A305V|419|N|protein_coding|CODING|GU280_gp10|1|T) NC_045512.2 29188 . A G 195.0 min_af_0.050000 AF=0.002515;DP=9144;DP4=5068,4049,15,8;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A305|419|N|protein_coding|CODING|GU280_gp10|1|G) NC_045512.2 29195 . GC G 248.0 min_af_0.050000 AF=0.002343;DP=8962;DP4=5061,3918,12,9;HRUN=5;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||ccc/|P309|419|N|protein_coding|CODING|GU280_gp10|1|G|INFO_REALIGN_3_PRIME);LOF=(N|GU280_gp10|1|1.00) NC_045512.2 29377 . TA T 103.0 min_af_0.050000 AF=0.001989;DP=4525;DP4=3220,1474,4,5;HRUN=5;SB=8;INDEL;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)