Mercurial > repos > iuc > snpfreqplot
view test-data/1085990.vcf @ 3:3d0adeee3f2b draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit c062eb1cd00ce9d565f3e2f3b042b3dd90d78ce4"
| author | iuc |
|---|---|
| date | Wed, 06 Jan 2021 10:55:53 +0000 |
| parents | 1062d6ad6503 |
| 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/012/246/12246267/tmp/lofreq2_call_parallelqn_l60x2/0.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_76,Description="Minimum SNV Quality (Phred) 76"> ##FILTER=<ID=min_indelqual_62,Description="Minimum Indel Quality (Phred) 62"> ##FILTER=<ID=min_snvqual_80,Description="Minimum SNV Quality (Phred) 80"> ##FILTER=<ID=min_indelqual_65,Description="Minimum Indel Quality (Phred) 65"> ##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/012/246/12246347/outputs/galaxy_dataset_1ca63e30-5487-4601-bda6-72c686cc7d32.dat NC_045512.2 /data/dnb03/galaxy_db/files/d/9/0/dataset_d9078927-a687-4f10-a32b-a57712d806a3.dat " ##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_Change| Amino_Acid_length | Gene_Name | Transcript_BioType | Gene_Coding | Transcript_ID | Exon_Rank | Genotype [ | ERRORS | WARNINGS ] )' "> ##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'"> ##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'"> #CHROM POS ID REF ALT QUAL FILTER INFO NC_045512.2 241 . C T 49314.0 PASS AF=0.994274;DP=3318;DP4=0,1,1344,1972;SB=0 NC_045512.2 396 . A G 97.0 min_af_0.050000 AF=0.001315;DP=12924;DP4=10266,2637,16,1;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q44R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q44R|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q44R|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q44R|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G) NC_045512.2 443 . GT G 109.0 min_af_0.050000 AF=0.000905;DP=13257;DP4=10220,3055,10,2;HRUN=4;SB=0;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_045512.2 527 . C T 185.0 min_af_0.050000 AF=0.003468;DP=5767;DP4=3187,2554,12,8;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L88|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L88|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON),SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L88|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON),SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L88|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T) NC_045512.2 558 . G T 365.0 min_af_0.050000 AF=0.006082;DP=5426;DP4=3138,2252,18,16;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G98V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G98V|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G98V|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G98V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T) NC_045512.2 656 . G T 88.0 min_af_0.050000 AF=0.001295;DP=12351;DP4=2406,9925,8,10;SB=18;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A131S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A131S|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A131S|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A131S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T) NC_045512.2 1295 . T A 171.0 min_af_0.050000 AF=0.002789;DP=6813;DP4=1575,5217,1,18;SB=10;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Agt|C344S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Agt|C344S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Agt|C164S|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Agt|C164S|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 1644 . A C 184.0 min_af_0.050000 AF=0.001854;DP=12942;DP4=10851,2059,10,16;SB=67;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 175.0 min_af_0.050000 AF=0.001771;DP=12990;DP4=10827,2131,10,17;SB=71;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 151.0 min_af_0.050000 AF=0.001603;DP=13099;DP4=10815,2261,8,14;SB=57;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 147.0 min_af_0.050000 AF=0.001594;DP=13171;DP4=10873,2272,9,15;SB=59;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 285.0 min_af_0.050000 AF=0.002544;DP=13363;DP4=10930,2369,25,10;SB=9;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 1897 . A G 87.0 min_af_0.050000 AF=0.001063;DP=15050;DP4=3734,11290,12,8;SB=30;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V544|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V544|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V364|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V364|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 1914 . G A 101.0 min_af_0.050000 AF=0.001163;DP=18060;DP4=6834,11191,7,16;SB=2;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 2240 . A T 906.0 min_af_0.050000 AF=0.008998;DP=7335;DP4=1191,6074,1,66;SB=37;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 2248 . TG T 66.0 min_af_0.050000 AF=0.003336;DP=1199;DP4=1120,82,4,0;HRUN=2;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||gga/|G662|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||gga/|G662|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||gga/|G482|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||gga/|G482|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) NC_045512.2 3037 . C T 9439.0 PASS AF=0.992278;DP=259;DP4=0,0,128,131;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 3412 . TA T 98.0 min_af_0.050000 AF=0.001304;DP=7669;DP4=1394,6276,1,9;HRUN=5;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||aag/|K1051|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aag/|K1051|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aag/|K233|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aag/|K233|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 3904 . A G 157.0 min_af_0.050000 AF=0.001423;DP=16871;DP4=13947,2891,19,6;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P1213|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P1213|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P395|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P395|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 4276 . C T 89.0 min_af_0.050000 AF=0.000980;DP=17342;DP4=4361,12963,6,11;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y1337|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y1337|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y519|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y519|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 4455 . C T 49314.0 PASS AF=0.783453;DP=4738;DP4=510,475,1930,1820;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A1397V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A1397V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A579V|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A579V|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 5283 . A G 97.0 min_af_0.050000 AF=0.006051;DP=1322;DP4=756,557,0,9;SB=33;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aGc|N1673S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aGc|N1673S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aGc|N855S|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aGc|N855S|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 5284 . C T 114.0 min_af_0.050000 AF=0.006798;DP=1324;DP4=754,560,1,8;SB=22;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 5291 . CT C 137.0 min_af_0.050000 AF=0.003193;DP=2819;DP4=2233,578,5,4;HRUN=2;SB=10;INDEL;EFF=FRAME_SHIFT(HIGH||ctt/|L1676|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ctt/|L1676|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ctt/|L858|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ctt/|L858|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 5365 . C T 104.0 min_af_0.050000 AF=0.003156;DP=3169;DP4=2400,758,8,3;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y1700|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y1700|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y882|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y882|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 5629 . G A 324.0 min_af_0.050000 AF=0.007767;DP=3090;DP4=2578,487,21,4;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T1788|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T1788|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T970|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T970|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 6173 . AT A 206.0 min_af_0.050000 AF=0.002274;DP=6597;DP4=430,6155,0,15;HRUN=2;SB=2;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 6176 . GA G 85.0 min_af_0.050000 AF=0.000988;DP=8096;DP4=422,7697,0,8;HRUN=1;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||gat/|D1971|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),FRAME_SHIFT(HIGH||gat/|D1971|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),FRAME_SHIFT(HIGH||gat/|D1153|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),FRAME_SHIFT(HIGH||gat/|D1153|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.14) NC_045512.2 6177 . AT A 186.0 min_af_0.050000 AF=0.001680;DP=8929;DP4=413,8512,0,15;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 147.0 min_af_0.050000 AF=0.000724;DP=55250;DP4=41638,13544,34,16;SB=6;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 6374 . G T 93.0 min_af_0.050000 AF=0.000994;DP=19124;DP4=9189,9907,9,11;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Tat|D2037Y|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Tat|D2037Y|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Tat|D1219Y|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Tat|D1219Y|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 6396 . TA T 142.0 min_af_0.050000 AF=0.000800;DP=21237;DP4=9622,11810,11,6;HRUN=4;SB=8;INDEL;EFF=FRAME_SHIFT(HIGH||aaa/|K2045|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K2045|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K1227|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K1227|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 6456 . G A 103.0 min_af_0.050000 AF=0.000659;DP=45552;DP4=8833,36673,5,30;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C2064Y|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C2064Y|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C1246Y|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C1246Y|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 6503 . G A 88.0 min_af_0.050000 AF=0.000611;DP=40914;DP4=6252,34625,5,24;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 6513 . G T 249.0 min_af_0.050000 AF=0.001124;DP=40021;DP4=5694,34255,5,55;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aTt|S2083I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aTt|S2083I|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aTt|S1265I|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aTt|S1265I|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 7246 . GT G 113.0 min_af_0.050000 AF=0.010067;DP=596;DP4=270,327,3,3;HRUN=5;SB=0;INDEL;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 7889 . GT G 115.0 min_af_0.050000 AF=0.001985;DP=5039;DP4=1008,4028,3,7;HRUN=5;SB=3;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/|F2543|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F2543|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F1725|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F1725|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 9656 . A G 748.0 min_af_0.050000;sb_fdr AF=0.010109;DP=5243;DP4=2338,2850,51,3;SB=137;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M3131V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M3131V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M368V|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M368V|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 9811 . CT C 124.0 min_af_0.050000 AF=0.001097;DP=12759;DP4=1985,10818,1,13;HRUN=5;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||ttg/|L3184|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L3184|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L421|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L421|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 10409 . A G 102.0 min_af_0.050000 AF=0.002045;DP=5868;DP4=2189,3666,5,7;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Gat|N3382D|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Gat|N3382D|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Gat|N119D|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Gat|N119D|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 10511 . G A 49314.0 PASS AF=0.781399;DP=2301;DP4=353,134,1375,438;SB=8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D3416N|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D3416N|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D153N|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D153N|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 10783 . AC A 1328.0 min_af_0.050000 AF=0.030864;DP=1782;DP4=775,955,10,45;HRUN=1;SB=41;INDEL;EFF=FRAME_SHIFT(HIGH||caa/|Q3507|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),FRAME_SHIFT(HIGH||caa/|Q3507|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),FRAME_SHIFT(HIGH||caa/|Q244|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),FRAME_SHIFT(HIGH||caa/|Q244|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.14) NC_045512.2 10986 . G T 245.0 min_af_0.050000 AF=0.004993;DP=4206;DP4=1217,2968,7,14;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGa/aTa|R3574I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGa/aTa|R3574I|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGa/aTa|R5I|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGa/aTa|R5I|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 11003 . C T 136.0 min_af_0.050000 AF=0.003531;DP=4531;DP4=1176,3339,6,10;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Tac|H3580Y|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Tac|H3580Y|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Tac|H11Y|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Tac|H11Y|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 11071 . G GTTC 49314.0 PASS AF=0.921222;DP=13811;DP4=910,220,10234,2489;HRUN=2;SB=0;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 3604.0 min_af_0.050000 AF=0.024274;DP=14007;DP4=10839,2872,285,55;HRUN=8;SB=14;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 6655.0 min_af_0.050000 AF=0.021513;DP=14038;DP4=10846,2884,246,56;HRUN=8;SB=4;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 117.0 min_af_0.050000 AF=0.000855;DP=14038;DP4=10846,2884,11,1;HRUN=8;SB=3;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 116.0 min_af_0.050000 AF=0.001273;DP=14138;DP4=11112,3018,6,12;HRUN=8;SB=43;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 300.0 min_af_0.050000 AF=0.008197;DP=14151;DP4=11058,2972,63,56;SB=92;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 436.0 min_af_0.050000 AF=0.005129;DP=14232;DP4=11065,3081,62,22;SB=4;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 11983 . A T 101.0 min_af_0.050000 AF=0.001169;DP=15398;DP4=12255,3117,13,6;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaA/gaT|E3906D|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaA/gaT|E3906D|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaA/gaT|E47D|82|ORF1ab|protein_coding|CODING|YP_009725303.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaA/gaT|E47D|82|ORF1ab|protein_coding|CODING|YP_009742614.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 12164 . G T 645.0 min_af_0.050000 AF=0.003440;DP=18898;DP4=5086,13740,17,49;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A3967S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A3967S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A25S|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A25S|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 12458 . A G 22986.0 PASS AF=0.118809;DP=7693;DP4=4150,2622,687,233;SB=151;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 12831 . A G 88.0 min_af_0.050000 AF=0.000898;DP=20042;DP4=16187,3831,14,5;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q4189R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q4189R|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q49R|112|ORF1ab|protein_coding|CODING|YP_009725305.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q49R|112|ORF1ab|protein_coding|CODING|YP_009742616.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 13006 . T C 128.0 min_af_0.050000 AF=0.001106;DP=22613;DP4=4970,17609,8,18;SB=4;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 86.0 min_af_0.050000 AF=0.000804;DP=26106;DP4=4889,21186,8,14;SB=12;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 95.0 min_af_0.050000 AF=0.000506;DP=69235;DP4=45709,23472,20,21;SB=15;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 13048 . T C 181.0 min_af_0.050000 AF=0.000682;DP=70402;DP4=45971,24198,44,166;SB=390;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P4261|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P4261|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P8|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P8|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 13049 . G A 164.0 min_af_0.050000 AF=0.000651;DP=70714;DP4=46084,24548,36,18;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A4262T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A4262T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A9T|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A9T|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 13073 . T C 106.0 min_af_0.050000 AF=0.000530;DP=71755;DP4=46248,25458,25,18;SB=3;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 110.0 min_af_0.050000 AF=0.000604;DP=57907;DP4=46186,11671,29,10;SB=3;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 362.0 min_af_0.050000 AF=0.000845;DP=57968;DP4=45262,12745,39,10;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 275.0 min_af_0.050000 AF=0.001106;DP=58773;DP4=45596,13058,79,15;SB=7;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 225.0 min_af_0.050000 AF=0.001046;DP=58324;DP4=13189,45056,12,53;SB=2;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 168.0 min_af_0.050000 AF=0.000823;DP=58314;DP4=13132,45114,15,36;SB=6;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 201.0 min_af_0.050000 AF=0.000834;DP=59945;DP4=13428,46442,16,42;SB=4;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 13288 . AT A 246.0 min_af_0.050000 AF=0.000600;DP=58346;DP4=12587,45733,5,30;HRUN=4;SB=3;INDEL;EFF=FRAME_SHIFT(HIGH||tgt/|C4343|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tgt/|C4343|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tgt/|C90|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tgt/|C90|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.11) NC_045512.2 13345 . T C 83.0 min_af_0.050000 AF=0.000573;DP=55875;DP4=12086,43726,9,28;SB=1;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 13350 . GT G 253.0 min_af_0.050000 AF=0.000632;DP=55344;DP4=11847,43567,6,29;HRUN=4;SB=1;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 13565 . T G 345.0 min_af_0.050000 AF=0.004812;DP=6235;DP4=1296,4904,18,12;SB=54;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 13571 . G T 479.0 min_af_0.050000 AF=0.006221;DP=6269;DP4=1318,4908,5,37;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G4436V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G44V|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 13650 . T G 148.0 min_af_0.050000;sb_fdr AF=0.000779;DP=43663;DP4=33531,10080,3,32;SB=168;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttT/ttG|F4462L|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttT/ttG|F70L|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|G|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 14267 . C T 87.0 min_af_0.050000 AF=0.001143;DP=13128;DP4=8606,4502,9,7;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T4668M|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T276M|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 14408 . C T 49314.0 PASS AF=0.993192;DP=3966;DP4=0,0,1935,2031;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 15324 . C T 49314.0 PASS AF=0.988437;DP=11935;DP4=1,2,9099,2830;SB=8;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 328.0 min_af_0.050000 AF=0.002827;DP=13441;DP4=2511,10857,40,27;SB=127;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 15568 . A C 180.0 min_af_0.050000 AF=0.002297;DP=10448;DP4=8328,2090,17,9;SB=10;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Cct|T5102P|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Cct|T710P|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|C|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 15673 . T G 106.0 min_af_0.050000;sb_fdr AF=0.004279;DP=4674;DP4=2599,2037,25,1;SB=50;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttt/Gtt|F5137V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttt/Gtt|F745V|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|G|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 15682 . T A 1300.0 min_af_0.050000 AF=0.017751;DP=4563;DP4=2587,1892,47,35;SB=0;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 1323.0 min_af_0.050000 AF=0.017982;DP=4560;DP4=2573,1902,46,36;SB=0;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 16026 . A T 151.0 min_af_0.050000 AF=0.004022;DP=3481;DP4=1737,1726,1,15;SB=32;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttA/ttT|L5254F|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttA/ttT|L862F|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 16030 . A G 152.0 min_af_0.050000;sb_fdr AF=0.004060;DP=3448;DP4=1751,1682,0,14;SB=43;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I5256V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I864V|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|G|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 17122 . G A 82.0 min_af_0.050000 AF=0.001070;DP=14013;DP4=7804,6183,14,7;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A5620T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A296T|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 17146 . A G 85.0 min_af_0.050000 AF=0.001464;DP=9561;DP4=7533,1983,9,5;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I5628V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I304V|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 18687 . CT C 132.0 min_af_0.050000 AF=0.000757;DP=21142;DP4=16971,4200,11,5;HRUN=4;SB=4;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 18859 . G A 80.0 min_af_0.050000 AF=0.000826;DP=20592;DP4=4201,16371,5,12;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A6199T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A274T|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 18941 . A T 392.0 min_af_0.050000 AF=0.002016;DP=24798;DP4=8527,16211,9,44;SB=20;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 22000 . CA C 81.0 min_af_0.050000 AF=0.001893;DP=3697;DP4=1829,1873,5,2;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 22091 . A G 359.0 min_af_0.050000 AF=0.010671;DP=2249;DP4=1794,428,21,3;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M177V|1273|S|protein_coding|CODING|GU280_gp02|1|G) NC_045512.2 22643 . T A 168.0 min_af_0.050000 AF=0.003589;DP=4458;DP4=3614,824,12,4;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Agt|C361S|1273|S|protein_coding|CODING|GU280_gp02|1|A) NC_045512.2 22644 . G C 129.0 min_af_0.050000 AF=0.003124;DP=4481;DP4=3615,850,11,3;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tCt|C361S|1273|S|protein_coding|CODING|GU280_gp02|1|C) NC_045512.2 22645 . T A 151.0 min_af_0.050000 AF=0.003350;DP=4478;DP4=3605,849,14,3;SB=0;EFF=STOP_GAINED(HIGH|NONSENSE|tgT/tgA|C361*|1273|S|protein_coding|CODING|GU280_gp02|1|A) NC_045512.2 22805 . AC A 70.0 min_af_0.050000 AF=0.001232;DP=4871;DP4=723,4147,0,6;HRUN=1;SB=2;INDEL;EFF=FRAME_SHIFT(HIGH||act/|T415|1273|S|protein_coding|CODING|GU280_gp02|1|A);LOF=(S|GU280_gp02|1|1.00) NC_045512.2 22899 . G T 250.0 min_af_0.050000 AF=0.002593;DP=12339;DP4=9701,2594,28,9;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G446V|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512.2 23131 . TG T 97.0 min_af_0.050000 AF=0.000820;DP=12195;DP4=2479,9746,1,9;HRUN=1;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||gtt/|V524|1273|S|protein_coding|CODING|GU280_gp02|1|T);LOF=(S|GU280_gp02|1|1.00) NC_045512.2 23143 . TA T 127.0 min_af_0.050000 AF=0.001144;DP=12243;DP4=2290,9978,0,14;HRUN=5;SB=10;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 23205 . G A 87.0 min_af_0.050000 AF=0.000720;DP=30549;DP4=19078,11434,15,7;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGc/gAc|G548D|1273|S|protein_coding|CODING|GU280_gp02|1|A) NC_045512.2 23238 . T C 182.0 min_af_0.050000 AF=0.001117;DP=31346;DP4=19348,11952,9,31;SB=62;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTt/tCt|F559S|1273|S|protein_coding|CODING|GU280_gp02|1|C) NC_045512.2 23261 . A G 132.0 min_af_0.050000 AF=0.001092;DP=26563;DP4=18642,7879,25,8;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aga/Gga|R567G|1273|S|protein_coding|CODING|GU280_gp02|1|G) NC_045512.2 23302 . G A 137.0 min_af_0.050000 AF=0.001764;DP=10768;DP4=5127,5611,17,4;SB=24;EFF=SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q580|1273|S|protein_coding|CODING|GU280_gp02|1|A) NC_045512.2 23306 . C G 116.0 min_af_0.050000 AF=0.001570;DP=10826;DP4=5174,5631,14,3;SB=22;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Gtt|L582V|1273|S|protein_coding|CODING|GU280_gp02|1|G) NC_045512.2 23403 . A G 49314.0 PASS AF=0.991045;DP=24567;DP4=3,5,5490,19063;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D614G|1273|S|protein_coding|CODING|GU280_gp02|1|G) NC_045512.2 23417 . G T 465.0 min_af_0.050000 AF=0.002290;DP=24458;DP4=5401,18993,18,40;SB=9;EFF=STOP_GAINED(HIGH|NONSENSE|Gaa/Taa|E619*|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512.2 24729 . C T 88.0 min_af_0.050000 AF=0.001045;DP=15304;DP4=11983,3304,14,2;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A1056V|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512.2 24776 . GA G 68.0 min_af_0.050000 AF=0.000587;DP=15338;DP4=12278,3058,6,3;HRUN=4;SB=4;INDEL;EFF=FRAME_SHIFT(HIGH||aag/|K1073|1273|S|protein_coding|CODING|GU280_gp02|1|G|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00) NC_045512.2 24883 . G A 138.0 min_af_0.050000 AF=0.002752;DP=5813;DP4=2679,3117,8,8;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R1107|1273|S|protein_coding|CODING|GU280_gp02|1|A) NC_045512.2 24933 . G T 358.0 min_af_0.050000 AF=0.002817;DP=14552;DP4=2925,11563,9,51;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G1124V|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512.2 24942 . A T 251.0 min_af_0.050000 AF=0.002129;DP=14564;DP4=2931,11594,5,30;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gTt|D1127V|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512.2 25132 . C A 105.0 min_af_0.050000 AF=0.009537;DP=734;DP4=504,222,5,3;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcA|A1190|1273|S|protein_coding|CODING|GU280_gp02|1|A) NC_045512.2 25379 . A T 122.0 min_af_0.050000 AF=0.001291;DP=16270;DP4=13436,2805,11,10;SB=28;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Tca|T1273S|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512.2 25543 . G A 86.0 min_af_0.050000 AF=0.000993;DP=17112;DP4=3351,13735,4,14;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A51T|275|ORF3a|protein_coding|CODING|GU280_gp03|1|A) NC_045512.2 25635 . C T 81.0 min_af_0.050000 AF=0.000911;DP=17568;DP4=4208,13332,5,15;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C81|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T) NC_045512.2 25646 . T G 149.0 min_af_0.050000;sb_fdr AF=0.001557;DP=17345;DP4=4081,13232,23,4;SB=106;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTg/tGg|L85W|275|ORF3a|protein_coding|CODING|GU280_gp03|1|G) NC_045512.2 25797 . CA C 136.0 min_af_0.050000 AF=0.004646;DP=1937;DP4=832,1134,5,4;HRUN=5;SB=2;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 26042 . C T 456.0 min_af_0.050000 AF=0.003753;DP=11725;DP4=8878,2799,31,15;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T217I|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T) NC_045512.2 26044 . C G 445.0 min_af_0.050000 AF=0.003696;DP=11634;DP4=8840,2742,30,14;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q218E|275|ORF3a|protein_coding|CODING|GU280_gp03|1|G) NC_045512.2 26046 . A G 446.0 min_af_0.050000 AF=0.003765;DP=11688;DP4=8854,2787,32,14;SB=5;EFF=SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q218|275|ORF3a|protein_coding|CODING|GU280_gp03|1|G) NC_045512.2 26089 . T A 116.0 min_af_0.050000 AF=0.002761;DP=4709;DP4=2229,2464,3,12;SB=14;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Aac|Y233N|275|ORF3a|protein_coding|CODING|GU280_gp03|1|A) NC_045512.2 26103 . T A 159.0 min_af_0.050000 AF=0.003338;DP=4793;DP4=2379,2397,14,2;SB=26;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtT/gtA|V237|275|ORF3a|protein_coding|CODING|GU280_gp03|1|A) NC_045512.2 26270 . C T 88.0 min_af_0.050000 AF=0.001211;DP=11557;DP4=2704,8836,4,10;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T9I|75|E|protein_coding|CODING|GU280_gp04|1|T) NC_045512.2 26542 . C A 168.0 min_af_0.050000 AF=0.004989;DP=2806;DP4=185,2601,1,13;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 786.0 min_af_0.050000 AF=0.004062;DP=19450;DP4=16700,2664,68,12;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTt/aGt|I8S|222|M|protein_coding|CODING|GU280_gp05|1|G) NC_045512.2 26554 . A G 217.0 min_af_0.050000 AF=0.001613;DP=19843;DP4=16861,2946,28,4;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gGa|E11G|222|M|protein_coding|CODING|GU280_gp05|1|G) NC_045512.2 26635 . C T 83.0 min_af_0.050000 AF=0.000830;DP=21692;DP4=17729,3934,19,3;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A38V|222|M|protein_coding|CODING|GU280_gp05|1|T) NC_045512.2 26695 . G C 144.0 min_af_0.050000;sb_fdr AF=0.002401;DP=7079;DP4=3264,3797,0,17;SB=45;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGg/tCg|W58S|222|M|protein_coding|CODING|GU280_gp05|1|C) NC_045512.2 26713 . GT G 108.0 min_af_0.050000 AF=0.001325;DP=7547;DP4=3518,4048,3,7;HRUN=4;SB=4;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 26889 . C T 105.0 min_af_0.050000 AF=0.000846;DP=36631;DP4=17521,19069,15,18;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cca/Tca|P123S|222|M|protein_coding|CODING|GU280_gp05|1|T) NC_045512.2 26895 . C T 124.0 min_af_0.050000 AF=0.001078;DP=20410;DP4=17437,2947,21,3;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H125Y|222|M|protein_coding|CODING|GU280_gp05|1|T) NC_045512.2 27059 . C T 383.0 min_af_0.050000 AF=0.003588;DP=11426;DP4=4376,7002,17,25;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y179|222|M|protein_coding|CODING|GU280_gp05|1|T) NC_045512.2 27079 . G A 86.0 min_af_0.050000 AF=0.000875;DP=21704;DP4=4481,17197,2,17;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R186H|222|M|protein_coding|CODING|GU280_gp05|1|A) NC_045512.2 27105 . G A 117.0 min_af_0.050000 AF=0.001008;DP=21817;DP4=4582,17206,6,16;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A195T|222|M|protein_coding|CODING|GU280_gp05|1|A) NC_045512.2 27120 . A G 85.0 min_af_0.050000 AF=0.000830;DP=21676;DP4=4482,17172,4,14;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agg/Ggg|R200G|222|M|protein_coding|CODING|GU280_gp05|1|G) NC_045512.2 27214 . G A 86.0 min_af_0.050000 AF=0.001126;DP=13325;DP4=11074,2235,9,6;SB=15;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V5I|61|ORF6|protein_coding|CODING|GU280_gp06|1|A) NC_045512.2 27335 . C T 214.0 min_af_0.050000 AF=0.004064;DP=4921;DP4=2786,2115,15,5;SB=9;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T45I|61|ORF6|protein_coding|CODING|GU280_gp06|1|T) NC_045512.2 27344 . A T 333.0 min_af_0.050000 AF=0.005777;DP=4847;DP4=2763,2055,20,8;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAa/aTa|K48I|61|ORF6|protein_coding|CODING|GU280_gp06|1|T) NC_045512.2 27345 . A T 322.0 min_af_0.050000 AF=0.005784;DP=4841;DP4=2760,2050,20,8;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 354.0 min_af_0.050000 AF=0.006365;DP=4556;DP4=2590,1937,21,8;SB=8;EFF=SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q51|61|ORF6|protein_coding|CODING|GU280_gp06|1|G) NC_045512.2 28333 . C A 829.0 min_af_0.050000 AF=0.006612;DP=13007;DP4=2288,10630,42,45;SB=100;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccC/ccA|P20|419|N|protein_coding|CODING|GU280_gp10|1|A) NC_045512.2 28346 . G T 1405.0 min_af_0.050000 AF=0.008030;DP=12951;DP4=2278,10563,52,53;SB=128;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Tgc|G25C|419|N|protein_coding|CODING|GU280_gp10|1|T) NC_045512.2 28849 . C T 253.0 min_af_0.050000 AF=0.008879;DP=2140;DP4=1054,1067,9,10;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N192|419|N|protein_coding|CODING|GU280_gp10|1|T) NC_045512.2 29029 . T C 2047.0 min_af_0.050000 AF=0.004975;DP=36379;DP4=28535,7633,126,74;SB=64;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A252|419|N|protein_coding|CODING|GU280_gp10|1|C) NC_045512.2 29039 . A T 5675.0 min_af_0.050000 AF=0.010564;DP=37106;DP4=28670,8011,189,214;SB=413;EFF=STOP_GAINED(HIGH|NONSENSE|Aag/Tag|K256*|419|N|protein_coding|CODING|GU280_gp10|1|T) NC_045512.2 29044 . G A 616.0 min_af_0.050000 AF=0.002272;DP=34327;DP4=28857,5335,105,15;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaG/aaA|K257|419|N|protein_coding|CODING|GU280_gp10|1|A) NC_045512.2 29049 . G A 646.0 min_af_0.050000 AF=0.002444;DP=34783;DP4=28968,5690,85,10;SB=8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R259Q|419|N|protein_coding|CODING|GU280_gp10|1|A) NC_045512.2 29186 . G A 114.0 min_af_0.050000 AF=0.001532;DP=12404;DP4=6845,5536,15,6;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A305T|419|N|protein_coding|CODING|GU280_gp10|1|A) NC_045512.2 29187 . C T 142.0 min_af_0.050000 AF=0.001691;DP=12417;DP4=6915,5477,13,9;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A305V|419|N|protein_coding|CODING|GU280_gp10|1|T) NC_045512.2 29188 . A G 134.0 min_af_0.050000 AF=0.001629;DP=12279;DP4=6876,5376,13,11;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A305|419|N|protein_coding|CODING|GU280_gp10|1|G) NC_045512.2 29195 . GC G 297.0 min_af_0.050000 AF=0.002159;DP=12041;DP4=6921,5152,14,12;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 29235 . G A 83.0 min_af_0.050000 AF=0.000626;DP=36745;DP4=6926,29793,7,17;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGc/gAc|G321D|419|N|protein_coding|CODING|GU280_gp10|1|A) NC_045512.2 29312 . A G 145.0 min_af_0.050000 AF=0.000883;DP=33979;DP4=4770,29170,1,30;SB=9;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aaa/Gaa|K347E|419|N|protein_coding|CODING|GU280_gp10|1|G) NC_045512.2 29320 . A G 106.0 min_af_0.050000 AF=0.000762;DP=34141;DP4=5096,29012,4,26;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q349|419|N|protein_coding|CODING|GU280_gp10|1|G) NC_045512.2 29331 . T C 99.0 min_af_0.050000 AF=0.000719;DP=33388;DP4=4576,28723,2,67;SB=23;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTg/cCg|L353P|419|N|protein_coding|CODING|GU280_gp10|1|C)