Mercurial > repos > iuc > snpfreqplot
view test-data/1084592.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/012/246/12246258/tmp/lofreq2_call_parallelo8d8yqgo/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_80,Description="Minimum SNV Quality (Phred) 80"> ##FILTER=<ID=min_indelqual_66,Description="Minimum Indel Quality (Phred) 66"> ##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/012/246/12246325/outputs/galaxy_dataset_6f0d993e-795a-409c-9e60-c42e81b8063a.dat NC_045512.2 /data/dnb03/galaxy_db/files/6/9/2/dataset_692b463b-8a0c-40e3-8a87-942e48d53fcd.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_045512.2 164 . C T 133.0 min_af_0.050000 AF=0.001348;DP=16325;DP4=12679,3617,21,6;SB=0 NC_045512.2 241 . C T 49314.0 PASS AF=0.990942;DP=5741;DP4=1,0,2961,2774;SB=0 NC_045512.2 323 . GT G 75.0 min_af_0.050000 AF=0.000602;DP=16624;DP4=3541,13119,3,7;HRUN=4;SB=3;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_045512.2 343 . G A 92.0 min_af_0.050000 AF=0.000967;DP=26891;DP4=13149,13701,12,17;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V26|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V26|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON),SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V26|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON),SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V26|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A) NC_045512.2 424 . AGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTT A 49314.0 PASS AF=0.867361;DP=12779;DP4=908,822,9479,1605;HRUN=1;SB=1918;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gtagaagttgaaaaaggcgttttgcctcaacttgaa/gaa|VEVEKGVLPQLE54E|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gtagaagttgaaaaaggcgttttgcctcaacttgaa/gaa|VEVEKGVLPQLE54E|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gtagaagttgaaaaaggcgttttgcctcaacttgaa/gaa|VEVEKGVLPQLE54E|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gtagaagttgaaaaaggcgttttgcctcaacttgaa/gaa|VEVEKGVLPQLE54E|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A|INFO_REALIGN_3_PRIME) NC_045512.2 457 . T TA 1257.0 min_af_0.050000 AF=0.006406;DP=11239;DP4=9516,1651,67,5;HRUN=1;SB=11;INDEL;EFF=FRAME_SHIFT(HIGH||gaa/Agaa|E65R?|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|TA),FRAME_SHIFT(HIGH||gaa/Agaa|E65R?|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|TA|WARNING_TRANSCRIPT_NO_STOP_CODON),FRAME_SHIFT(HIGH||gaa/Agaa|E65R?|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|TA|WARNING_TRANSCRIPT_NO_STOP_CODON),FRAME_SHIFT(HIGH||gaa/Agaa|E65R?|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|TA);LOF=(ORF1ab|GU280_gp01|28|0.07) NC_045512.2 509 . GGTCATGTTATGGTT G 158.0 min_af_0.050000 AF=0.003328;DP=5709;DP4=3637,2595,8,11;HRUN=2;SB=7;INDEL;EFF=FRAME_SHIFT(HIGH||ggtcatgttatggttgag/|GHVMVE82|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ggtcatgttatggttgag/|GHVMVE82|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ggtcatgttatggttgag/|GHVMVE82|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ggtcatgttatggttgag/|GHVMVE82|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07) NC_045512.2 558 . G T 440.0 min_af_0.050000 AF=0.007488;DP=4941;DP4=2892,2007,24,13;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_045512.2 602 . G A 134.0 min_af_0.050000 AF=0.001451;DP=14475;DP4=3277,11172,8,16;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gaa/Aaa|E113K|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gaa/Aaa|E113K|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gaa/Aaa|E113K|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gaa/Aaa|E113K|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A) NC_045512.2 685 . AAAGTCATTT A 186.0 min_af_0.050000 AF=0.001184;DP=14362;DP4=3266,11121,4,13;HRUN=3;SB=0;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_045512.2 951 . A G 160.0 min_af_0.050000 AF=0.003730;DP=4021;DP4=506,3495,0,17;SB=8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tAc/tGc|Y229C|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tAc/tGc|Y229C|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tAc/tGc|Y49C|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tAc/tGc|Y49C|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 1019 . C T 109.0 min_af_0.050000 AF=0.000957;DP=21953;DP4=17831,4091,17,7;SB=7;EFF=STOP_GAINED(HIGH|NONSENSE|Cag/Tag|Q252*|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),STOP_GAINED(HIGH|NONSENSE|Cag/Tag|Q252*|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),STOP_GAINED(HIGH|NONSENSE|Cag/Tag|Q72*|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),STOP_GAINED(HIGH|NONSENSE|Cag/Tag|Q72*|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.04);NMD=(ORF1ab|GU280_gp01|28|0.04) NC_045512.2 1020 . A G 108.0 min_af_0.050000 AF=0.000957;DP=21933;DP4=17771,4130,20,5;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q252R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q252R|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q72R|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q72R|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 1026 . CT C 166.0 min_af_0.050000 AF=0.000872;DP=21786;DP4=17611,4236,13,6;HRUN=4;SB=6;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/|F255|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F255|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F75|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F75|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.11) NC_045512.2 1027 . T C 192.0 min_af_0.050000 AF=0.001376;DP=21810;DP4=17520,4226,28,6;SB=0;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 736.0 min_af_0.050000;sb_fdr AF=0.008634;DP=6370;DP4=2492,3819,4,51;SB=70;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 1133 . A T 481.0 min_af_0.050000 AF=0.006411;DP=6551;DP4=2807,3701,35,7;SB=68;EFF=STOP_GAINED(HIGH|NONSENSE|Aag/Tag|K290*|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),STOP_GAINED(HIGH|NONSENSE|Aag/Tag|K290*|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),STOP_GAINED(HIGH|NONSENSE|Aag/Tag|K110*|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),STOP_GAINED(HIGH|NONSENSE|Aag/Tag|K110*|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.04);NMD=(ORF1ab|GU280_gp01|28|0.04) NC_045512.2 1201 . C T 184.0 min_af_0.050000 AF=0.001608;DP=18660;DP4=3443,15178,7,23;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C312|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C312|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C132|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C132|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 1211 . T C 100.0 min_af_0.050000 AF=0.001014;DP=18739;DP4=3499,15213,6,15;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgc/Cgc|C316R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgc/Cgc|C316R|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgc/Cgc|C136R|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgc/Cgc|C136R|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 1644 . A C 438.0 min_af_0.050000 AF=0.003210;DP=14641;DP4=11631,2951,20,31;SB=94;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 496.0 min_af_0.050000 AF=0.003406;DP=14679;DP4=11564,3059,19,34;SB=108;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 395.0 min_af_0.050000 AF=0.003129;DP=14702;DP4=11472,3173,20,31;SB=87;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 351.0 min_af_0.050000 AF=0.002908;DP=14789;DP4=11547,3193,16,29;SB=90;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 289.0 min_af_0.050000 AF=0.002467;DP=14590;DP4=11407,3111,29,7;SB=0;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 275.0 min_af_0.050000 AF=0.002280;DP=14476;DP4=11396,3040,21,17;SB=29;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 1721 . G A 140.0 min_af_0.050000 AF=0.001466;DP=14325;DP4=11313,2989,14,7;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A486T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A486T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A306T|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A306T|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 1868 . G A 132.0 min_af_0.050000 AF=0.001298;DP=16183;DP4=3249,12900,4,20;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A535T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A535T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A355T|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A355T|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 1874 . G A 95.0 min_af_0.050000 AF=0.001055;DP=16116;DP4=3127,12965,3,15;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A537T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A537T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A357T|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A357T|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 1886 . G A 84.0 min_af_0.050000 AF=0.001075;DP=15820;DP4=2886,12908,4,17;SB=0;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 137.0 min_af_0.050000 AF=0.001452;DP=15147;DP4=2713,12407,6,18;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 2904 . TA T 78.0 min_af_0.050000 AF=0.001265;DP=6322;DP4=5093,1224,5,3;HRUN=5;SB=7;INDEL;EFF=FRAME_SHIFT(HIGH||act/|T882|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||act/|T882|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||act/|T64|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||act/|T64|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07) NC_045512.2 3036 . TC T 93.0 min_af_0.050000 AF=0.002984;DP=2011;DP4=1107,916,3,3;HRUN=1;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||ttc/|F924|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),FRAME_SHIFT(HIGH||ttc/|F924|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),FRAME_SHIFT(HIGH||ttc/|F106|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),FRAME_SHIFT(HIGH||ttc/|F106|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.14) NC_045512.2 3037 . C T 49314.0 PASS AF=0.991580;DP=2019;DP4=0,0,1111,902;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 3259 . G T 128.0 min_af_0.050000 AF=0.002216;DP=6770;DP4=5516,1236,14,1;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caG/caT|Q998H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caG/caT|Q998H|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caG/caT|Q180H|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caG/caT|Q180H|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 3412 . TA T 76.0 min_af_0.050000 AF=0.001168;DP=6847;DP4=1290,5560,1,7;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 4174 . TA T 155.0 min_af_0.050000 AF=0.000954;DP=19915;DP4=15786,4180,15,4;HRUN=5;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||aag/|K1305|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aag/|K1305|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aag/|K487|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aag/|K487|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 4185 . G T 321.0 min_af_0.050000 AF=0.002271;DP=20253;DP4=15843,4355,24,24;SB=46;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 4308 . A G 307.0 min_af_0.050000 AF=0.001970;DP=21317;DP4=4425,16849,9,34;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K1348R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K1348R|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K530R|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K530R|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 4321 . CT C 96.0 min_af_0.050000 AF=0.000624;DP=20829;DP4=4119,17027,3,10;HRUN=4;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||tac/|Y1354|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tac/|Y1354|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tac/|Y536|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tac/|Y536|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 4391 . C T 91.0 min_af_0.050000 AF=0.001118;DP=21462;DP4=4942,16483,5,24;SB=1;EFF=STOP_GAINED(HIGH|NONSENSE|Cga/Tga|R1376*|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),STOP_GAINED(HIGH|NONSENSE|Cga/Tga|R1376*|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),STOP_GAINED(HIGH|NONSENSE|Cga/Tga|R558*|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),STOP_GAINED(HIGH|NONSENSE|Cga/Tga|R558*|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.04);NMD=(ORF1ab|GU280_gp01|28|0.04) NC_045512.2 4412 . GA G 74.0 min_af_0.050000 AF=0.000953;DP=7343;DP4=4106,3237,2,5;HRUN=2;SB=5;INDEL;EFF=FRAME_SHIFT(HIGH||gaa/|E1383|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||gaa/|E1383|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||gaa/|E565|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||gaa/|E565|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 5284 . C T 108.0 min_af_0.050000 AF=0.002361;DP=5082;DP4=3452,1616,2,10;SB=34;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 298.0 min_af_0.050000 AF=0.002476;DP=8887;DP4=7154,1717,15,7;HRUN=2;SB=7;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 5305 . G T 135.0 min_af_0.050000 AF=0.001876;DP=9060;DP4=7211,1817,14,4;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttT|L1680F|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttT|L1680F|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttT|L862F|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttT|L862F|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 5411 . G A 238.0 min_af_0.050000 AF=0.003764;DP=6110;DP4=3843,2238,8,16;SB=23;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A1716T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A1716T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A898T|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A898T|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 5743 . G C 189.0 min_af_0.050000 AF=0.005262;DP=3421;DP4=1740,1660,3,16;SB=26;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 311.0 min_af_0.050000 AF=0.007656;DP=3396;DP4=1744,1626,8,18;SB=13;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 5809 . AGACGGTGCTTTACTT A 92.0 min_af_0.050000 AF=0.000900;DP=9999;DP4=2218,7782,1,8;HRUN=1;SB=1;INDEL;EFF=CODON_DELETION(MODERATE||gacggtgctttactt/|DGALL1849|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),CODON_DELETION(MODERATE||gacggtgctttactt/|DGALL1849|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),CODON_DELETION(MODERATE||gacggtgctttactt/|DGALL1031|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),CODON_DELETION(MODERATE||gacggtgctttactt/|DGALL1031|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 5924 . G A 89.0 min_af_0.050000 AF=0.000850;DP=23540;DP4=13235,10277,7,14;SB=13;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V1887I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V1887I|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V1069I|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V1069I|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 6044 . AATT A 89.0 min_af_0.050000 AF=0.001604;DP=4363;DP4=1797,2576,4,3;HRUN=2;SB=3;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aatttt/att|NF1927I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aatttt/att|NF1927I|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aatttt/att|NF1109I|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aatttt/att|NF1109I|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 6139 . AT A 118.0 min_af_0.050000 AF=0.000973;DP=14384;DP4=2789,11592,3,11;HRUN=5;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||ttc/|F1960|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttc/|F1960|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttc/|F1142|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttc/|F1142|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 194.0 min_af_0.050000 AF=0.001019;DP=18642;DP4=2648,15985,2,17;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 6179 . TA T 68.0 min_af_0.050000 AF=0.000477;DP=18879;DP4=2626,16309,0,9;HRUN=1;SB=2;INDEL;EFF=FRAME_SHIFT(HIGH||tat/|Y1972|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),FRAME_SHIFT(HIGH||tat/|Y1972|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),FRAME_SHIFT(HIGH||tat/|Y1154|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),FRAME_SHIFT(HIGH||tat/|Y1154|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.14) NC_045512.2 6199 . T C 159.0 min_af_0.050000 AF=0.001119;DP=49166;DP4=31656,17424,42,17;SB=4;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S1978|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S1978|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S1160|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S1160|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 6242 . C T 150.0 min_af_0.050000 AF=0.000761;DP=51238;DP4=31718,19455,32,17;SB=1;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 6254 . G A 127.0 min_af_0.050000 AF=0.000758;DP=39566;DP4=31533,7989,26,8;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 6270 . C T 81.0 min_af_0.050000 AF=0.000632;DP=39548;DP4=30669,8836,22,9;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T2002M|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T2002M|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T1184M|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T1184M|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 6271 . G A 176.0 min_af_0.050000 AF=0.001023;DP=39089;DP4=30156,8871,25,21;SB=32;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 6297 . G A 180.0 min_af_0.050000 AF=0.000958;DP=38631;DP4=29557,9033,26,11;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R2011H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R2011H|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R1193H|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R1193H|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 6312 . CA C 294.0 min_af_0.050000 AF=0.000902;DP=37682;DP4=29256,8543,26,8;HRUN=4;SB=0;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 6396 . T C 258.0 min_af_0.050000 AF=0.002203;DP=14981;DP4=6634,8302,5,31;SB=38;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTa/cCa|L2044P|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTa/cCa|L2044P|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTa/cCa|L1226P|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTa/cCa|L1226P|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 6409 . T C 102.0 min_af_0.050000 AF=0.000752;DP=34578;DP4=6634,27908,5,23;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S2048|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S2048|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S1230|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S1230|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 6503 . G A 102.0 min_af_0.050000 AF=0.000761;DP=31528;DP4=5228,26256,5,25;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 199.0 min_af_0.050000 AF=0.001168;DP=30810;DP4=4748,25994,7,49;SB=1;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 6906 . C T 41177.0 PASS AF=0.995383;DP=1083;DP4=1,0,564,518;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S2214L|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S2214L|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S1396L|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S1396L|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 7246 . GT G 95.0 min_af_0.050000 AF=0.005029;DP=1193;DP4=555,642,3,3;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 7614 . G C 134.0 min_af_0.050000 AF=0.010056;DP=895;DP4=349,535,6,3;SB=7;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 135.0 min_af_0.050000 AF=0.010045;DP=896;DP4=350,535,6,3;SB=7;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 7772 . CT C 79.0 min_af_0.050000 AF=0.000827;DP=9676;DP4=7597,2126,5,3;HRUN=3;SB=4;INDEL;EFF=FRAME_SHIFT(HIGH||tac/|Y2504|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tac/|Y2504|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tac/|Y1686|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tac/|Y1686|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 7788 . C A 130.0 min_af_0.050000 AF=0.003436;DP=3784;DP4=1622,2148,11,2;SB=24;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gAt|A2508D|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gAt|A2508D|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gAt|A1690D|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gAt|A1690D|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 7813 . TTC T 77.0 min_af_0.050000 AF=0.001577;DP=3805;DP4=1781,2043,3,3;HRUN=2;SB=0;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 7889 . GT G 703.0 min_af_0.050000 AF=0.004789;DP=10024;DP4=2088,7910,10,38;HRUN=5;SB=0;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 7911 . G C 105.0 min_af_0.050000 AF=0.001495;DP=10036;DP4=2129,7889,2,13;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tCt|C2549S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tCt|C2549S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tCt|C1731S|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tCt|C1731S|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 8017 . G A 112.0 min_af_0.050000 AF=0.002980;DP=5034;DP4=4162,854,8,7;SB=21;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A2584|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A2584|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A1766|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A1766|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 8387 . A C 82.0 min_af_0.050000 AF=0.003079;DP=3897;DP4=3112,767,8,5;SB=8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aac/Cac|N2708H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aac/Cac|N2708H|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aac/Cac|N1890H|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aac/Cac|N1890H|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 8937 . C T 98.0 min_af_0.050000 AF=0.001505;DP=9303;DP4=7370,1913,10,4;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A2891V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A2891V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A128V|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A128V|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 8991 . C T 141.0 min_af_0.050000 AF=0.001933;DP=9310;DP4=7384,1900,17,4;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A2909V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A2909V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A146V|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A146V|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 9593 . T C 83.0 min_af_0.050000 AF=0.001116;DP=12543;DP4=9868,2657,13,3;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L3110|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L3110|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L347|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L347|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 9656 . A G 276.0 min_af_0.050000;sb_fdr AF=0.005870;DP=3918;DP4=1706,2185,22,1;SB=67;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 9807 . G A 135.0 min_af_0.050000 AF=0.001628;DP=11669;DP4=2191,9457,4,15;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C3181Y|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C3181Y|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C418Y|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C418Y|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 9808 . C T 149.0 min_af_0.050000 AF=0.001800;DP=11666;DP4=2188,9439,6,31;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C3181|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C3181|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C418|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C418|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 10450 . C T 569.0 min_af_0.050000 AF=0.010680;DP=3839;DP4=2984,812,31,10;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P3395|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P3395|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P132|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P132|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 10481 . G A 110.0 min_af_0.050000 AF=0.003086;DP=3564;DP4=2636,916,11,1;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G3406S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G3406S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G143S|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G143S|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 10615 . C T 122.0 min_af_0.050000 AF=0.003522;DP=3407;DP4=1050,2343,7,6;SB=8;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D3450|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D3450|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D187|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D187|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 10679 . T C 451.0 min_af_0.050000 AF=0.010126;DP=3259;DP4=866,2359,7,26;SB=2;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 11083 . G T 248.0 min_af_0.050000 AF=0.002203;DP=17707;DP4=13818,3821,39,10;SB=0;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 11095 . CT C 240.0 min_af_0.050000 AF=0.001401;DP=17844;DP4=13909,3979,18,7;HRUN=5;SB=3;INDEL;EFF=FRAME_SHIFT(HIGH||tta/|L3612|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tta/|L3612|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tta/|L43|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tta/|L43|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 11104 . T C 146.0 min_af_0.050000 AF=0.001454;DP=17883;DP4=13846,3990,25,4;SB=4;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P3613|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P3613|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P44|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P44|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 11139 . C T 105.0 min_af_0.050000 AF=0.001114;DP=17949;DP4=13766,4153,16,6;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A3625V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A3625V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A56V|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A56V|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 11248 . G A 90.0 min_af_0.050000 AF=0.001085;DP=17516;DP4=3720,13767,7,17;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atG/atA|M3661I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atG/atA|M3661I|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atG/atA|M92I|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atG/atA|M92I|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 11321 . G A 115.0 min_af_0.050000 AF=0.001101;DP=19067;DP4=3969,15072,6,17;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A3686T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A3686T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A117T|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A117T|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 11354 . G A 145.0 min_af_0.050000 AF=0.001076;DP=25103;DP4=9900,15171,11,18;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A3697T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A3697T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A128T|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A128T|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 11406 . T G 80.0 min_af_0.050000 AF=0.001365;DP=8792;DP4=6687,2087,7,7;SB=12;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTc/gGc|V3714G|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTc/gGc|V3714G|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTc/gGc|V145G|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTc/gGc|V145G|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 11540 . GT G 98.0 min_af_0.050000 AF=0.001671;DP=5387;DP4=1684,3719,5,4;HRUN=5;SB=8;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/|F3760|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F3760|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F191|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F191|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) NC_045512.2 11654 . T C 120.0 min_af_0.050000 AF=0.001515;DP=13857;DP4=6675,7149,9,13;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttt/Ctt|F3797L|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttt/Ctt|F3797L|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttt/Ctt|F228L|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttt/Ctt|F228L|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 11939 . G A 81.0 min_af_0.050000 AF=0.000866;DP=19641;DP4=16008,3601,13,6;SB=8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V3892I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V3892I|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V33I|82|ORF1ab|protein_coding|CODING|YP_009725303.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V33I|82|ORF1ab|protein_coding|CODING|YP_009742614.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 11952 . A T 80.0 min_af_0.050000 AF=0.000943;DP=19088;DP4=15213,3849,13,6;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aTt|N3896I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aTt|N3896I|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aTt|N37I|82|ORF1ab|protein_coding|CODING|YP_009725303.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aTt|N37I|82|ORF1ab|protein_coding|CODING|YP_009742614.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 12128 . G A 91.0 min_af_0.050000 AF=0.000925;DP=20531;DP4=4035,16468,3,20;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A3955T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A3955T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A13T|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A13T|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 12129 . C T 87.0 min_af_0.050000 AF=0.000876;DP=20539;DP4=4021,16498,3,15;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A3955V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A3955V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A13V|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A13V|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 12141 . C T 93.0 min_af_0.050000 AF=0.000878;DP=21647;DP4=5102,16508,3,16;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T3959I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T3959I|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T17I|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T17I|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 12161 . C T 92.0 min_af_0.050000 AF=0.000874;DP=21732;DP4=5048,16660,6,15;SB=2;EFF=STOP_GAINED(HIGH|NONSENSE|Cag/Tag|Q3966*|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),STOP_GAINED(HIGH|NONSENSE|Cag/Tag|Q3966*|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),STOP_GAINED(HIGH|NONSENSE|Cag/Tag|Q24*|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),STOP_GAINED(HIGH|NONSENSE|Cag/Tag|Q24*|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.04);NMD=(ORF1ab|GU280_gp01|28|0.04) NC_045512.2 12164 . G T 351.0 min_af_0.050000 AF=0.002070;DP=21735;DP4=5033,16647,15,33;SB=6;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 12201 . A G 204.0 min_af_0.050000 AF=0.001584;DP=20834;DP4=4220,16578,7,29;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K3979R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K3979R|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K37R|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K37R|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 12224 . G A 103.0 min_af_0.050000 AF=0.000998;DP=20040;DP4=3616,16391,5,18;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A3987T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A3987T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A45T|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A45T|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 12458 . A G 322.0 min_af_0.050000 AF=0.002236;DP=17442;DP4=13770,3621,34,6;SB=3;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 12513 . C T 139.0 min_af_0.050000 AF=0.001298;DP=17726;DP4=13800,3892,14,9;SB=11;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T4083M|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T4083M|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T141M|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T141M|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 12578 . G T 99.0 min_af_0.050000 AF=0.002130;DP=6103;DP4=2421,3667,9,5;SB=10;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Tat|D4105Y|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Tat|D4105Y|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Tat|D163Y|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Tat|D163Y|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 12754 . C T 193.0 min_af_0.050000 AF=0.001165;DP=29183;DP4=14327,14756,21,71;SB=65;EFF=SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C4163|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C4163|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C23|112|ORF1ab|protein_coding|CODING|YP_009725305.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C23|112|ORF1ab|protein_coding|CODING|YP_009742616.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 12999 . G A 88.0 min_af_0.050000 AF=0.000980;DP=17347;DP4=4073,13246,5,14;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aAt|S4245N|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aAt|S4245N|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aAt|S105N|112|ORF1ab|protein_coding|CODING|YP_009725305.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aAt|S105N|112|ORF1ab|protein_coding|CODING|YP_009742616.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 13034 . G A 201.0 min_af_0.050000 AF=0.000910;DP=47277;DP4=29099,18123,31,13;SB=5;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 135.0 min_af_0.050000 AF=0.000711;DP=47843;DP4=29048,18629,26,114;SB=238;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 162.0 min_af_0.050000 AF=0.000791;DP=48027;DP4=29118,18852,25,20;SB=2;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 13050 . C T 185.0 min_af_0.050000 AF=0.000853;DP=48077;DP4=29117,18902,27,20;SB=1;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 13059 . C T 119.0 min_af_0.050000 AF=0.000665;DP=48140;DP4=28964,19130,18,19;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T4265I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T4265I|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T12I|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T12I|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 13061 . G A 149.0 min_af_0.050000 AF=0.000747;DP=48218;DP4=28907,19226,43,19;SB=8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gta/Ata|V4266I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gta/Ata|V4266I|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gta/Ata|V13I|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gta/Ata|V13I|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 13084 . T C 155.0 min_af_0.050000 AF=0.000894;DP=35812;DP4=28538,7231,27,8;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A4273|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A4273|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A20|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A20|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 13094 . G A 91.0 min_af_0.050000 AF=0.000756;DP=35712;DP4=27866,7809,23,7;SB=0;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 284.0 min_af_0.050000 AF=0.001022;DP=34241;DP4=26326,7960,28,7;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 311.0 min_af_0.050000 AF=0.001594;DP=34502;DP4=26344,8069,53,15;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 13201 . G T 11905.0 min_af_0.050000 AF=0.045618;DP=13043;DP4=6344,6083,306,296;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccG/ccT|P4312|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|ccG/ccT|P4312|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|ccG/ccT|P59|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ccG/ccT|P59|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 13235 . G A 191.0 min_af_0.050000 AF=0.001363;DP=30081;DP4=7582,22442,11,32;SB=0;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 13254 . G A 125.0 min_af_0.050000 AF=0.000926;DP=34575;DP4=8035,26482,10,29;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C4330Y|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C4330Y|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C77Y|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C77Y|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 13260 . G A 110.0 min_af_0.050000 AF=0.000832;DP=34837;DP4=8162,26632,9,26;SB=1;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 141.0 min_af_0.050000 AF=0.000576;DP=34699;DP4=8173,26639,4,16;HRUN=4;SB=0;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 13334 . G A 93.0 min_af_0.050000 AF=0.000719;DP=33393;DP4=6325,27020,8,20;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A4357T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A4357T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A104T|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A104T|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 13345 . T C 142.0 min_af_0.050000 AF=0.000923;DP=37923;DP4=11024,26838,17,19;SB=15;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 67.0 min_af_0.050000 AF=0.000345;DP=37715;DP4=10940,26835,4,9;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 13373 . TG T 74.0 min_af_0.050000 AF=0.000556;DP=16174;DP4=9855,6326,3,6;HRUN=1;SB=7;INDEL;EFF=FRAME_SHIFT(HIGH||tgt/|C4370|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),FRAME_SHIFT(HIGH||tgt/|C4370|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),FRAME_SHIFT(HIGH||tgt/|C117|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),FRAME_SHIFT(HIGH||tgt/|C117|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.11) NC_045512.2 13451 . G A 139.0 min_af_0.050000 AF=0.002377;DP=6732;DP4=5314,1401,11,5;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4396T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4396T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4T|12|ORF1ab|protein_coding|CODING|YP_009725312.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4T|931|ORF1ab|protein_coding|CODING|YP_009725307.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 13565 . T G 126.0 min_af_0.050000 AF=0.002191;DP=6845;DP4=1460,5365,11,6;SB=38;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 626.0 min_af_0.050000 AF=0.007100;DP=6901;DP4=1486,5364,11,39;SB=0;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 13616 . A G 107.0 min_af_0.050000 AF=0.001711;DP=10521;DP4=1399,9100,2,17;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K4451R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K59R|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|G|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 13836 . G A 153.0 min_af_0.050000 AF=0.000927;DP=34520;DP4=6715,27756,10,24;SB=7;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R4524|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R132|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 13966 . G A 87.0 min_af_0.050000 AF=0.001010;DP=15845;DP4=13708,2113,14,3;SB=3;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 361.0 min_af_0.050000 AF=0.003139;DP=13381;DP4=10986,2346,23,20;SB=49;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 13988 . G A 99.0 min_af_0.050000 AF=0.001272;DP=12581;DP4=10082,2474,15,2;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R4575H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R183H|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 14408 . C T 33427.0 PASS AF=0.987778;DP=900;DP4=0,3,371,524;SB=5;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 14624 . G A 100.0 min_af_0.050000 AF=0.001576;DP=8885;DP4=6982,1886,13,3;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C4787Y|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C395Y|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 14653 . G T 110.0 min_af_0.050000 AF=0.001667;DP=8999;DP4=6980,2002,13,3;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Ttt|V4797F|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Ttt|V405F|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 14848 . CTATTTG C 71.0 min_af_0.050000 AF=0.000856;DP=8180;DP4=1608,6620,1,6;HRUN=1;SB=0;INDEL;EFF=CODON_DELETION(MODERATE||tttgta/|FV4863|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C|INFO_REALIGN_3_PRIME),CODON_DELETION(MODERATE||tttgta/|FV471|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME) NC_045512.2 15016 . G T 479.0 min_af_0.050000 AF=0.014688;DP=2451;DP4=1905,509,26,10;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Tca|A4918S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Tca|A526S|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 15128 . G A 80.0 min_af_0.050000 AF=0.003114;DP=2890;DP4=662,2204,3,10;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C4955Y|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C563Y|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 15157 . CA C 88.0 min_af_0.050000 AF=0.002424;DP=2888;DP4=652,2250,1,6;HRUN=5;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||aaa/|K4966|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K574|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07) NC_045512.2 15279 . C T 202.0 min_af_0.050000 AF=0.002300;DP=10437;DP4=8333,2073,23,6;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H5005|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H613|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=0.989112;DP=8817;DP4=1,1,6751,2058;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 15587 . C T 109.0 min_af_0.050000 AF=0.000895;DP=27936;DP4=22151,5748,24,5;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A5108V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A716V|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 15602 . G A 148.0 min_af_0.050000 AF=0.001137;DP=28150;DP4=22229,5881,25,8;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R5113H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R721H|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 15610 . C T 81.0 min_af_0.050000 AF=0.000720;DP=27789;DP4=22076,5684,17,5;SB=1;EFF=STOP_GAINED(HIGH|NONSENSE|Caa/Taa|Q5116*|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),STOP_GAINED(HIGH|NONSENSE|Caa/Taa|Q724*|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 15628 . T C 97.0 min_af_0.050000 AF=0.000810;DP=27146;DP4=21748,5352,23,2;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C5122R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C730R|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|C|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 15673 . T G 138.0 min_af_0.050000;sb_fdr AF=0.002916;DP=9601;DP4=4640,4919,28,2;SB=65;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 3086.0 min_af_0.050000 AF=0.019651;DP=9567;DP4=4771,4605,113,78;SB=16;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 3070.0 min_af_0.050000 AF=0.019492;DP=9645;DP4=4821,4634,112,78;SB=14;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 15752 . C T 130.0 min_af_0.050000 AF=0.000956;DP=27194;DP4=5580,21576,5,26;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A5163V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A771V|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 15761 . G C 111.0 min_af_0.050000 AF=0.000914;DP=27359;DP4=5595,21715,7,21;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gCt|G5166A|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gCt|G774A|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|C|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 15784 . T TGAC 140.0 min_af_0.050000 AF=0.000612;DP=27777;DP4=5858,22028,5,12;HRUN=3;SB=4;INDEL;EFF=STOP_GAINED+CODON_CHANGE_PLUS_CODON_INSERTION(HIGH||ttt/tGACtt|F5174*L|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|TGAC),STOP_GAINED+CODON_CHANGE_PLUS_CODON_INSERTION(HIGH||ttt/tGACtt|F782*L|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|TGAC|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 15788 . AGTC A 140.0 min_af_0.050000 AF=0.000617;DP=27575;DP4=5626,21971,5,12;HRUN=1;SB=4;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aagtca/aaa|KS5175K|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aagtca/aaa|KS783K|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 15959 . C G 86.0 min_af_0.050000 AF=0.001104;DP=16300;DP4=12597,3665,14,5;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gGc|A5232G|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gGc|A840G|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|G|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 16073 . C T 104.0 min_af_0.050000 AF=0.001226;DP=15503;DP4=3133,12344,4,17;SB=0;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 16386 . C T 95.0 min_af_0.050000 AF=0.006667;DP=1050;DP4=288,752,3,4;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C5374|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C50|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 16800 . TA T 143.0 min_af_0.050000 AF=0.001533;DP=9133;DP4=7069,2052,12,2;HRUN=5;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||aac/|N5514|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aac/|N190|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07) NC_045512.2 16949 . C T 101.0 min_af_0.050000 AF=0.003001;DP=3665;DP4=1707,1944,5,7;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P5562L|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P238L|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 17035 . G A 90.0 min_af_0.050000 AF=0.001462;DP=8890;DP4=2031,6845,4,9;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A5591T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A267T|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 17140 . G A 85.0 min_af_0.050000 AF=0.001241;DP=12090;DP4=9631,2440,12,4;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A5626T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A302T|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 17144 . G A 117.0 min_af_0.050000 AF=0.001660;DP=12046;DP4=9540,2484,14,6;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R5627H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R303H|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 17200 . TTAAAA T 188.0 min_af_0.050000 AF=0.001439;DP=11115;DP4=8773,2405,10,6;HRUN=2;SB=8;INDEL;EFF=FRAME_SHIFT(HIGH||aaatat/|KY5647|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaatat/|KY323|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07) NC_045512.2 17339 . C T 81.0 min_af_0.050000 AF=0.001134;DP=12349;DP4=3036,9291,3,11;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A5692V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A368V|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 17808 . G T 151.0 min_af_0.050000 AF=0.009872;DP=1013;DP4=826,177,9,1;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaG/aaT|K5848N|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaG/aaT|K524N|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 18641 . T A 530.0 min_af_0.050000 AF=0.003382;DP=15673;DP4=11486,4127,27,27;SB=35;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTa/aAa|I6126K|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTa/aAa|I201K|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 18687 . CT C 156.0 min_af_0.050000 AF=0.001118;DP=14308;DP4=11344,2973,10,6;HRUN=4;SB=9;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 18715 . T C 109.0 min_af_0.050000 AF=0.001262;DP=14258;DP4=11215,3019,14,6;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C6151R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C226R|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 18736 . TTTGA T 79.0 min_af_0.050000 AF=0.000635;DP=14178;DP4=11228,2983,7,2;HRUN=3;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||gattac/|DY6159|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||gattac/|DY234|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07) NC_045512.2 19172 . C T 142.0 min_af_0.050000 AF=0.001388;DP=15855;DP4=3216,12613,7,16;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T6303I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T378I|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 19188 . AT A 219.0 min_af_0.050000 AF=0.001329;DP=15807;DP4=3164,12631,6,15;HRUN=4;SB=3;INDEL;EFF=FRAME_SHIFT(HIGH||tgg/|W6310|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tgg/|W385|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07) NC_045512.2 19199 . G A 96.0 min_af_0.050000 AF=0.001074;DP=15832;DP4=3167,12645,6,13;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C6312Y|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C387Y|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 19452 . T A 120.0 min_af_0.050000 AF=0.030612;DP=196;DP4=112,78,1,5;SB=10;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcA|A6396|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcA|A471|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 19468 . T A 100.0 min_af_0.050000 AF=0.013605;DP=441;DP4=123,312,3,3;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgc/Agc|C6402S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgc/Agc|C477S|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 19679 . G T 305.0 min_af_0.050000 AF=0.002634;DP=14427;DP4=11435,2935,30,8;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G6472V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G20V|345|ORF1ab|protein_coding|CODING|YP_009725310.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 19821 . A G 97.0 min_af_0.050000 AF=0.001163;DP=13752;DP4=2628,11106,4,12;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P6519|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P67|345|ORF1ab|protein_coding|CODING|YP_009725310.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 19870 . G A 130.0 min_af_0.050000 AF=0.001286;DP=16326;DP4=4782,11514,9,15;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V6536M|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V84M|345|ORF1ab|protein_coding|CODING|YP_009725310.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 20317 . G T 81.0 min_af_0.050000 AF=0.006459;DP=929;DP4=629,294,5,1;SB=1;EFF=STOP_GAINED(HIGH|NONSENSE|Gaa/Taa|E6685*|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),STOP_GAINED(HIGH|NONSENSE|Gaa/Taa|E233*|345|ORF1ab|protein_coding|CODING|YP_009725310.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 20839 . G A 95.0 min_af_0.050000 AF=0.000824;DP=25489;DP4=12509,12947,18,8;SB=13;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 20926 . C T 100.0 min_af_0.050000 AF=0.001257;DP=13527;DP4=10536,2964,13,8;SB=9;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P6888S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P90S|297|ORF1ab|protein_coding|CODING|YP_009725311.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 21054 . C T 135.0 min_af_0.050000 AF=0.001728;DP=12156;DP4=2309,9817,5,20;SB=0;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 21066 . TA T 181.0 min_af_0.050000 AF=0.001502;DP=11985;DP4=2225,9771,3,15;HRUN=5;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||aat/|N6936|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aat/|N138|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 21634 . A AC 95.0 min_af_0.050000 AF=0.003008;DP=2327;DP4=624,1696,2,5;HRUN=5;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||cct/ccCt|P26P?|1273|S|protein_coding|CODING|GU280_gp02|1|AC|INFO_REALIGN_3_PRIME) NC_045512.2 22573 . T C 83.0 min_af_0.050000 AF=0.001085;DP=13831;DP4=11344,2466,18,2;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P337|1273|S|protein_coding|CODING|GU280_gp02|1|C) NC_045512.2 22583 . GT G 209.0 min_af_0.050000 AF=0.001487;DP=14121;DP4=11424,2680,17,4;HRUN=5;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/|F342|1273|S|protein_coding|CODING|GU280_gp02|1|G|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00) NC_045512.2 22591 . C T 138.0 min_af_0.050000 AF=0.001470;DP=14282;DP4=11424,2830,18,7;SB=5;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N343|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512.2 22639 . C T 94.0 min_af_0.050000 AF=0.001122;DP=14257;DP4=11431,2802,13,4;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S359|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512.2 22643 . T A 465.0 min_af_0.050000 AF=0.003306;DP=14216;DP4=11344,2812,33,14;SB=10;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Agt|C361S|1273|S|protein_coding|CODING|GU280_gp02|1|A) NC_045512.2 22644 . G C 442.0 min_af_0.050000 AF=0.003220;DP=14284;DP4=11347,2879,32,14;SB=10;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tCt|C361S|1273|S|protein_coding|CODING|GU280_gp02|1|C) NC_045512.2 22645 . T A 374.0 min_af_0.050000 AF=0.003012;DP=14276;DP4=11332,2884,35,14;SB=8;EFF=STOP_GAINED(HIGH|NONSENSE|tgT/tgA|C361*|1273|S|protein_coding|CODING|GU280_gp02|1|A) NC_045512.2 22852 . A G 87.0 min_af_0.050000 AF=0.001083;DP=13851;DP4=3408,10413,2,15;SB=5;EFF=SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T430|1273|S|protein_coding|CODING|GU280_gp02|1|G) NC_045512.2 22899 . G T 187.0 min_af_0.050000 AF=0.004985;DP=3410;DP4=2519,874,10,7;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G446V|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512.2 22900 . T A 595.0 min_af_0.050000 AF=0.012915;DP=3252;DP4=2361,843,7,37;SB=145;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggT/ggA|G446|1273|S|protein_coding|CODING|GU280_gp02|1|A) NC_045512.2 23132 . GT G 293.0 min_af_0.050000 AF=0.004197;DP=4289;DP4=758,3519,3,15;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 23202 . C T 84.0 min_af_0.050000 AF=0.000879;DP=19331;DP4=14178,5113,15,7;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T547I|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512.2 23209 . A G 118.0 min_af_0.050000 AF=0.001076;DP=19518;DP4=14128,5360,16,7;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T549|1273|S|protein_coding|CODING|GU280_gp02|1|G) NC_045512.2 23389 . T C 89.0 min_af_0.050000 AF=0.000975;DP=17437;DP4=3751,13662,3,14;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A609|1273|S|protein_coding|CODING|GU280_gp02|1|C) NC_045512.2 23403 . A G 49314.0 PASS AF=0.991866;DP=17334;DP4=2,4,3724,13599;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D614G|1273|S|protein_coding|CODING|GU280_gp02|1|G) NC_045512.2 23412 . G A 80.0 min_af_0.050000 AF=0.000918;DP=17437;DP4=3771,13642,2,16;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C617Y|1273|S|protein_coding|CODING|GU280_gp02|1|A) NC_045512.2 23417 . G T 181.0 min_af_0.050000 AF=0.001558;DP=17328;DP4=3727,13562,4,24;SB=3;EFF=STOP_GAINED(HIGH|NONSENSE|Gaa/Taa|E619*|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512.2 23425 . T C 88.0 min_af_0.050000 AF=0.000985;DP=17263;DP4=3692,13549,3,15;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P621|1273|S|protein_coding|CODING|GU280_gp02|1|C) NC_045512.2 23439 . C T 100.0 min_af_0.050000 AF=0.001053;DP=17099;DP4=3589,13484,4,14;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A626V|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512.2 23462 . C T 126.0 min_af_0.050000 AF=0.001338;DP=17185;DP4=3035,14116,6,20;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R634C|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512.2 23493 . A G 90.0 min_af_0.050000 AF=0.000907;DP=20942;DP4=6938,13963,23,16;SB=29;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q644R|1273|S|protein_coding|CODING|GU280_gp02|1|G) NC_045512.2 23552 . ATACCCATTGGTGCAGGTATATGCGCTAGT A 145.0 min_af_0.050000 AF=0.001893;DP=5811;DP4=4532,1270,7,4;HRUN=1;SB=5;INDEL;EFF=FRAME_SHIFT(HIGH||cccattggtgcaggtatatgcgctagttat/|PIGAGICASY665|1273|S|protein_coding|CODING|GU280_gp02|1|A|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00) NC_045512.2 23568 . GTA G 66.0 min_af_0.050000 AF=0.001026;DP=5846;DP4=4545,1316,5,1;HRUN=1;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||atatgc/|IC670|1273|S|protein_coding|CODING|GU280_gp02|1|G|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00) NC_045512.2 23616 . G A 89.0 min_af_0.050000 AF=0.003866;DP=2328;DP4=1117,1202,1,8;SB=13;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R685H|1273|S|protein_coding|CODING|GU280_gp02|1|A) NC_045512.2 24182 . A C 147.0 min_af_0.050000 AF=0.020997;DP=381;DP4=276,97,4,4;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Cct|T874P|1273|S|protein_coding|CODING|GU280_gp02|1|C) NC_045512.2 24728 . G A 82.0 min_af_0.050000 AF=0.000723;DP=27644;DP4=22524,5093,18,2;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A1056T|1273|S|protein_coding|CODING|GU280_gp02|1|A) NC_045512.2 24729 . C T 323.0 min_af_0.050000 AF=0.001663;DP=27657;DP4=22503,5095,36,12;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A1056V|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512.2 24752 . C T 95.0 min_af_0.050000 AF=0.000795;DP=28914;DP4=22721,6154,23,6;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H1064Y|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512.2 24770 . G A 136.0 min_af_0.050000 AF=0.000946;DP=28532;DP4=22916,5573,25,4;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A1070T|1273|S|protein_coding|CODING|GU280_gp02|1|A) NC_045512.2 24793 . T C 92.0 min_af_0.050000 AF=0.000755;DP=29133;DP4=22850,6250,21,5;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T1077|1273|S|protein_coding|CODING|GU280_gp02|1|C) NC_045512.2 24794 . G A 113.0 min_af_0.050000 AF=0.000855;DP=29231;DP4=22852,6337,22,6;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A1078T|1273|S|protein_coding|CODING|GU280_gp02|1|A) NC_045512.2 24799 . T C 150.0 min_af_0.050000 AF=0.000995;DP=29150;DP4=22833,6271,29,7;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P1079|1273|S|protein_coding|CODING|GU280_gp02|1|C) NC_045512.2 24800 . G A 114.0 min_af_0.050000 AF=0.000854;DP=29273;DP4=22886,6348,22,4;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A1080T|1273|S|protein_coding|CODING|GU280_gp02|1|A) NC_045512.2 24933 . G T 1263.0 min_af_0.050000 AF=0.004328;DP=27725;DP4=5738,21835,28,110;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G1124V|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512.2 24939 . G A 96.0 min_af_0.050000 AF=0.000787;DP=27943;DP4=5902,22003,3,25;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C1126Y|1273|S|protein_coding|CODING|GU280_gp02|1|A) NC_045512.2 24942 . A T 756.0 min_af_0.050000 AF=0.002979;DP=27862;DP4=5854,21905,11,79;SB=14;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gTt|D1127V|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512.2 24966 . A T 102.0 min_af_0.050000 AF=0.000825;DP=27895;DP4=6029,21831,14,11;SB=37;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aTc|N1135I|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512.2 24985 . G A 81.0 min_af_0.050000 AF=0.000720;DP=27773;DP4=5873,21863,3,23;SB=4;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttG/ttA|L1141|1273|S|protein_coding|CODING|GU280_gp02|1|A) NC_045512.2 24986 . C T 113.0 min_af_0.050000 AF=0.000866;DP=27711;DP4=5859,21820,2,25;SB=10;EFF=STOP_GAINED(HIGH|NONSENSE|Caa/Taa|Q1142*|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512.2 25007 . A G 87.0 min_af_0.050000 AF=0.000720;DP=27762;DP4=6070,21661,5,19;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aag/Gag|K1149E|1273|S|protein_coding|CODING|GU280_gp02|1|G) NC_045512.2 25049 . G T 81.0 min_af_0.050000 AF=0.000780;DP=25627;DP4=4432,21148,5,26;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Tat|D1163Y|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512.2 25345 . T C 133.0 min_af_0.050000 AF=0.001541;DP=12330;DP4=9912,2395,16,4;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S1261|1273|S|protein_coding|CODING|GU280_gp02|1|C) NC_045512.2 25452 . C T 83.0 min_af_0.050000 AF=0.002103;DP=4754;DP4=2545,2198,5,6;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I20|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T) NC_045512.2 25527 . G A 91.0 min_af_0.050000 AF=0.001163;DP=13756;DP4=2772,10956,6,12;SB=6;EFF=STOP_GAINED(HIGH|NONSENSE|tgG/tgA|W45*|275|ORF3a|protein_coding|CODING|GU280_gp03|1|A) NC_045512.2 25543 . G A 191.0 min_af_0.050000 AF=0.001876;DP=13859;DP4=2806,11016,10,18;SB=12;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A51T|275|ORF3a|protein_coding|CODING|GU280_gp03|1|A) NC_045512.2 25785 . G T 1368.0 PASS AF=0.078772;DP=749;DP4=366,323,30,29;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tgG/tgT|W131C|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T) NC_045512.2 25963 . G A 80.0 min_af_0.050000 AF=0.000889;DP=20248;DP4=15478,4744,17,5;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gaa/Aaa|E191K|275|ORF3a|protein_coding|CODING|GU280_gp03|1|A) NC_045512.2 26042 . C T 2421.0 min_af_0.050000 AF=0.008776;DP=20282;DP4=15383,4712,142,41;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T217I|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T) NC_045512.2 26044 . C G 2272.0 min_af_0.050000 AF=0.008352;DP=20115;DP4=15297,4638,134,37;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q218E|275|ORF3a|protein_coding|CODING|GU280_gp03|1|G) NC_045512.2 26046 . A G 2419.0 min_af_0.050000 AF=0.008854;DP=20216;DP4=15316,4716,140,41;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q218|275|ORF3a|protein_coding|CODING|GU280_gp03|1|G) NC_045512.2 26054 . C T 177.0 min_af_0.050000 AF=0.001501;DP=19993;DP4=15345,4610,21,10;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T221I|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T) NC_045512.2 26057 . A C 149.0 min_af_0.050000 AF=0.002423;DP=11556;DP4=6976,4538,18,14;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAc/gCc|D222A|275|ORF3a|protein_coding|CODING|GU280_gp03|1|C) NC_045512.2 26089 . T A 308.0 min_af_0.050000 AF=0.004038;DP=7430;DP4=3377,4013,7,26;SB=23;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Aac|Y233N|275|ORF3a|protein_coding|CODING|GU280_gp03|1|A) NC_045512.2 26103 . T A 739.0 min_af_0.050000;sb_fdr AF=0.007772;DP=7591;DP4=3673,3855,56,5;SB=118;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtT/gtA|V237|275|ORF3a|protein_coding|CODING|GU280_gp03|1|A) NC_045512.2 26141 . A T 370.0 min_af_0.050000 AF=0.004848;DP=7425;DP4=4276,3106,13,23;SB=19;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAc/gTc|D250V|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T) NC_045512.2 26194 . A T 163.0 min_af_0.050000 AF=0.001439;DP=20158;DP4=4634,15473,14,19;SB=19;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acg/Tcg|T268S|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T) NC_045512.2 26209 . G A 120.0 min_af_0.050000 AF=0.001098;DP=20035;DP4=4361,15644,4,20;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V273M|275|ORF3a|protein_coding|CODING|GU280_gp03|1|A) NC_045512.2 26444 . C T 133.0 min_af_0.050000 AF=0.009395;DP=958;DP4=226,723,2,7;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tTt|S67F|75|E|protein_coding|CODING|GU280_gp04|1|T) NC_045512.2 26542 . C A 294.0 min_af_0.050000 AF=0.005601;DP=4285;DP4=300,3952,0,24;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aAt|T7N|222|M|protein_coding|CODING|GU280_gp05|1|A) NC_045512.2 26545 . T G 596.0 min_af_0.050000 AF=0.002632;DP=27734;DP4=23608,4048,50,25;SB=43;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTt/aGt|I8S|222|M|protein_coding|CODING|GU280_gp05|1|G) NC_045512.2 26554 . A G 231.0 min_af_0.050000 AF=0.001343;DP=28305;DP4=23755,4496,36,6;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gGa|E11G|222|M|protein_coding|CODING|GU280_gp05|1|G) NC_045512.2 26566 . A G 106.0 min_af_0.050000 AF=0.001211;DP=28909;DP4=23882,4962,34,6;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K15R|222|M|protein_coding|CODING|GU280_gp05|1|G) NC_045512.2 26695 . G C 248.0 min_af_0.050000 AF=0.003064;DP=9137;DP4=3972,5129,3,25;SB=34;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGg/tCg|W58S|222|M|protein_coding|CODING|GU280_gp05|1|C) NC_045512.2 26769 . G A 113.0 min_af_0.050000 AF=0.000875;DP=28587;DP4=5339,23210,6,24;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A83T|222|M|protein_coding|CODING|GU280_gp05|1|A) NC_045512.2 26774 . GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTTT G 115.0 min_af_0.050000 AF=0.000525;DP=28594;DP4=5378,23236,0,15;HRUN=2;SB=10;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgtttgcg/gcg|ACLVGLMWLSYFIASFRLFA85A|222|M|protein_coding|CODING|GU280_gp05|1|G|INFO_REALIGN_3_PRIME) NC_045512.2 26774 . GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT G 83.0 min_af_0.050000 AF=0.000420;DP=28594;DP4=5378,23236,0,12;HRUN=2;SB=8;INDEL;EFF=FRAME_SHIFT(HIGH||gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/|ACLVGLMWLSYFIASFRLF85|222|M|protein_coding|CODING|GU280_gp05|1|G);LOF=(M|GU280_gp05|1|1.00) NC_045512.2 26775 . GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT G 351.0 min_af_0.050000 AF=0.001157;DP=28524;DP4=5373,23234,4,29;HRUN=1;SB=2;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc|CLVGLMWLSYFIASF86F|222|M|protein_coding|CODING|GU280_gp05|1|G|INFO_REALIGN_3_PRIME) NC_045512.2 26779 . GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT G 869.0 min_af_0.050000 AF=0.002271;DP=28626;DP4=5385,23256,8,57;HRUN=1;SB=6;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 26786 . AGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT A 940.0 min_af_0.050000 AF=0.002413;DP=28595;DP4=5340,23218,9,60;HRUN=2;SB=5;INDEL;EFF=FRAME_SHIFT(HIGH||ggcttgatgtggctcagctacttcattgcttctttc/|GLMWLSYFIASF89|222|M|protein_coding|CODING|GU280_gp05|1|A);LOF=(M|GU280_gp05|1|1.00) NC_045512.2 26798 . G A 105.0 min_af_0.050000 AF=0.000868;DP=28812;DP4=5462,23064,5,20;SB=0;EFF=STOP_GAINED(HIGH|NONSENSE|tgG/tgA|W92*|222|M|protein_coding|CODING|GU280_gp05|1|A) NC_045512.2 26839 . C T 208.0 min_af_0.050000 AF=0.001347;DP=28947;DP4=4990,23908,12,31;SB=11;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T106M|222|M|protein_coding|CODING|GU280_gp05|1|T) NC_045512.2 26885 . C T 108.0 min_af_0.050000 AF=0.000780;DP=42334;DP4=17203,25082,14,21;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N121|222|M|protein_coding|CODING|GU280_gp05|1|T) NC_045512.2 26888 . G A 81.0 min_af_0.050000 AF=0.000638;DP=42299;DP4=17150,25099,12,22;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V122|222|M|protein_coding|CODING|GU280_gp05|1|A) NC_045512.2 26889 . C T 167.0 min_af_0.050000 AF=0.000971;DP=42214;DP4=17062,25099,15,30;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cca/Tca|P123S|222|M|protein_coding|CODING|GU280_gp05|1|T) NC_045512.2 27097 . GT G 88.0 min_af_0.050000 AF=0.000583;DP=20569;DP4=4890,15748,3,9;HRUN=4;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/|F193|222|M|protein_coding|CODING|GU280_gp05|1|G|INFO_REALIGN_3_PRIME);LOF=(M|GU280_gp05|1|1.00) NC_045512.2 27131 . CTATAAAT C 110.0 min_af_0.050000 AF=0.000623;DP=20859;DP4=5002,15909,3,10;HRUN=1;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||tataaatta/|YKL204|222|M|protein_coding|CODING|GU280_gp05|1|C|INFO_REALIGN_3_PRIME);LOF=(M|GU280_gp05|1|1.00) NC_045512.2 27133 . ATAAATT A 226.0 min_af_0.050000 AF=0.001049;DP=20965;DP4=5016,15929,9,13;HRUN=1;SB=11;INDEL;EFF=STOP_GAINED+CODON_CHANGE_PLUS_CODON_DELETION(HIGH||tataaatta/taa|YKL204*|222|M|protein_coding|CODING|GU280_gp05|1|A) NC_045512.2 27190 . AAGTGACAACAGATGTTTCATCTCGTTGACTT A 97.0 min_af_0.050000 AF=0.000617;DP=24308;DP4=20706,18252,14,1;HRUN=2;SB=28;INDEL;EFF=GENE_FUSION(HIGH|||||M+ORF6||CODING|||A),FRAME_SHIFT+STOP_LOST+SPLICE_SITE_REGION(HIGH||taa/|*223|222|M|protein_coding|CODING|GU280_gp05|1|A),FRAME_SHIFT+START_LOST(HIGH||atgtttcatctcgttgacttt/|MFHLVDF1|61|ORF6|protein_coding|CODING|GU280_gp06|1|A);LOF=(ORF6|GU280_gp06|1|1.00) NC_045512.2 27214 . G A 104.0 min_af_0.050000 AF=0.001051;DP=22836;DP4=18857,3927,21,5;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V5I|61|ORF6|protein_coding|CODING|GU280_gp06|1|A) NC_045512.2 27285 . T A 292.0 min_af_0.050000 AF=0.001761;DP=22714;DP4=18427,4236,40,2;SB=17;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaA|N28K|61|ORF6|protein_coding|CODING|GU280_gp06|1|A) NC_045512.2 27335 . C T 588.0 min_af_0.050000 AF=0.006257;DP=7831;DP4=4278,3502,31,18;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T45I|61|ORF6|protein_coding|CODING|GU280_gp06|1|T) NC_045512.2 27344 . A T 1040.0 min_af_0.050000 AF=0.009986;DP=7811;DP4=4348,3381,53,26;SB=11;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAa/aTa|K48I|61|ORF6|protein_coding|CODING|GU280_gp06|1|T) NC_045512.2 27345 . A T 1026.0 min_af_0.050000 AF=0.009985;DP=7812;DP4=4358,3374,52,26;SB=10;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaA/aaT|K48N|61|ORF6|protein_coding|CODING|GU280_gp06|1|T) NC_045512.2 27354 . A G 1255.0 min_af_0.050000 AF=0.011517;DP=7641;DP4=4387,3162,62,27;SB=15;EFF=SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q51|61|ORF6|protein_coding|CODING|GU280_gp06|1|G) NC_045512.2 27720 . TATA T 301.0 PASS AF=0.056701;DP=194;DP4=56,129,6,5;HRUN=1;SB=9;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ataaca/aca|IT110T|121|ORF7a|protein_coding|CODING|GU280_gp07|1|T|INFO_REALIGN_3_PRIME) NC_045512.2 28019 . T C 80.0 min_af_0.050000 AF=0.006079;DP=987;DP4=283,698,0,6;SB=7;EFF=SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y42|121|ORF8|protein_coding|CODING|GU280_gp09|1|C) NC_045512.2 28148 . T C 122.0 min_af_0.050000 AF=0.001204;DP=19103;DP4=16383,2676,25,3;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P85|121|ORF8|protein_coding|CODING|GU280_gp09|1|C) NC_045512.2 28195 . G A 84.0 min_af_0.050000 AF=0.000961;DP=19771;DP4=16165,3583,15,4;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R101H|121|ORF8|protein_coding|CODING|GU280_gp09|1|A) NC_045512.2 28232 . C T 88.0 min_af_0.050000 AF=0.000926;DP=19437;DP4=16091,3321,16,2;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D113|121|ORF8|protein_coding|CODING|GU280_gp09|1|T) NC_045512.2 28326 . G T 189.0 min_af_0.050000 AF=0.001431;DP=20959;DP4=4181,16743,5,28;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G18V|419|N|protein_coding|CODING|GU280_gp10|1|T) NC_045512.2 28380 . G A 100.0 min_af_0.050000 AF=0.000983;DP=20349;DP4=3516,16795,6,21;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGa/cAa|R36Q|419|N|protein_coding|CODING|GU280_gp10|1|A) NC_045512.2 28406 . TTACCCAATA T 99.0 min_af_0.050000 AF=0.000588;DP=20419;DP4=3137,17295,0,12;HRUN=3;SB=6;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ttacccaataat/tat|LPNN45Y|419|N|protein_coding|CODING|GU280_gp10|1|T) NC_045512.2 28436 . G A 96.0 min_af_0.050000 AF=0.000921;DP=22792;DP4=5504,17257,4,21;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A55T|419|N|protein_coding|CODING|GU280_gp10|1|A) NC_045512.2 28714 . C T 124.0 min_af_0.050000 AF=0.001581;DP=12018;DP4=8559,3430,15,9;SB=4;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G147|419|N|protein_coding|CODING|GU280_gp10|1|T) NC_045512.2 28801 . C A 85.0 min_af_0.050000 AF=0.001339;DP=11202;DP4=8430,2743,10,10;SB=18;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agC/agA|S176R|419|N|protein_coding|CODING|GU280_gp10|1|A) NC_045512.2 28876 . C T 84.0 min_af_0.050000 AF=0.002074;DP=5303;DP4=2390,2902,5,6;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S201|419|N|protein_coding|CODING|GU280_gp10|1|T) NC_045512.2 28987 . CCAA C 414.0 min_af_0.050000 AF=0.002606;DP=11513;DP4=2411,9107,7,23;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 29027 . G T 203.0 min_af_0.050000 AF=0.001223;DP=29446;DP4=18810,10572,30,14;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A252S|419|N|protein_coding|CODING|GU280_gp10|1|T) NC_045512.2 29029 . T C 1891.0 min_af_0.050000 AF=0.005500;DP=29452;DP4=18773,10482,91,92;SB=41;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A252|419|N|protein_coding|CODING|GU280_gp10|1|C) NC_045512.2 29039 . A T 6489.0 min_af_0.050000 AF=0.014020;DP=29815;DP4=18712,10662,202,224;SB=108;EFF=STOP_GAINED(HIGH|NONSENSE|Aag/Tag|K256*|419|N|protein_coding|CODING|GU280_gp10|1|T) NC_045512.2 29049 . G A 590.0 min_af_0.050000 AF=0.003061;DP=23194;DP4=18861,4251,67,9;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R259Q|419|N|protein_coding|CODING|GU280_gp10|1|A) NC_045512.2 29067 . CTAAAGCATACAATG C 141.0 min_af_0.050000 AF=0.000696;DP=22988;DP4=18360,4666,14,2;HRUN=1;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||aaagcatacaatgtaaca/|KAYNVT266|419|N|protein_coding|CODING|GU280_gp10|1|C|INFO_REALIGN_3_PRIME);LOF=(N|GU280_gp10|1|1.00) NC_045512.2 29095 . C T 83.0 min_af_0.050000 AF=0.000864;DP=23152;DP4=18350,4772,17,5;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F274|419|N|protein_coding|CODING|GU280_gp10|1|T) NC_045512.2 29110 . A G 84.0 min_af_0.050000 AF=0.000869;DP=23018;DP4=18316,4667,14,8;SB=9;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P279|419|N|protein_coding|CODING|GU280_gp10|1|G) NC_045512.2 29114 . C T 94.0 min_af_0.050000 AF=0.000914;DP=22969;DP4=18282,4644,17,7;SB=5;EFF=STOP_GAINED(HIGH|NONSENSE|Caa/Taa|Q281*|419|N|protein_coding|CODING|GU280_gp10|1|T) NC_045512.2 29187 . C T 173.0 min_af_0.050000 AF=0.002658;DP=8276;DP4=4583,3668,9,13;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A305V|419|N|protein_coding|CODING|GU280_gp10|1|T) NC_045512.2 29188 . A G 140.0 min_af_0.050000 AF=0.002202;DP=8175;DP4=4555,3592,7,14;SB=13;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A305|419|N|protein_coding|CODING|GU280_gp10|1|G) NC_045512.2 29195 . GC G 376.0 min_af_0.050000 AF=0.003461;DP=8089;DP4=4612,3478,15,13;HRUN=5;SB=1;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 29227 . G T 10969.0 min_af_0.050000 AF=0.028346;DP=22155;DP4=4416,17071,181,465;SB=50;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcG/tcT|S318|419|N|protein_coding|CODING|GU280_gp10|1|T) NC_045512.2 29229 . G A 85.0 min_af_0.050000 AF=0.000857;DP=23341;DP4=4584,18726,4,21;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R319H|419|N|protein_coding|CODING|GU280_gp10|1|A) NC_045512.2 29247 . C T 127.0 min_af_0.050000 AF=0.001148;DP=23526;DP4=4650,18843,5,23;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T325I|419|N|protein_coding|CODING|GU280_gp10|1|T) NC_045512.2 29254 . G A 281.0 min_af_0.050000 AF=0.001700;DP=23530;DP4=4654,18818,10,39;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S327|419|N|protein_coding|CODING|GU280_gp10|1|A) NC_045512.2 29259 . C T 85.0 min_af_0.050000 AF=0.000897;DP=23401;DP4=4563,18811,7,16;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T329M|419|N|protein_coding|CODING|GU280_gp10|1|T) NC_045512.2 29279 . G A 136.0 min_af_0.050000 AF=0.001077;DP=23215;DP4=4317,18858,4,26;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A336T|419|N|protein_coding|CODING|GU280_gp10|1|A) NC_045512.2 29280 . C T 85.0 min_af_0.050000 AF=0.000821;DP=23150;DP4=4303,18812,2,21;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A336V|419|N|protein_coding|CODING|GU280_gp10|1|T) NC_045512.2 29287 . A T 94.0 min_af_0.050000 AF=0.000906;DP=23185;DP4=4260,18897,3,19;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaA/aaT|K338N|419|N|protein_coding|CODING|GU280_gp10|1|T) NC_045512.2 29348 . G A 93.0 min_af_0.050000 AF=0.000890;DP=22464;DP4=3870,18549,4,17;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A359T|419|N|protein_coding|CODING|GU280_gp10|1|A) NC_045512.2 29377 . TA T 111.0 min_af_0.050000 AF=0.003745;DP=2136;DP4=1755,642,5,3;HRUN=5;SB=3;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)