Mercurial > repos > iuc > snpfreqplot
view test-data/1085445.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/012/246/12246263/tmp/lofreq2_call_parallel9r7g_vq5/0.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_64,Description="Minimum Indel Quality (Phred) 64"> ##FILTER=<ID=min_snvqual_81,Description="Minimum SNV Quality (Phred) 81"> ##FILTER=<ID=min_indelqual_67,Description="Minimum Indel Quality (Phred) 67"> ##FILTER=<ID=min_af_0.050000,Description="Minimum allele frequency 0.050000"> ##FILTER=<ID=min_dp_5,Description="Minimum Coverage 5"> ##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000"> ##SnpEffVersion="4.5covid19 (build 2020-04-15 22:26), by Pablo Cingolani" ##SnpEffCmd="SnpEff -i vcf -o vcf -formatEff -classic -no-downstream -no-intergenic -no-upstream -stats /data/dnb03/galaxy_db/job_working_directory/012/246/12246330/outputs/galaxy_dataset_12727ea3-b173-47f2-a640-8b761bc6dbc9.dat NC_045512.2 /data/dnb03/galaxy_db/files/6/d/3/dataset_6d370681-43dc-4f44-ad01-c8a251815384.dat " ##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_Change| Amino_Acid_length | Gene_Name | Transcript_BioType | Gene_Coding | Transcript_ID | Exon_Rank | Genotype [ | ERRORS | WARNINGS ] )' "> ##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'"> ##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'"> #CHROM POS ID REF ALT QUAL FILTER INFO NC_045512.2 241 . C T 49314.0 PASS AF=0.991443;DP=8180;DP4=12,7,3967,4190;SB=5 NC_045512.2 361 . A G 108.0 min_af_0.050000 AF=0.000916;DP=24022;DP4=10476,13511,11,15;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G32|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G32|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G32|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G32|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G) NC_045512.2 385 . A G 83.0 min_af_0.050000 AF=0.000852;DP=23474;DP4=10007,13442,12,11;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S40|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S40|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON),SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S40|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON),SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S40|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G) NC_045512.2 443 . GT G 392.0 min_af_0.050000 AF=0.002591;DP=11579;DP4=8340,3245,18,12;HRUN=4;SB=8;INDEL;EFF=FRAME_SHIFT(HIGH||ttg/|L61|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L61|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L61|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L61|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07) NC_045512.2 507 . ATGGTCATGTTATGGT A 231.0 min_af_0.050000 AF=0.002668;DP=5998;DP4=3100,2886,12,4;HRUN=1;SB=10;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggtcatgttatggttgag/gag|GHVMVE82E|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggtcatgttatggttgag/gag|GHVMVE82E|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggtcatgttatggttgag/gag|GHVMVE82E|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggtcatgttatggttgag/gag|GHVMVE82E|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A|INFO_REALIGN_3_PRIME) NC_045512.2 509 . GGTCATGTTATGGTT G 80.0 min_af_0.050000 AF=0.001176;DP=5951;DP4=3124,2862,7,0;HRUN=2;SB=17;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_045512.2 509 . GGTCATGTT G 95.0 min_af_0.050000 AF=0.001344;DP=5951;DP4=3124,2862,3,5;HRUN=2;SB=3;INDEL;EFF=FRAME_SHIFT(HIGH||ggtcatgtt/|GHV82|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),FRAME_SHIFT(HIGH||ggtcatgtt/|GHV82|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON),FRAME_SHIFT(HIGH||ggtcatgtt/|GHV82|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON),FRAME_SHIFT(HIGH||ggtcatgtt/|GHV82|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G);LOF=(ORF1ab|GU280_gp01|28|0.07) NC_045512.2 514 . TGTTATG T 95.0 min_af_0.050000 AF=0.001356;DP=5899;DP4=3143,2829,3,5;HRUN=1;SB=3;INDEL;EFF=CODON_DELETION(MODERATE||atggtt/|MV85|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),CODON_DELETION(MODERATE||atggtt/|MV85|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),CODON_DELETION(MODERATE||atggtt/|MV85|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),CODON_DELETION(MODERATE||atggtt/|MV85|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME) NC_045512.2 518 . ATGGTT A 79.0 min_af_0.050000 AF=0.001180;DP=5933;DP4=3134,2801,3,4;HRUN=1;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||atggtt/|MV85|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),FRAME_SHIFT(HIGH||atggtt/|MV85|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON),FRAME_SHIFT(HIGH||atggtt/|MV85|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON),FRAME_SHIFT(HIGH||atggtt/|MV85|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A);LOF=(ORF1ab|GU280_gp01|28|0.07) NC_045512.2 558 . G T 263.0 min_af_0.050000 AF=0.004646;DP=5596;DP4=3200,2366,18,9;SB=3;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_045512.2 601 . C T 114.0 min_af_0.050000 AF=0.001426;DP=12622;DP4=3414,9185,8,11;SB=7;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G112|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G112|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON),SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G112|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON),SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G112|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T) NC_045512.2 683 . CTA C 109.0 min_af_0.050000 AF=0.000870;DP=12642;DP4=3760,8924,6,5;HRUN=1;SB=10;INDEL;EFF=FRAME_SHIFT(HIGH||cta/|L140|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),FRAME_SHIFT(HIGH||cta/|L140|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|C|WARNING_TRANSCRIPT_NO_STOP_CODON),FRAME_SHIFT(HIGH||cta/|L140|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|C|WARNING_TRANSCRIPT_NO_STOP_CODON),FRAME_SHIFT(HIGH||cta/|L140|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C);LOF=(ORF1ab|GU280_gp01|28|0.07) NC_045512.2 685 . AAAGTCATTT A 721.0 min_af_0.050000 AF=0.003737;DP=12578;DP4=3649,8908,17,30;HRUN=3;SB=4;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_045512.2 891 . G A 82.0 min_af_0.050000 AF=0.003096;DP=2584;DP4=700,1876,4,4;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G209D|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G209D|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G29D|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G29D|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 1001 . GA G 70.0 min_af_0.050000 AF=0.000521;DP=19212;DP4=14170,5050,7,3;HRUN=4;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||aag/|K247|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aag/|K247|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aag/|K67|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aag/|K67|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.11) NC_045512.2 1011 . ATG A 158.0 min_af_0.050000 AF=0.000902;DP=17731;DP4=14217,3504,14,2;HRUN=1;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||tatgaa/|YE249|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),FRAME_SHIFT(HIGH||tatgaa/|YE249|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),FRAME_SHIFT(HIGH||tatgaa/|YE69|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),FRAME_SHIFT(HIGH||tatgaa/|YE69|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.11) NC_045512.2 1018 . G A 194.0 min_af_0.050000 AF=0.001555;DP=18008;DP4=14268,3704,24,6;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttG/ttA|L251|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),SYNONYMOUS_CODING(LOW|SILENT|ttG/ttA|L251|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),SYNONYMOUS_CODING(LOW|SILENT|ttG/ttA|L71|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ttG/ttA|L71|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 1019 . C T 96.0 min_af_0.050000 AF=0.000990;DP=18175;DP4=14292,3861,14,5;SB=2;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 1059 . C T 49314.0 PASS AF=0.914482;DP=18230;DP4=1138,343,12822,3919;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T265I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T265I|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T85I|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T85I|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 1115 . A T 112.0 min_af_0.050000 AF=0.002090;DP=6697;DP4=2661,4022,1,13;SB=19;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 1140 . A G 82.0 min_af_0.050000 AF=0.001915;DP=6788;DP4=2923,3852,5,8;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K292R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K292R|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K112R|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K112R|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 1288 . C T 96.0 min_af_0.050000 AF=0.001212;DP=15681;DP4=3701,11913,4,57;SB=31;EFF=SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C341|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C341|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C161|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C161|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 1644 . A C 204.0 min_af_0.050000 AF=0.001874;DP=14945;DP4=11652,3256,18,14;SB=22;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 204.0 min_af_0.050000 AF=0.001794;DP=15048;DP4=11650,3368,14,14;SB=26;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 169.0 min_af_0.050000 AF=0.001647;DP=15179;DP4=11625,3520,18,12;SB=13;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 171.0 min_af_0.050000 AF=0.001899;DP=15272;DP4=11693,3542,22,12;SB=9;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 1698 . C T 85.0 min_af_0.050000 AF=0.001095;DP=15526;DP4=11739,3762,12,7;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A478V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A478V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A298V|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A298V|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 1701 . CT C 201.0 min_af_0.050000 AF=0.001361;DP=15428;DP4=11734,3700,17,4;HRUN=5;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||tct/|S481|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tct/|S481|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tct/|S301|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tct/|S301|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) NC_045512.2 1702 . T C 336.0 min_af_0.050000 AF=0.002654;DP=15449;DP4=11702,3680,34,10;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 131.0 min_af_0.050000 AF=0.001431;DP=15372;DP4=11672,3674,11,12;SB=23;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 1733 . A G 97.0 min_af_0.050000 AF=0.001812;DP=7174;DP4=3582,3573,16,1;SB=35;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T490A|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T490A|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T310A|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T310A|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 1914 . G A 164.0 min_af_0.050000 AF=0.001604;DP=14959;DP4=3270,11663,2,22;SB=8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R550H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R550H|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R370H|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R370H|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 1928 . G A 122.0 min_af_0.050000 AF=0.001310;DP=14507;DP4=2942,11544,2,17;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A555T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A555T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A375T|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A375T|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 2240 . A T 102.0 min_af_0.050000 AF=0.005411;DP=1848;DP4=440,1398,1,9;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Ttt|I659F|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Ttt|I659F|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Ttt|I479F|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Ttt|I479F|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 2371 . C A 84.0 min_af_0.050000 AF=0.033898;DP=118;DP4=57,56,3,2;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcA|A702|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcA|A702|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcA|A522|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcA|A522|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 3037 . C T 49314.0 PASS AF=0.989605;DP=1924;DP4=1,3,905,1013;SB=2;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 3178 . T C 85.0 min_af_0.050000 AF=0.001409;DP=9934;DP4=6039,3875,10,7;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P971|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P971|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P153|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P153|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 3290 . C G 201.0 min_af_0.050000 AF=0.002822;DP=7796;DP4=6032,1737,15,7;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q1009E|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q1009E|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q191E|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q191E|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 3373 . C A 4347.0 PASS AF=0.062157;DP=3282;DP4=1695,1380,116,90;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaC/gaA|D1036E|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaC/gaA|D1036E|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaC/gaA|D218E|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaC/gaA|D218E|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 3412 . TA T 167.0 min_af_0.050000 AF=0.001903;DP=7881;DP4=1821,6068,4,11;HRUN=5;SB=1;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 3832 . CT C 207.0 min_af_0.050000 AF=0.003618;DP=4146;DP4=3478,655,12,3;HRUN=5;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||ttg/|L1191|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L1191|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L373|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L373|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 4142 . G A 162.0 min_af_0.050000 AF=0.001370;DP=21166;DP4=14320,6812,14,19;SB=23;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E1293K|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E1293K|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E475K|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E475K|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 4179 . A G 90.0 min_af_0.050000 AF=0.001176;DP=19554;DP4=14327,5191,20,8;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K1305R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K1305R|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K487R|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K487R|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 4289 . G A 89.0 min_af_0.050000 AF=0.001013;DP=19750;DP4=5529,14191,8,13;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A1342T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A1342T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A524T|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A524T|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 4308 . A G 267.0 min_af_0.050000 AF=0.001968;DP=20834;DP4=5011,15773,12,32;SB=2;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 5291 . CT C 168.0 min_af_0.050000 AF=0.001809;DP=7188;DP4=5641,1540,12,1;HRUN=2;SB=4;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 5387 . G A 82.0 min_af_0.050000 AF=0.001671;DP=6582;DP4=4204,2365,8,3;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A1708T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A1708T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A890T|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A890T|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 5400 . C T 116.0 min_af_0.050000 AF=0.002168;DP=6458;DP4=4180,2261,9,6;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A1712V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A1712V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A894V|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A894V|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 5743 . G C 265.0 min_af_0.050000 AF=0.005125;DP=4683;DP4=2467,2189,5,19;SB=27;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 406.0 min_af_0.050000 AF=0.007072;DP=4666;DP4=2466,2162,10,26;SB=26;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y1827H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y1827H|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y1009H|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y1009H|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 5765 . G A 192.0 min_af_0.050000 AF=0.004055;DP=4686;DP4=2625,2040,4,16;SB=29;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G1834S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G1834S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G1016S|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G1016S|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 5766 . G C 133.0 min_af_0.050000 AF=0.003178;DP=4720;DP4=2667,2035,3,12;SB=21;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gCt|G1834A|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gCt|G1834A|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gCt|G1016A|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gCt|G1016A|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 6181 . TA T 74.0 min_af_0.050000 AF=0.000612;DP=14709;DP4=2144,12612,0,9;HRUN=3;SB=4;INDEL;EFF=FRAME_SHIFT(HIGH||aaa/|K1973|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K1973|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K1155|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K1155|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 6242 . C T 165.0 min_af_0.050000 AF=0.000825;DP=46066;DP4=29941,16067,31,16;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H1993Y|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H1993Y|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H1175Y|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H1175Y|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 6254 . G A 105.0 min_af_0.050000 AF=0.000684;DP=39491;DP4=30022,9423,21,10;SB=5;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 6271 . G A 379.0 min_af_0.050000 AF=0.001604;DP=39896;DP4=29246,10561,43,29;SB=19;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 6364 . G A 108.0 min_af_0.050000 AF=0.001237;DP=16980;DP4=8010,8945,14,9;SB=6;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A2033|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A2033|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A1215|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A1215|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 6396 . TA T 87.0 min_af_0.050000 AF=0.000649;DP=18497;DP4=8545,10129,7,5;HRUN=4;SB=3;INDEL;EFF=FRAME_SHIFT(HIGH||aaa/|K2045|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K2045|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K1227|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K1227|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) NC_045512.2 6402 . C T 109.0 min_af_0.050000 AF=0.000771;DP=36334;DP4=8494,27803,7,23;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCa/cTa|P2046L|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCa/cTa|P2046L|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCa/cTa|P1228L|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCa/cTa|P1228L|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 6409 . T C 104.0 min_af_0.050000 AF=0.000721;DP=36080;DP4=8420,27622,5,22;SB=1;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 7431 . CATTTT C 70.0 min_af_0.050000 AF=0.004202;DP=952;DP4=599,351,2,2;HRUN=1;SB=2;INDEL;EFF=FRAME_SHIFT(HIGH||ttttattat/|FYY2390|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttttattat/|FYY2390|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttttattat/|FYY1572|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttttattat/|FYY1572|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 7736 . G A 87.0 min_af_0.050000 AF=0.001450;DP=9654;DP4=7167,2470,12,4;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V2491I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V2491I|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V1673I|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V1673I|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 7738 . T C 96.0 min_af_0.050000 AF=0.001449;DP=9661;DP4=7170,2476,11,4;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtT/gtC|V2491|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|gtT/gtC|V2491|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|gtT/gtC|V1673|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|gtT/gtC|V1673|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 7771 . T G 119.0 min_af_0.050000 AF=0.001861;DP=9671;DP4=7169,2479,8,10;SB=19;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caT/caG|H2502Q|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caT/caG|H2502Q|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caT/caG|H1684Q|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caT/caG|H1684Q|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 7889 . GT G 495.0 min_af_0.050000 AF=0.003791;DP=9496;DP4=2286,7193,8,28;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 8927 . GT G 77.0 min_af_0.050000 AF=0.001225;DP=6529;DP4=5082,1441,6,2;HRUN=5;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/|F2889|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F2889|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F126|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F126|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) NC_045512.2 9014 . G A 94.0 min_af_0.050000 AF=0.001833;DP=7092;DP4=5255,1822,9,4;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A2917T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A2917T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A154T|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A154T|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 9479 . G T 578.0 min_af_0.050000 AF=0.027073;DP=1182;DP4=216,934,17,15;SB=47;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Tgt|G3072C|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Tgt|G3072C|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Tgt|G309C|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Tgt|G309C|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 9656 . A G 85.0 min_af_0.050000 AF=0.002371;DP=4218;DP4=1823,2383,10,0;SB=36;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 9737 . A AG 93.0 min_af_0.050000 AF=0.000941;DP=9561;DP4=2070,7513,4,5;HRUN=1;SB=9;INDEL;EFF=FRAME_SHIFT(HIGH||agt/agGt|S3158R?|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|AG|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||agt/agGt|S3158R?|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|AG|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||agt/agGt|S395R?|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|AG|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||agt/agGt|S395R?|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|AG|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) NC_045512.2 9919 . T C 86.0 min_af_0.050000 AF=0.008837;DP=679;DP4=478,194,3,3;SB=4;EFF=SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S3218|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S3218|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S455|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S455|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 10615 . C T 116.0 min_af_0.050000 AF=0.002812;DP=4623;DP4=1510,3095,5,9;SB=1;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 10635 . C T 136.0 min_af_0.050000 AF=0.002999;DP=4668;DP4=1550,3104,5,9;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A3457V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A3457V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A194V|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A194V|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 10874 . A T 122.0 min_af_0.050000 AF=0.007206;DP=1249;DP4=654,586,4,5;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Tat|N3537Y|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Tat|N3537Y|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Tat|N274Y|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Tat|N274Y|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 11082 . TG T 110.0 min_af_0.050000 AF=0.000734;DP=16355;DP4=12351,4023,10,2;HRUN=1;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||ttg/|L3606|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),FRAME_SHIFT(HIGH||ttg/|L3606|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),FRAME_SHIFT(HIGH||ttg/|L37|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),FRAME_SHIFT(HIGH||ttg/|L37|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.14) NC_045512.2 11083 . G T 328.0 min_af_0.050000 AF=0.003159;DP=16459;DP4=12330,4055,43,15;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 11250 . G A 84.0 min_af_0.050000 AF=0.000966;DP=17602;DP4=4658,12920,6,11;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R3662H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R3662H|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R93H|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R93H|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 11292 . GT G 105.0 min_af_0.050000 AF=0.000711;DP=18275;DP4=5121,13165,5,8;HRUN=4;SB=4;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/|F3677|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F3677|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F108|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F108|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 101.0 min_af_0.050000 AF=0.001376;DP=12355;DP4=6380,5954,10,7;SB=1;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 11895 . A G 117.0 min_af_0.050000 AF=0.001058;DP=21736;DP4=13835,7875,13,11;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q3877R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q3877R|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q18R|82|ORF1ab|protein_coding|CODING|YP_009725303.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q18R|82|ORF1ab|protein_coding|CODING|YP_009742614.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 11952 . A T 108.0 min_af_0.050000 AF=0.001249;DP=17618;DP4=13412,4175,18,4;SB=0;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 12031 . G A 88.0 min_af_0.050000 AF=0.001927;DP=8304;DP4=4111,4170,10,7;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q3922|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q3922|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q63|82|ORF1ab|protein_coding|CODING|YP_009725303.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q63|82|ORF1ab|protein_coding|CODING|YP_009742614.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 12035 . G A 91.0 min_af_0.050000 AF=0.001697;DP=8249;DP4=4097,4133,7,9;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A3924T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A3924T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A65T|82|ORF1ab|protein_coding|CODING|YP_009725303.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A65T|82|ORF1ab|protein_coding|CODING|YP_009742614.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 12128 . G A 124.0 min_af_0.050000 AF=0.001125;DP=20441;DP4=4710,15706,10,14;SB=13;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 12143 . G A 171.0 min_af_0.050000 AF=0.001269;DP=22057;DP4=6298,15713,9,20;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A3960T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A3960T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A18T|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A18T|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 12164 . G T 158.0 min_af_0.050000 AF=0.001229;DP=21965;DP4=6177,15735,10,23;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A3967S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A3967S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A25S|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A25S|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 12201 . A G 203.0 min_af_0.050000 AF=0.001756;DP=20503;DP4=5036,15425,12,27;SB=4;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 12458 . A G 2325.0 min_af_0.050000 AF=0.010507;DP=15038;DP4=11454,3422,135,23;SB=19;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 12673 . T C 83.0 min_af_0.050000 AF=0.001026;DP=14614;DP4=3924,10673,5,11;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A4136|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A4136|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A194|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A194|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 12684 . A G 90.0 min_af_0.050000 AF=0.001091;DP=14670;DP4=3905,10744,3,13;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q4140R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q4140R|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|cAg/cGg|Q198R|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|cAg/cGg|Q198R|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 12703 . T C 99.0 min_af_0.050000 AF=0.001164;DP=14610;DP4=3877,10708,6,16;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P4146|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P4146|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P6|112|ORF1ab|protein_coding|CODING|YP_009725305.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P6|112|ORF1ab|protein_coding|CODING|YP_009742616.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 13006 . T C 100.0 min_af_0.050000 AF=0.001091;DP=18324;DP4=4970,13320,5,18;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A4247|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A4247|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A107|112|ORF1ab|protein_coding|CODING|YP_009725305.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A107|112|ORF1ab|protein_coding|CODING|YP_009742616.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 13034 . G A 287.0 min_af_0.050000 AF=0.001172;DP=43512;DP4=25678,17773,36,17;SB=6;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 13039 . A G 153.0 min_af_0.050000 AF=0.000801;DP=43670;DP4=25606,18020,23,15;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T4258|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T4258|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T5|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T5|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 13049 . G A 126.0 min_af_0.050000 AF=0.000745;DP=44275;DP4=25781,18447,22,16;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A4262T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A4262T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A9T|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A9T|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 13050 . C T 160.0 min_af_0.050000 AF=0.000857;DP=44323;DP4=25765,18501,28,14;SB=5;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 13123 . TG T 90.0 min_af_0.050000 AF=0.000496;DP=32271;DP4=23537,8806,12,4;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 13126 . G T 894.0 min_af_0.050000 AF=0.003763;DP=32684;DP4=23617,8932,96,30;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggG/ggT|G4287|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|ggG/ggT|G4287|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|ggG/ggT|G34|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ggG/ggT|G34|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 13129 . A G 415.0 min_af_0.050000 AF=0.002114;DP=32636;DP4=23626,8909,60,24;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 13142 . AATT A 68.0 min_af_0.050000 AF=0.000345;DP=31908;DP4=23436,8544,7,4;HRUN=2;SB=3;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aattgt/agt|NC4293S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aattgt/agt|NC4293S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aattgt/agt|NC40S|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aattgt/agt|NC40S|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 13178 . G A 92.0 min_af_0.050000 AF=0.001099;DP=15464;DP4=7168,8274,7,12;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G4305S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G4305S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G52S|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G52S|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 13184 . G A 88.0 min_af_0.050000 AF=0.001085;DP=15669;DP4=7536,8107,10,8;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4307T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4307T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A54T|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A54T|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 13235 . G A 184.0 min_af_0.050000 AF=0.001314;DP=30447;DP4=8620,21776,11,31;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 13240 . G A 120.0 min_af_0.050000 AF=0.001047;DP=30554;DP4=8647,21862,13,25;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S4325|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S4325|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S72|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S72|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 13255 . C T 121.0 min_af_0.050000 AF=0.000922;DP=32523;DP4=8871,23617,11,19;SB=5;EFF=SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C4330|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C4330|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C77|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C77|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 13257 . G A 103.0 min_af_0.050000 AF=0.000795;DP=32720;DP4=8969,23719,5,23;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R4331H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R4331H|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R78H|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R78H|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 13299 . TA T 67.0 min_af_0.050000 AF=0.000373;DP=32129;DP4=8835,23401,3,9;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 13345 . T C 114.0 min_af_0.050000 AF=0.000845;DP=34302;DP4=11365,22885,12,23;SB=0;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 13385 . G A 203.0 min_af_0.050000 AF=0.003101;DP=9673;DP4=7564,2070,23,10;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G4374S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G4374S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G121S|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G121S|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 13482 . A G 84.0 min_af_0.050000 AF=0.002138;DP=5145;DP4=2849,2284,8,3;SB=4;EFF=SPLICE_SITE_REGION+SYNONYMOUS_STOP(LOW|SILENT|tAa/tGa|*4406|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V4406|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V14|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|G|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 13541 . CT C 128.0 min_af_0.050000 AF=0.001323;DP=9073;DP4=2350,6760,4,8;HRUN=4;SB=2;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/|F4427|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F35|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.04) NC_045512.2 13565 . T G 710.0 min_af_0.050000 AF=0.006207;DP=9345;DP4=2347,6927,31,27;SB=52;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 498.0 min_af_0.050000 AF=0.004930;DP=9533;DP4=2456,7025,10,39;SB=2;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 13586 . TA T 114.0 min_af_0.050000 AF=0.001250;DP=9600;DP4=2526,7104,3,9;HRUN=5;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||act/|T4443|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||act/|T51|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07) NC_045512.2 13729 . G A 97.0 min_af_0.050000 AF=0.000758;DP=31659;DP4=23911,7707,19,7;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A4489T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A97T|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 13982 . G A 334.0 min_af_0.050000 AF=0.003336;DP=13191;DP4=10186,2952,21,25;SB=55;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 14197 . G A 131.0 min_af_0.050000 AF=0.001509;DP=12592;DP4=2965,9602,4,17;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4645T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A253T|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 14408 . C T 49314.0 PASS AF=0.993579;DP=1869;DP4=2,1,961,905;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P4715L|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P323L|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 14625 . CT C 95.0 min_af_0.050000 AF=0.000978;DP=10228;DP4=7598,2681,7,3;HRUN=4;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||tca/|S4789|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tca/|S397|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 14638 . G A 81.0 min_af_0.050000 AF=0.001254;DP=10364;DP4=7602,2745,9,5;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4792T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A400T|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 15380 . G T 19339.0 PASS AF=0.137502;DP=5629;DP4=2428,2416,397,383;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aTc|S5039I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aTc|S647I|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 15481 . T C 525.0 min_af_0.050000 AF=0.004225;DP=12307;DP4=3137,9071,51,40;SB=87;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Cca|S5073P|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Cca|S681P|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|C|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 15537 . T C 82.0 min_af_0.050000 AF=0.000714;DP=32206;DP4=19463,12697,24,11;SB=4;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A5091|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A699|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|C|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 15602 . G A 81.0 min_af_0.050000 AF=0.000869;DP=25304;DP4=18787,6490,16,6;SB=0;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 15673 . T G 170.0 min_af_0.050000;sb_fdr AF=0.002959;DP=11154;DP4=5550,5555,29,5;SB=44;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 3591.0 min_af_0.050000 AF=0.019897;DP=11057;DP4=5644,5185,123,101;SB=3;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 3576.0 min_af_0.050000 AF=0.019571;DP=11088;DP4=5677,5189,119,98;SB=3;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 15784 . T TGAC 112.0 min_af_0.050000 AF=0.000564;DP=24832;DP4=6387,18537,7,7;HRUN=3;SB=12;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 113.0 min_af_0.050000 AF=0.000570;DP=24581;DP4=6120,18483,7,7;HRUN=1;SB=12;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 16946 . C T 81.0 min_af_0.050000 AF=0.002242;DP=4461;DP4=1946,2504,5,6;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A5561V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A237V|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 17035 . G A 130.0 min_af_0.050000 AF=0.002105;DP=8076;DP4=2373,5684,6,12;SB=0;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 17146 . A G 124.0 min_af_0.050000 AF=0.001762;DP=11915;DP4=8858,3024,17,7;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I5628V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I304V|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 17200 . TTAAAA T 215.0 min_af_0.050000 AF=0.001499;DP=12007;DP4=8894,3153,15,3;HRUN=2;SB=3;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 17410 . C T 89.0 min_af_0.050000 AF=0.001226;DP=13051;DP4=3103,9927,5,12;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R5716C|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R392C|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 18687 . CT C 125.0 min_af_0.050000 AF=0.001021;DP=13716;DP4=10356,3385,9,5;HRUN=4;SB=4;INDEL;EFF=FRAME_SHIFT(HIGH||tcc/|S6143|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tcc/|S218|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07) NC_045512.2 18839 . C T 87.0 min_af_0.050000 AF=0.001144;DP=13109;DP4=3502,9590,6,9;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A6192V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A267V|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 19029 . C T 142.0 min_af_0.050000 AF=0.001333;DP=18002;DP4=13296,4678,17,7;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H6255|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H330|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 19132 . G T 183.0 min_af_0.050000 AF=0.002631;DP=7981;DP4=4498,3460,10,12;SB=4;EFF=STOP_GAINED(HIGH|NONSENSE|Gaa/Taa|E6290*|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),STOP_GAINED(HIGH|NONSENSE|Gaa/Taa|E365*|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 19137 . A C 139.0 min_af_0.050000 AF=0.002242;DP=8029;DP4=4529,3481,8,10;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttA/ttC|L6291F|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttA/ttC|L366F|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 19173 . A G 184.0 min_af_0.050000 AF=0.001475;DP=18300;DP4=4405,13862,8,20;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T6303|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T378|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 19199 . G A 95.0 min_af_0.050000 AF=0.000992;DP=18154;DP4=4265,13867,5,14;SB=1;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 19554 . CT C 88.0 min_af_0.050000 AF=0.002555;DP=2348;DP4=169,2178,0,6;HRUN=3;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/|F6431|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F506|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.04) NC_045512.2 19804 . A G 95.0 min_af_0.050000 AF=0.001057;DP=17023;DP4=4133,12868,6,14;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aac/Gac|N6514D|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aac/Gac|N62D|345|ORF1ab|protein_coding|CODING|YP_009725310.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 20555 . C T 1517.0 min_af_0.050000 AF=0.008538;DP=12766;DP4=9871,2780,90,22;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tTt|S6764F|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tTt|S312F|345|ORF1ab|protein_coding|CODING|YP_009725310.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 20769 . TA T 71.0 min_af_0.050000 AF=0.000640;DP=12508;DP4=3063,9486,3,5;HRUN=3;SB=3;INDEL;EFF=FRAME_SHIFT(HIGH||aaa/|K6836|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K38|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 20791 . G A 100.0 min_af_0.050000 AF=0.001350;DP=14075;DP4=2871,11181,6,16;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A6843T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A45T|297|ORF1ab|protein_coding|CODING|YP_009725311.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 21066 . TA T 267.0 min_af_0.050000 AF=0.001799;DP=13898;DP4=3162,10753,8,17;HRUN=5;SB=4;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 21093 . TA T 69.0 min_af_0.050000 AF=0.000600;DP=13336;DP4=2749,10687,2,6;HRUN=3;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||aaa/|K6944|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K146|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 21123 . G T 2708.0 min_af_0.050000 AF=0.013197;DP=13412;DP4=3026,10193,36,152;SB=5;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggG/ggT|G6953|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),SYNONYMOUS_CODING(LOW|SILENT|ggG/ggT|G155|297|ORF1ab|protein_coding|CODING|YP_009725311.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 21204 . G T 1022.0 min_af_0.050000 AF=0.041982;DP=1191;DP4=795,343,25,27;SB=27;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaG/aaT|K6980N|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaG/aaT|K182N|297|ORF1ab|protein_coding|CODING|YP_009725311.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) NC_045512.2 21650 . A C 117.0 min_af_0.050000 AF=0.004405;DP=2270;DP4=628,1631,2,8;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Cat|N30H|1273|S|protein_coding|CODING|GU280_gp02|1|C) NC_045512.2 21656 . TTCAC T 72.0 min_af_0.050000 AF=0.002225;DP=2247;DP4=622,1639,2,3;HRUN=3;SB=2;INDEL;EFF=FRAME_SHIFT(HIGH||ttcaca/|FT32|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512.2 21736 . CT C 78.0 min_af_0.050000 AF=0.000985;DP=8122;DP4=6241,1886,6,2;HRUN=4;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||tcc/|S60|1273|S|protein_coding|CODING|GU280_gp02|1|C|INFO_REALIGN_3_PRIME) NC_045512.2 21954 . G A 81.0 min_af_0.050000 AF=0.001578;DP=6970;DP4=1556,5401,2,9;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C131Y|1273|S|protein_coding|CODING|GU280_gp02|1|A) NC_045512.2 22000 . CA C 164.0 min_af_0.050000 AF=0.001817;DP=8255;DP4=2894,5378,9,6;HRUN=5;SB=12;INDEL;EFF=FRAME_SHIFT(HIGH||aac/|N148|1273|S|protein_coding|CODING|GU280_gp02|1|C|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00) NC_045512.2 22091 . A G 248.0 min_af_0.050000 AF=0.006641;DP=2861;DP4=2126,714,18,1;SB=12;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M177V|1273|S|protein_coding|CODING|GU280_gp02|1|G) NC_045512.2 22120 . CA C 69.0 min_af_0.050000 AF=0.003159;DP=1583;DP4=970,695,1,4;HRUN=5;SB=7;INDEL;EFF=FRAME_SHIFT(HIGH||aat/|N188|1273|S|protein_coding|CODING|GU280_gp02|1|C|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00) NC_045512.2 22583 . GTTT G 87.0 min_af_0.050000 AF=0.000843;DP=13055;DP4=10169,2877,8,3;HRUN=5;SB=1;INDEL;EFF=CODON_DELETION(MODERATE||ttt/|F342|1273|S|protein_coding|CODING|GU280_gp02|1|G|INFO_REALIGN_3_PRIME) NC_045512.2 22643 . T A 561.0 min_af_0.050000 AF=0.003894;DP=13611;DP4=10284,3268,43,11;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Agt|C361S|1273|S|protein_coding|CODING|GU280_gp02|1|A) NC_045512.2 22644 . G C 533.0 min_af_0.050000 AF=0.003793;DP=13710;DP4=10293,3357,41,11;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tCt|C361S|1273|S|protein_coding|CODING|GU280_gp02|1|C) NC_045512.2 22645 . T A 522.0 min_af_0.050000 AF=0.003723;DP=13699;DP4=10277,3356,44,11;SB=2;EFF=STOP_GAINED(HIGH|NONSENSE|tgT/tgA|C361*|1273|S|protein_coding|CODING|GU280_gp02|1|A) NC_045512.2 22851 . C T 115.0 min_af_0.050000 AF=0.001412;DP=12041;DP4=3221,8772,5,33;SB=11;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T430I|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512.2 22858 . C T 81.0 min_af_0.050000 AF=0.001258;DP=11921;DP4=3141,8751,5,11;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C432|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512.2 23131 . TG T 92.0 min_af_0.050000 AF=0.001755;DP=3989;DP4=819,3176,0,7;HRUN=1;SB=4;INDEL;EFF=FRAME_SHIFT(HIGH||gtt/|V524|1273|S|protein_coding|CODING|GU280_gp02|1|T);LOF=(S|GU280_gp02|1|1.00) NC_045512.2 23132 . GT G 125.0 min_af_0.050000 AF=0.002191;DP=4108;DP4=817,3296,0,9;HRUN=3;SB=6;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 23403 . A G 49314.0 PASS AF=0.991574;DP=16497;DP4=5,22,4298,12165;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D614G|1273|S|protein_coding|CODING|GU280_gp02|1|G) NC_045512.2 23417 . G T 370.0 min_af_0.050000 AF=0.002551;DP=16465;DP4=4287,12132,12,30;SB=1;EFF=STOP_GAINED(HIGH|NONSENSE|Gaa/Taa|E619*|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512.2 23554 . ACCCATTGGTGCAGGTATATGCGCTAGTT A 194.0 min_af_0.050000 AF=0.002880;DP=4514;DP4=3258,1249,11,2;HRUN=3;SB=2;INDEL;EFF=FRAME_SHIFT(HIGH||cccattggtgcaggtatatgcgctagttat/|PIGAGICASY665|1273|S|protein_coding|CODING|GU280_gp02|1|A);LOF=(S|GU280_gp02|1|1.00) NC_045512.2 23582 . TATCAGACTCAGACTA T 519.0 min_af_0.050000 AF=0.006436;DP=4506;DP4=3258,1232,14,15;HRUN=1;SB=22;INDEL;EFF=CODON_DELETION(MODERATE||cagactcagactaat/|QTQTN675|1273|S|protein_coding|CODING|GU280_gp02|1|T|INFO_REALIGN_3_PRIME) NC_045512.2 24728 . G A 138.0 min_af_0.050000 AF=0.001075;DP=23260;DP4=18198,5032,20,6;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A1056T|1273|S|protein_coding|CODING|GU280_gp02|1|A) NC_045512.2 24729 . C T 267.0 min_af_0.050000 AF=0.001633;DP=23275;DP4=18189,5042,31,9;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A1056V|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512.2 24770 . G A 85.0 min_af_0.050000 AF=0.000776;DP=24482;DP4=18807,5645,16,4;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A1070T|1273|S|protein_coding|CODING|GU280_gp02|1|A) NC_045512.2 24771 . C T 100.0 min_af_0.050000 AF=0.000857;DP=24506;DP4=18807,5671,17,5;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A1070V|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512.2 24794 . G A 173.0 min_af_0.050000 AF=0.001191;DP=25181;DP4=18729,6412,23,8;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A1078T|1273|S|protein_coding|CODING|GU280_gp02|1|A) NC_045512.2 24910 . TAC T 77.0 min_af_0.050000 AF=0.000771;DP=10375;DP4=5736,4681,6,2;HRUN=1;SB=5;INDEL;EFF=FRAME_SHIFT(HIGH||aca/|T1117|1273|S|protein_coding|CODING|GU280_gp02|1|T|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00) NC_045512.2 24933 . G T 547.0 min_af_0.050000 AF=0.002715;DP=23942;DP4=5894,17971,24,44;SB=13;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G1124V|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512.2 24938 . T C 90.0 min_af_0.050000 AF=0.000836;DP=23912;DP4=5888,17993,5,17;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C1126R|1273|S|protein_coding|CODING|GU280_gp02|1|C) NC_045512.2 24942 . A T 433.0 min_af_0.050000 AF=0.002206;DP=24029;DP4=5968,18000,7,48;SB=13;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gTt|D1127V|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512.2 24986 . C T 213.0 min_af_0.050000 AF=0.001391;DP=23728;DP4=5830,17860,9,24;SB=1;EFF=STOP_GAINED(HIGH|NONSENSE|Caa/Taa|Q1142*|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512.2 25344 . C T 81.0 min_af_0.050000;sb_fdr AF=0.002408;DP=11212;DP4=8717,2463,4,24;SB=118;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tTt|S1261F|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512.2 25563 . G T 49314.0 PASS AF=0.910164;DP=12456;DP4=238,777,2686,8750;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caG/caT|Q57H|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T) NC_045512.2 25567 . G A 86.0 min_af_0.050000 AF=0.001207;DP=12424;DP4=2908,9492,5,12;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A59T|275|ORF3a|protein_coding|CODING|GU280_gp03|1|A) NC_045512.2 25572 . CA C 112.0 min_af_0.050000 AF=0.000961;DP=12491;DP4=2976,9571,1,11;HRUN=4;SB=5;INDEL;EFF=FRAME_SHIFT(HIGH||atc/|I62|275|ORF3a|protein_coding|CODING|GU280_gp03|1|C|INFO_REALIGN_3_PRIME);LOF=(ORF3a|GU280_gp03|1|1.00) NC_045512.2 25635 . C T 95.0 min_af_0.050000 AF=0.001259;DP=11913;DP4=2737,9155,4,11;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C81|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T) NC_045512.2 25646 . T G 88.0 min_af_0.050000;sb_fdr AF=0.001532;DP=11748;DP4=2658,9069,16,2;SB=83;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTg/tGg|L85W|275|ORF3a|protein_coding|CODING|GU280_gp03|1|G) NC_045512.2 25797 . CA C 93.0 min_af_0.050000 AF=0.004626;DP=1297;DP4=521,784,1,5;HRUN=5;SB=3;INDEL;EFF=FRAME_SHIFT(HIGH||aac/|N137|275|ORF3a|protein_coding|CODING|GU280_gp03|1|C|INFO_REALIGN_3_PRIME);LOF=(ORF3a|GU280_gp03|1|1.00) NC_045512.2 26042 . C T 1956.0 min_af_0.050000 AF=0.008189;DP=17706;DP4=12836,4716,99,50;SB=11;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T217I|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T) NC_045512.2 26044 . C G 1842.0 min_af_0.050000 AF=0.007844;DP=17592;DP4=12777,4670,91,48;SB=13;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q218E|275|ORF3a|protein_coding|CODING|GU280_gp03|1|G) NC_045512.2 26046 . A G 1895.0 min_af_0.050000 AF=0.008153;DP=17662;DP4=12782,4734,95,51;SB=14;EFF=SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q218|275|ORF3a|protein_coding|CODING|GU280_gp03|1|G) NC_045512.2 26057 . A C 226.0 min_af_0.050000 AF=0.003504;DP=11131;DP4=6545,4539,21,19;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAc/gCc|D222A|275|ORF3a|protein_coding|CODING|GU280_gp03|1|C) NC_045512.2 26089 . T A 325.0 min_af_0.050000 AF=0.003996;DP=7758;DP4=3605,4118,5,28;SB=35;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Aac|Y233N|275|ORF3a|protein_coding|CODING|GU280_gp03|1|A) NC_045512.2 26103 . T A 508.0 min_af_0.050000 AF=0.005526;DP=7963;DP4=3881,4036,34,10;SB=36;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtT/gtA|V237|275|ORF3a|protein_coding|CODING|GU280_gp03|1|A) NC_045512.2 26157 . TGTTA T 86.0 min_af_0.050000 AF=0.001022;DP=7827;DP4=4500,3335,7,1;HRUN=1;SB=8;INDEL;EFF=FRAME_SHIFT(HIGH||gttaat/|VN256|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T);LOF=(ORF3a|GU280_gp03|1|1.00) NC_045512.2 26189 . A G 161.0 min_af_0.050000 AF=0.001616;DP=17322;DP4=4576,12716,9,21;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gGa|E266G|275|ORF3a|protein_coding|CODING|GU280_gp03|1|G) NC_045512.2 26542 . C A 369.0 min_af_0.050000 AF=0.006926;DP=4043;DP4=233,3778,5,23;SB=16;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aAt|T7N|222|M|protein_coding|CODING|GU280_gp05|1|A) NC_045512.2 26545 . T G 1128.0 min_af_0.050000 AF=0.004540;DP=24230;DP4=20240,3866,88,26;SB=12;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTt/aGt|I8S|222|M|protein_coding|CODING|GU280_gp05|1|G) NC_045512.2 26554 . A G 296.0 min_af_0.050000 AF=0.001728;DP=24881;DP4=20503,4324,36,11;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gGa|E11G|222|M|protein_coding|CODING|GU280_gp05|1|G) NC_045512.2 26566 . A G 125.0 min_af_0.050000 AF=0.001328;DP=25594;DP4=20737,4806,27,9;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K15R|222|M|protein_coding|CODING|GU280_gp05|1|G) NC_045512.2 26573 . TGAACAATGGAACCTAGTAATAGGTTTCCTA T 159.0 min_af_0.050000 AF=0.000710;DP=25348;DP4=20879,4448,14,4;HRUN=1;SB=2;INDEL;EFF=CODON_DELETION(MODERATE||gaacaatggaacctagtaataggtttccta/|EQWNLVIGFL18|222|M|protein_coding|CODING|GU280_gp05|1|T) NC_045512.2 26574 . GAACAATGGAACCTAGTAATAGGTTTCCTA G 99.0 min_af_0.050000 AF=0.000510;DP=25466;DP4=20936,4518,12,1;HRUN=2;SB=3;INDEL;EFF=FRAME_SHIFT(HIGH||gaacaatggaacctagtaataggtttccta/|EQWNLVIGFL18|222|M|protein_coding|CODING|GU280_gp05|1|G);LOF=(M|GU280_gp05|1|1.00) NC_045512.2 26635 . C T 180.0 min_af_0.050000 AF=0.001185;DP=27851;DP4=21620,6185,28,10;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A38V|222|M|protein_coding|CODING|GU280_gp05|1|T) NC_045512.2 26763 . G A 81.0 min_af_0.050000 AF=0.000763;DP=27529;DP4=6306,21191,4,17;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A81T|222|M|protein_coding|CODING|GU280_gp05|1|A) NC_045512.2 26769 . G A 94.0 min_af_0.050000 AF=0.000832;DP=27645;DP4=6442,21176,4,19;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A83T|222|M|protein_coding|CODING|GU280_gp05|1|A) NC_045512.2 26774 . GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT G 153.0 min_af_0.050000 AF=0.000651;DP=27645;DP4=6489,21183,1,17;HRUN=2;SB=10;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 106.0 min_af_0.050000 AF=0.000508;DP=27555;DP4=6490,21192,2,12;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 914.0 min_af_0.050000 AF=0.002420;DP=27690;DP4=6485,21216,9,58;HRUN=1;SB=12;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 26784 . GTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT G 242.0 min_af_0.050000 AF=0.000902;DP=27725;DP4=6544,21238,5,20;HRUN=1;SB=0;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gtaggcttgatgtggctcagctacttcattgcttctttc/gtc|VGLMWLSYFIASF88V|222|M|protein_coding|CODING|GU280_gp05|1|G|INFO_REALIGN_3_PRIME) NC_045512.2 26786 . AGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT A 574.0 min_af_0.050000 AF=0.001701;DP=27628;DP4=6442,21191,4,43;HRUN=2;SB=18;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 88.0 min_af_0.050000 AF=0.000750;DP=27989;DP4=6584,21171,7,16;SB=3;EFF=STOP_GAINED(HIGH|NONSENSE|tgG/tgA|W92*|222|M|protein_coding|CODING|GU280_gp05|1|A) NC_045512.2 26814 . G A 89.0 min_af_0.050000 AF=0.000826;DP=27845;DP4=6505,21101,5,19;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A98T|222|M|protein_coding|CODING|GU280_gp05|1|A) NC_045512.2 26839 . C T 115.0 min_af_0.050000 AF=0.001001;DP=27978;DP4=5992,21948,9,20;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T106M|222|M|protein_coding|CODING|GU280_gp05|1|T) NC_045512.2 26887 . T C 178.0 min_af_0.050000 AF=0.000942;DP=40361;DP4=17436,22867,21,21;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V122A|222|M|protein_coding|CODING|GU280_gp05|1|C) NC_045512.2 26889 . C T 94.0 min_af_0.050000 AF=0.000744;DP=40302;DP4=17327,22937,12,20;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cca/Tca|P123S|222|M|protein_coding|CODING|GU280_gp05|1|T) NC_045512.2 27076 . A G 91.0 min_af_0.050000 AF=0.001012;DP=20750;DP4=5415,15300,7,25;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q185R|222|M|protein_coding|CODING|GU280_gp05|1|G) NC_045512.2 27131 . CTATAAAT C 85.0 min_af_0.050000 AF=0.000517;DP=21269;DP4=5687,15657,2,9;HRUN=1;SB=1;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 27145 . C T 105.0 min_af_0.050000 AF=0.000947;DP=22170;DP4=5499,16643,8,14;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T208I|222|M|protein_coding|CODING|GU280_gp05|1|T) NC_045512.2 27214 . G A 95.0 min_af_0.050000 AF=0.000906;DP=20964;DP4=16303,4623,16,4;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 122.0 min_af_0.050000 AF=0.001097;DP=20974;DP4=15962,4976,20,4;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaA|N28K|61|ORF6|protein_coding|CODING|GU280_gp06|1|A) NC_045512.2 27335 . C T 348.0 min_af_0.050000 AF=0.003743;DP=9350;DP4=5145,4165,25,12;SB=8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T45I|61|ORF6|protein_coding|CODING|GU280_gp06|1|T) NC_045512.2 27344 . A T 857.0 min_af_0.050000 AF=0.007391;DP=9336;DP4=5187,4074,34,35;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAa/aTa|K48I|61|ORF6|protein_coding|CODING|GU280_gp06|1|T) NC_045512.2 27345 . A T 824.0 min_af_0.050000 AF=0.007162;DP=9355;DP4=5202,4083,34,35;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaA/aaT|K48N|61|ORF6|protein_coding|CODING|GU280_gp06|1|T) NC_045512.2 27354 . A G 835.0 min_af_0.050000 AF=0.007265;DP=9085;DP4=5193,3824,37,30;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q51|61|ORF6|protein_coding|CODING|GU280_gp06|1|G) NC_045512.2 27384 . T C 18042.0 min_af_0.050000 AF=0.039210;DP=22979;DP4=5329,16742,231,675;SB=4;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D61|61|ORF6|protein_coding|CODING|GU280_gp06|1|C) NC_045512.2 27476 . C T 120.0 min_af_0.050000 AF=0.001083;DP=21237;DP4=4263,16944,7,18;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T28I|121|ORF7a|protein_coding|CODING|GU280_gp07|1|T) NC_045512.2 27484 . T C 255.0 min_af_0.050000 AF=0.001917;DP=20866;DP4=3996,16822,10,37;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|Tta/Cta|L31|121|ORF7a|protein_coding|CODING|GU280_gp07|1|C) NC_045512.2 27883 . C A 5191.0 PASS AF=0.163062;DP=1202;DP4=757,245,152,47;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gAc|A43D|43|ORF7b|protein_coding|CODING|GU280_gp08|1|A) NC_045512.2 27916 . G T 383.0 min_af_0.050000 AF=0.018272;DP=1204;DP4=884,296,18,5;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gTa|G8V|121|ORF8|protein_coding|CODING|GU280_gp09|1|T) NC_045512.2 28116 . G A 100.0 min_af_0.050000 AF=0.001102;DP=18155;DP4=14658,3471,15,7;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D75N|121|ORF8|protein_coding|CODING|GU280_gp09|1|A) NC_045512.2 28121 . C T 85.0 min_af_0.050000 AF=0.000927;DP=18332;DP4=14718,3591,13,4;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I76|121|ORF8|protein_coding|CODING|GU280_gp09|1|T) NC_045512.2 28333 . C A 188.0 min_af_0.050000 AF=0.001670;DP=19759;DP4=4578,15135,15,20;SB=20;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccC/ccA|P20|419|N|protein_coding|CODING|GU280_gp10|1|A) NC_045512.2 28346 . G T 237.0 min_af_0.050000 AF=0.001681;DP=19634;DP4=4549,15043,16,18;SB=24;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Tgc|G25C|419|N|protein_coding|CODING|GU280_gp10|1|T) NC_045512.2 28347 . G A 4058.0 min_af_0.050000 AF=0.013345;DP=19633;DP4=4498,14865,67,200;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGc/gAc|G25D|419|N|protein_coding|CODING|GU280_gp10|1|A) NC_045512.2 28383 . CA C 138.0 min_af_0.050000 AF=0.000833;DP=19212;DP4=4193,15092,3,13;HRUN=4;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||aaa/|K38|419|N|protein_coding|CODING|GU280_gp10|1|C|INFO_REALIGN_3_PRIME);LOF=(N|GU280_gp10|1|1.00) NC_045512.2 28391 . C T 95.0 min_af_0.050000 AF=0.001045;DP=19144;DP4=4089,15033,6,15;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R40C|419|N|protein_coding|CODING|GU280_gp10|1|T) NC_045512.2 28406 . TTACCCAATA T 68.0 min_af_0.050000 AF=0.000476;DP=18921;DP4=3692,15258,2,7;HRUN=3;SB=1;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ttacccaataat/tat|LPNN45Y|419|N|protein_coding|CODING|GU280_gp10|1|T) NC_045512.2 28420 . T C 82.0 min_af_0.050000 AF=0.000929;DP=20450;DP4=5421,14999,5,18;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T49|419|N|protein_coding|CODING|GU280_gp10|1|C) NC_045512.2 28727 . G A 132.0 min_af_0.050000 AF=0.001513;DP=12555;DP4=8651,3864,27,5;SB=10;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A152T|419|N|protein_coding|CODING|GU280_gp10|1|A) NC_045512.2 28881 . G A 10935.0 PASS AF=0.076973;DP=6184;DP4=2898,2809,253,223;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aAg|R203K|419|N|protein_coding|CODING|GU280_gp10|1|A) NC_045512.2 28882 . G A 10816.0 PASS AF=0.075656;DP=6252;DP4=2940,2836,252,223;SB=4;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R203|419|N|protein_coding|CODING|GU280_gp10|1|A) NC_045512.2 28883 . G C 10619.0 PASS AF=0.075804;DP=6253;DP4=2948,2825,255,222;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gga/Cga|G204R|419|N|protein_coding|CODING|GU280_gp10|1|C) NC_045512.2 28987 . CCAA C 654.0 min_af_0.050000 AF=0.003439;DP=12502;DP4=2863,9632,6,37;HRUN=2;SB=6;INDEL;EFF=CODON_DELETION(MODERATE||caa/|Q242|419|N|protein_coding|CODING|GU280_gp10|1|C|INFO_REALIGN_3_PRIME) NC_045512.2 29029 . T C 4700.0 min_af_0.050000 AF=0.011125;DP=28765;DP4=17309,11111,119,216;SB=198;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A252|419|N|protein_coding|CODING|GU280_gp10|1|C) NC_045512.2 29031 . A G 100.0 min_af_0.050000 AF=0.000797;DP=28875;DP4=17391,11440,12,18;SB=15;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAg/gGg|E253G|419|N|protein_coding|CODING|GU280_gp10|1|G) NC_045512.2 29039 . A T 8719.0 min_af_0.050000 AF=0.017926;DP=29232;DP4=17349,11343,226,304;SB=155;EFF=STOP_GAINED(HIGH|NONSENSE|Aag/Tag|K256*|419|N|protein_coding|CODING|GU280_gp10|1|T) NC_045512.2 29049 . G A 828.0 min_af_0.050000 AF=0.003925;DP=22418;DP4=17644,4672,80,15;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R259Q|419|N|protein_coding|CODING|GU280_gp10|1|A) NC_045512.2 29067 . CTAAAGCATACAATG C 83.0 min_af_0.050000 AF=0.000492;DP=22352;DP4=17230,5161,8,3;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 29187 . C T 206.0 min_af_0.050000 AF=0.002499;DP=10005;DP4=5490,4489,18,7;SB=9;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A305V|419|N|protein_coding|CODING|GU280_gp10|1|T) NC_045512.2 29188 . A G 173.0 min_af_0.050000 AF=0.002324;DP=9896;DP4=5450,4414,15,11;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A305|419|N|protein_coding|CODING|GU280_gp10|1|G) NC_045512.2 29195 . GC G 256.0 min_af_0.050000 AF=0.002255;DP=9758;DP4=5491,4296,11,11;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 29287 . A T 83.0 min_af_0.050000 AF=0.000864;DP=22003;DP4=4700,17278,0,19;SB=16;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaA/aaT|K338N|419|N|protein_coding|CODING|GU280_gp10|1|T) NC_045512.2 29511 . G T 3323.0 PASS AF=0.076433;DP=1884;DP4=1073,665,70,76;SB=28;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aTt|S413I|419|N|protein_coding|CODING|GU280_gp10|1|T) NC_045512.2 29800 . G A 706.0 min_af_0.050000 AF=0.046875;DP=704;DP4=154,517,6,27;SB=1