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sample-02.vcf
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##fileformat=VCFv4.0
##FILTER=<ID=PASS,Description="All filters passed">
##fileDate=20240114
##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 5 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.0005 --bonf dynamic --no-default-filter --no-default-filter -r NC_045512.2:1-7475 -o /data/jwd02f/main/066/348/66348157/tmp/lofreq2_call_parallelseq_lia6/0.vcf.gz reads.bam
##reference=reference.fa
##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth">
##INFO=<ID=AF,Number=1,Type=Float,Description="Lofreq Allele Frequency; Fraction of variant-supporting bases with q > --min-bq among all bases at the site">
##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias at this position">
##INFO=<ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">
##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position">
##FILTER=<ID=min_snvqual_70,Description="Minimum SNV Quality (Phred) 70">
##FILTER=<ID=min_indelqual_52,Description="Minimum Indel Quality (Phred) 52">
##FILTER=<ID=min_snvqual_76,Description="Minimum SNV Quality (Phred) 76">
##FILTER=<ID=min_indelqual_59,Description="Minimum Indel Quality (Phred) 59">
##contig=<ID=NC_045512.2>
##INFO=<ID=AmpliconBias,Number=0,Type=Flag,Description="Indicates that the AF value of the variant could not be corrected for potential amplicon bias.">
##bcftools_annotateVersion=1.10.2+htslib-1.10.2
##bcftools_annotateCommand=annotate --columns QUAL,INFO --annotations annotations.vcf.gz --mark-sites -AmpliconBias --output-type v --threads 1 input.vcf.gz; Date=Sun Jan 14 20:36:55 2024
##bcftools_annotateCommand=annotate --columns QUAL,INFO --annotations annotations.vcf.gz --mark-sites +AmpliconBias --output-type v --threads 1 input.vcf.gz; Date=Sun Jan 14 20:38:21 2024
##SnpEffVersion="4.5covid19 (build 2020-04-15 22:26), by Pablo Cingolani"
##SnpEffCmd="SnpEff -i vcf -o vcf -formatEff -classic -no-downstream -no-intergenic -no-upstream -stats /data/jwd05e/main/066/348/66348337/outputs/dataset_c288c94a-0348-41f7-b870-1606f9e31660.dat NC_045512.2 /data/dnb09/galaxy_db/files/7/7/2/dataset_772d0911-b66c-4438-8ce9-5422d2ce0169.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'">
##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000">
##SnpSiftVersion="SnpSift 4.3t (build 2017-11-24 10:18), by Pablo Cingolani"
##SnpSiftCmd="SnpSift Filter -f /data/dnb09/galaxy_db/files/b/e/1/dataset_be17d1cf-1b65-49e1-8faa-ce584dae98c1.dat -e /data/jwd02f/main/066/348/66348992/configs/tmp4t__jjl5"
##FILTER=<ID=SnpSift,Description="SnpSift 4.3t (build 2017-11-24 10:18), by Pablo Cingolani, Expression used: DP >= 1">
##SnpSiftCmd="SnpSift Filter -f /data/dnb09/galaxy_db/files/c/3/7/dataset_c371141d-e70d-4f7b-9ec8-cac242098745.dat -e /data/jwd05e/main/066/349/66349011/configs/tmp_zqshhmt --addFilter min_af_0.05Xmin_dp_1Xmin_dp_alt_10"
##FILTER=<ID=SnpSift,Description="SnpSift 4.3t (build 2017-11-24 10:18), by Pablo Cingolani, Expression used: ( ( DP4[2] + DP4[3] ) < ( 0.05 * DP ) ) | ( DP < 1 ) | ( ( AF * DP ) < ( 10 - 0.5 ) )">
#CHROM POS ID REF ALT QUAL FILTER INFO
NC_045512.2 241 . C T 10937.0 PASS DP=328;AF=0.902439;SB=0;DP4=0,0,164,164
NC_045512.2 507 . ATGGTCATGTTATGGT A 412.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2144;AF=0.009795;SB=0;DP4=1058,1065,10,11;INDEL;HRUN=1;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggtcatgttatggttgag/gag|GHVMVE82E|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggtcatgttatggttgag/gag|GHVMVE82E|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggtcatgttatggttgag/gag|GHVMVE82E|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggtcatgttatggttgag/gag|GHVMVE82E|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A|INFO_REALIGN_3_PRIME)
NC_045512.2 509 . GGTCATGTT G 351.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2126;AF=0.009407;SB=0;DP4=1025,1032,10,10;INDEL;HRUN=2;EFF=FRAME_SHIFT(HIGH||ggtcatgtt/|GHV82|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),FRAME_SHIFT(HIGH||ggtcatgtt/|GHV82|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON),FRAME_SHIFT(HIGH||ggtcatgtt/|GHV82|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON),FRAME_SHIFT(HIGH||ggtcatgtt/|GHV82|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 509 . GGTCATGTTA G 840.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2126;AF=0.018815;SB=0;DP4=1025,1032,20,20;INDEL;HRUN=2;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggtcatgttatg/gtg|GHVM82V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggtcatgttatg/gtg|GHVM82V|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggtcatgttatg/gtg|GHVM82V|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggtcatgttatg/gtg|GHVM82V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G)
NC_045512.2 509 . GGTCATGTTATGGTT G 504.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2126;AF=0.011759;SB=0;DP4=1025,1032,12,13;INDEL;HRUN=2;EFF=FRAME_SHIFT(HIGH||ggtcatgttatggttgag/|GHVMVE82|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ggtcatgttatggttgag/|GHVMVE82|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ggtcatgttatggttgag/|GHVMVE82|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ggtcatgttatggttgag/|GHVMVE82|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 513 . ATGTTATGGT A 92.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2104;AF=0.002852;SB=0;DP4=1045,1055,3,3;INDEL;HRUN=1;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gttatggttgag/gag|VMVE84E|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gttatggttgag/gag|VMVE84E|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||gttatggttgag/gag|VMVE84E|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||gttatggttgag/gag|VMVE84E|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A|INFO_REALIGN_3_PRIME)
NC_045512.2 514 . TGTTATG T 191.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2135;AF=0.005152;SB=0;DP4=1057,1068,5,6;INDEL;HRUN=1;EFF=CODON_DELETION(MODERATE||atggtt/|MV85|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),CODON_DELETION(MODERATE||atggtt/|MV85|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),CODON_DELETION(MODERATE||atggtt/|MV85|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),CODON_DELETION(MODERATE||atggtt/|MV85|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME)
NC_045512.2 515 . GTTA G 111.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2138;AF=0.003274;SB=0;DP4=1059,1070,3,4;INDEL;HRUN=2;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gttatg/gtg|VM84V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gttatg/gtg|VM84V|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gttatg/gtg|VM84V|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gttatg/gtg|VM84V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME)
NC_045512.2 517 . TA T 130.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2124;AF=0.003766;SB=0;DP4=1052,1064,4,4;INDEL;HRUN=1;EFF=FRAME_SHIFT(HIGH||atg/|M85|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),FRAME_SHIFT(HIGH||atg/|M85|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON),FRAME_SHIFT(HIGH||atg/|M85|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON),FRAME_SHIFT(HIGH||atg/|M85|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 518 . ATGGTT A 435.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2082;AF=0.010567;SB=0;DP4=1046,1057,11,11;INDEL;HRUN=1;EFF=FRAME_SHIFT(HIGH||atggtt/|MV85|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),FRAME_SHIFT(HIGH||atggtt/|MV85|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON),FRAME_SHIFT(HIGH||atggtt/|MV85|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON),FRAME_SHIFT(HIGH||atggtt/|MV85|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 671 . TACGGCGCCGATCTA T 120.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1488;AF=0.004704;SB=0;DP4=715,775,3,4;INDEL;HRUN=1;EFF=FRAME_SHIFT(HIGH||tacggcgccgatctaaag/|YGADLK136|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tacggcgccgatctaaag/|YGADLK136|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tacggcgccgatctaaag/|YGADLK136|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tacggcgccgatctaaag/|YGADLK136|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 1026 . C CT 82.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1146;AF=0.004363;SB=0;DP4=607,534,3,2;INDEL;HRUN=4;EFF=FRAME_SHIFT+STOP_GAINED(HIGH||gaa/Tgaa|E256*?|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|CT|INFO_REALIGN_3_PRIME),FRAME_SHIFT+STOP_GAINED(HIGH||gaa/Tgaa|E256*?|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|CT|INFO_REALIGN_3_PRIME),FRAME_SHIFT+STOP_GAINED(HIGH||gaa/Tgaa|E76*?|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|CT|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT+STOP_GAINED(HIGH||gaa/Tgaa|E76*?|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|CT|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14);NMD=(ORF1ab|GU280_gp01|28|0.04)
NC_045512.2 1800 . CA C 64.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1008;AF=0.003968;SB=0;DP4=497,509,2,2;INDEL;HRUN=4;EFF=FRAME_SHIFT(HIGH||aaa/|K513|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K513|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K333|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K333|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 1983 . T A 100.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2702;AF=0.003701;SB=0;DP4=1355,1329,5,5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTt/aAt|I573N|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTt/aAt|I573N|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTt/aAt|I393N|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTt/aAt|I393N|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 2007 . T C 135.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2927;AF=0.004441;SB=0;DP4=1454,1448,7,7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTt/aCt|I581T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTt/aCt|I581T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTt/aCt|I401T|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTt/aCt|I401T|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 2330 . T A 218.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=781;AF=0.016645;SB=0;DP4=360,384,7,7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Agt|C689S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Agt|C689S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Agt|C509S|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Agt|C509S|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 2621 . A T 91.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1643;AF=0.004869;SB=0;DP4=824,802,5,5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aac/Tac|N786Y|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aac/Tac|N786Y|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aac/Tac|N606Y|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aac/Tac|N606Y|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 2832 . A G 35943.0 PASS DP=1069;AF=0.910196;SB=3;DP4=1,0,491,575;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K856R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K856R|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K38R|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K38R|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 3037 . C T 5436.0 PASS DP=153;AF=0.947712;SB=0;DP4=0,0,75,78;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 3104 . T A 183.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=507;AF=0.021696;SB=0;DP4=263,230,8,6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tat/Aat|Y947N|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tat/Aat|Y947N|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tat/Aat|Y129N|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tat/Aat|Y129N|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 3530 . GATTACATAGCTACTAATGGACCACTTAAAGTGGGTGGTAGTTGTGTTT G 170.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1296;AF=0.006944;SB=0;DP4=660,639,5,4;INDEL;HRUN=1;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gattacatagctactaatggaccacttaaagtgggtggtagttgtgtttta/gta|DYIATNGPLKVGGSCVL1089V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gattacatagctactaatggaccacttaaagtgggtggtagttgtgtttta/gta|DYIATNGPLKVGGSCVL1089V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gattacatagctactaatggaccacttaaagtgggtggtagttgtgtttta/gta|DYIATNGPLKVGGSCVL271V|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gattacatagctactaatggaccacttaaagtgggtggtagttgtgtttta/gta|DYIATNGPLKVGGSCVL271V|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 3604 . CTG C 135.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1451;AF=0.005513;SB=0;DP4=747,750,4,4;INDEL;HRUN=1;EFF=FRAME_SHIFT(HIGH||tgt/|C1114|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tgt/|C1114|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tgt/|C296|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tgt/|C296|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 3876 . C T 92.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=54;AF=0.074074;SB=0;DP4=25,23,2,2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A1204V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A1204V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A386V|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A386V|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 4240 . T C 119.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=524;AF=0.015267;SB=0;DP4=255,256,4,4;EFF=SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y1325|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y1325|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y507|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y507|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 4528 . ATT A 67.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=748;AF=0.005348;SB=0;DP4=370,372,2,2;INDEL;HRUN=4;EFF=FRAME_SHIFT(HIGH||ttttac/|FY1422|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttttac/|FY1422|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttttac/|FY604|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttttac/|FY604|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14)
NC_045512.2 4531 . TTACTTTTACACCAGTAAAACAACTG T 75.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=724;AF=0.005525;SB=0;DP4=359,361,2,2;INDEL;HRUN=4;EFF=FRAME_SHIFT(HIGH||tacttttacaccagtaaaacaactgta/|YFYTSKTTV1423|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tacttttacaccagtaaaacaactgta/|YFYTSKTTV1423|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tacttttacaccagtaaaacaactgta/|YFYTSKTTV605|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tacttttacaccagtaaaacaactgta/|YFYTSKTTV605|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 4576 . A T 110.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=780;AF=0.010256;SB=2;DP4=371,396,7,5;EFF=SYNONYMOUS_CODING(LOW|SILENT|acA/acT|T1437|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|acA/acT|T1437|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|acA/acT|T619|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|acA/acT|T619|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 4578 . TTAACGATC T 73.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=774;AF=0.005168;SB=0;DP4=373,397,2,2;INDEL;HRUN=2;EFF=FRAME_SHIFT(HIGH||aacgatctaaat/|NDLN1439|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aacgatctaaat/|NDLN1439|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aacgatctaaat/|NDLN621|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aacgatctaaat/|NDLN621|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 4579 . T A 116.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=775;AF=0.010323;SB=0;DP4=370,393,4,4;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctT/ctA|L1438|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),SYNONYMOUS_CODING(LOW|SILENT|ctT/ctA|L1438|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),SYNONYMOUS_CODING(LOW|SILENT|ctT/ctA|L620|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ctT/ctA|L620|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 4891 . C T 1382.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1943;AF=0.037571;SB=2;DP4=911,940,42,38;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T1542|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T1542|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T724|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T724|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 5239 . C T 92.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1340;AF=0.00597;SB=0;DP4=632,695,4,4;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y1658|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y1658|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y840|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y840|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 5386 . T G 49314.0 PASS DP=1745;AF=0.866476;SB=5;DP4=2,6,861,870;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcG|A1707|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcG|A1707|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcG|A889|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcG|A889|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 5743 . G C 551.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2274;AF=0.01715;SB=1;DP4=1115,1091,30,27;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 676.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2270;AF=0.020264;SB=2;DP4=1110,1098,33,27;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 5817 . C T 138.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1923;AF=0.00624;SB=10;DP4=948,943,16,7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A1851V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A1851V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A1033V|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A1033V|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 5818 . TTTAC T 174.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1882;AF=0.005313;SB=0;DP4=954,945,5,5;INDEL;HRUN=3;EFF=FRAME_SHIFT(HIGH||cttaca/|LT1853|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||cttaca/|LT1853|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||cttaca/|LT1035|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||cttaca/|LT1035|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 6508 . T G 81.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=387;AF=0.01292;SB=0;DP4=202,177,3,3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N2081K|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N2081K|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N1263K|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N1263K|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 6512 . AGTT A 13635.0 PASS DP=386;AF=0.997409;SB=6;DP4=0,2,206,179;INDEL;HRUN=1;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||agttta/ata|SL2083I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||agttta/ata|SL2083I|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||agttta/ata|SL1265I|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||agttta/ata|SL1265I|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 6653 . GTTAATAGTGTCCCTTGGGATACTATAGCTA G 248.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=672;AF=0.016369;SB=0;DP4=329,332,5,6;INDEL;HRUN=2;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gttaatagtgtcccttgggatactatagctaat/gat|VNSVPWDTIAN2130D|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gttaatagtgtcccttgggatactatagctaat/gat|VNSVPWDTIAN2130D|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gttaatagtgtcccttgggatactatagctaat/gat|VNSVPWDTIAN1312D|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gttaatagtgtcccttgggatactatagctaat/gat|VNSVPWDTIAN1312D|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 6654 . TTAATAGTGTCCCTTGGGATACTATAGC T 146.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=672;AF=0.010417;SB=1;DP4=330,335,4,3;INDEL;HRUN=2;EFF=CODON_DELETION(MODERATE||agtgtcccttgggatactatagctaat/|SVPWDTIAN2132|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),CODON_DELETION(MODERATE||agtgtcccttgggatactatagctaat/|SVPWDTIAN2132|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME),CODON_DELETION(MODERATE||agtgtcccttgggatactatagctaat/|SVPWDTIAN1314|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),CODON_DELETION(MODERATE||agtgtcccttgggatactatagctaat/|SVPWDTIAN1314|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME)
NC_045512.2 6696 . C CT 138.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=542;AF=0.012915;SB=0;DP4=275,274,4,3;INDEL;HRUN=4;EFF=FRAME_SHIFT(HIGH||ctt/Tctt|L2146S?|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|CT|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ctt/Tctt|L2146S?|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|CT|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ctt/Tctt|L1328S?|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|CT|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ctt/Tctt|L1328S?|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|CT|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14)
NC_045512.2 6787 . T C 87.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=610;AF=0.009836;SB=0;DP4=311,292,3,3;EFF=SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T2174|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T2174|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T1356|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T1356|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 6811 . TACTA T 94.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=707;AF=0.007072;SB=1;DP4=349,353,3,2;INDEL;HRUN=1;EFF=FRAME_SHIFT(HIGH||actaga/|TR2183|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),FRAME_SHIFT(HIGH||actaga/|TR2183|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),FRAME_SHIFT(HIGH||actaga/|TR1365|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),FRAME_SHIFT(HIGH||actaga/|TR1365|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.14)
NC_045512.2 7175 . TTA T 114.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=637;AF=0.009419;SB=0;DP4=336,297,3,3;INDEL;HRUN=3;EFF=FRAME_SHIFT(HIGH||tta/|L2304|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),FRAME_SHIFT(HIGH||tta/|L2304|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),FRAME_SHIFT(HIGH||tta/|L1486|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),FRAME_SHIFT(HIGH||tta/|L1486|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.14)
NC_045512.2 7615 . GAATTGTGTT G 134.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1869;AF=0.00428;SB=0;DP4=918,943,4,4;INDEL;HRUN=2;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gttaattgtgat/gat|VNCD2453D|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gttaattgtgat/gat|VNCD2453D|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gttaattgtgat/gat|VNCD1635D|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gttaattgtgat/gat|VNCD1635D|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME)
NC_045512.2 7617 . ATTGTG A 260.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1862;AF=0.007519;SB=0;DP4=915,940,7,7;INDEL;HRUN=2;EFF=FRAME_SHIFT(HIGH||tgtgtt/|CV2452|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tgtgtt/|CV2452|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tgtgtt/|CV1634|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tgtgtt/|CV1634|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14)
NC_045512.2 7622 . GTTAA G 196.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1884;AF=0.005839;SB=0;DP4=925,949,5,6;INDEL;HRUN=2;EFF=FRAME_SHIFT(HIGH||aattgt/|NC2454|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aattgt/|NC2454|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aattgt/|NC1636|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aattgt/|NC1636|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 7625 . AATT A 178.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1854;AF=0.005933;SB=0;DP4=910,934,5,6;INDEL;HRUN=2;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aattgt/agt|NC2454S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aattgt/agt|NC2454S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aattgt/agt|NC1636S|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aattgt/agt|NC1636S|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 8361 . T G 92.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1004;AF=0.006972;SB=1;DP4=554,439,3,4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTt/aGt|I2699S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTt/aGt|I2699S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTt/aGt|I1881S|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTt/aGt|I1881S|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 8376 . CA C 142.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=961;AF=0.008325;SB=0;DP4=529,424,4,4;INDEL;HRUN=5;EFF=FRAME_SHIFT(HIGH||agt/|S2706|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||agt/|S2706|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||agt/|S1888|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||agt/|S1888|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 8393 . G A 39024.0 PASS DP=1122;AF=0.926916;SB=0;DP4=3,3,622,489;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A2710T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A2710T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A1892T|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A1892T|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 8585 . AT A 163.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1386;AF=0.006494;SB=0;DP4=651,726,4,5;INDEL;HRUN=2;EFF=FRAME_SHIFT(HIGH||att/|I2774|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||att/|I2774|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||att/|I11|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||att/|I11|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 8606 . CT C 148.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1239;AF=0.007264;SB=0;DP4=563,667,4,5;INDEL;HRUN=5;EFF=FRAME_SHIFT(HIGH||ttt/|F2782|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F2782|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F19|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F19|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 9541 . CTGTTTAACACCAGTTTACTCATTCTTACCTGG C 79.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1686;AF=0.002966;SB=0;DP4=910,771,3,2;INDEL;HRUN=1;EFF=FRAME_SHIFT(HIGH||acaccagtttactcattcttacctggtgtttat/|TPVYSFLPGVY3095|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||acaccagtttactcattcttacctggtgtttat/|TPVYSFLPGVY3095|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||acaccagtttactcattcttacctggtgtttat/|TPVYSFLPGVY332|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||acaccagtttactcattcttacctggtgtttat/|TPVYSFLPGVY332|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14)
NC_045512.2 9996 . C T 240.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1656;AF=0.010266;SB=3;DP4=810,824,13,9;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S3244L|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S3244L|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S481L|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S481L|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 10029 . C T 49314.0 PASS DP=1563;AF=0.864363;SB=9;DP4=4,0,774,771;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T3255I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T3255I|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T492I|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T492I|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 10323 . A G 85.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1985;AF=0.00403;SB=0;DP4=969,998,4,4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K3353R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K3353R|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K90R|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K90R|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 10352 . AAGTATAAGTTTGTTCGCATTCAACCAGGACAGACTTTTT A 76.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1871;AF=0.002672;SB=0;DP4=893,990,2,3;INDEL;HRUN=2;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aagtataagtttgttcgcattcaaccaggacagactttttca/aca|KYKFVRIQPGQTFS3363T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aagtataagtttgttcgcattcaaccaggacagactttttca/aca|KYKFVRIQPGQTFS3363T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aagtataagtttgttcgcattcaaccaggacagactttttca/aca|KYKFVRIQPGQTFS100T|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aagtataagtttgttcgcattcaaccaggacagactttttca/aca|KYKFVRIQPGQTFS100T|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 10408 . C T 99.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1385;AF=0.005776;SB=5;DP4=626,745,8,5;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y3381|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y3381|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y118|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y118|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 10449 . C A 46894.0 PASS DP=1422;AF=0.888186;SB=11;DP4=0,5,666,739;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cAc|P3395H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cAc|P3395H|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cAc|P132H|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cAc|P132H|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 10484 . T G 658.0 PASS DP=742;AF=0.044474;SB=5;DP4=366,334,18,24;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Gca|S3407A|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Gca|S3407A|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Gca|S144A|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Gca|S144A|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 10541 . C A 492.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=929;AF=0.03014;SB=1;DP4=454,439,15,17;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Aac|H3426N|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Aac|H3426N|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Aac|H163N|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Aac|H163N|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 10698 . GA G 87.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=775;AF=0.006452;SB=0;DP4=371,409,2,3;INDEL;HRUN=1;EFF=FRAME_SHIFT(HIGH||gga/|G3478|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),FRAME_SHIFT(HIGH||gga/|G3478|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),FRAME_SHIFT(HIGH||gga/|G215|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),FRAME_SHIFT(HIGH||gga/|G215|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.14)
NC_045512.2 10769 . TATG T 124.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1282;AF=0.00546;SB=0;DP4=646,629,4,3;INDEL;HRUN=1;EFF=STOP_GAINED+CODON_CHANGE_PLUS_CODON_DELETION(HIGH||tatgaa/taa|YE3502*|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),STOP_GAINED+CODON_CHANGE_PLUS_CODON_DELETION(HIGH||tatgaa/taa|YE3502*|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME),STOP_GAINED+CODON_CHANGE_PLUS_CODON_DELETION(HIGH||tatgaa/taa|YE239*|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),STOP_GAINED+CODON_CHANGE_PLUS_CODON_DELETION(HIGH||tatgaa/taa|YE239*|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.04);NMD=(ORF1ab|GU280_gp01|28|0.04)
NC_045512.2 10935 . TTGATGTTGTTA T 59.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1527;AF=0.00262;SB=0;DP4=761,764,2,2;INDEL;HRUN=4;EFF=FRAME_SHIFT(HIGH||tttgatgttgttaga/|FDVVR3557|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),FRAME_SHIFT(HIGH||tttgatgttgttaga/|FDVVR3557|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),FRAME_SHIFT(HIGH||tttgatgttgttaga/|FDVVR294|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),FRAME_SHIFT(HIGH||tttgatgttgttaga/|FDVVR294|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 10977 . C T 99.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1287;AF=0.006216;SB=5;DP4=620,648,9,5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A3571V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A3571V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A2V|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A2V|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 11039 . T C 87.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1303;AF=0.00614;SB=0;DP4=629,661,5,5;EFF=SYNONYMOUS_CODING(LOW|SILENT|Tta/Cta|L3592|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|Tta/Cta|L3592|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|Tta/Cta|L23|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|Tta/Cta|L23|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 11178 . T G 122.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1657;AF=0.006035;SB=0;DP4=808,837,6,6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTg/tGg|L3638W|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTg/tGg|L3638W|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTg/tGg|L69W|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTg/tGg|L69W|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 11266 . GGATATGGTTGATACTAGTTTGTCTGGTT G 77.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1595;AF=0.003135;SB=0;DP4=766,832,2,3;INDEL;HRUN=2;EFF=FRAME_SHIFT(HIGH||gatatggttgatactagtttgtctggtttt/|DMVDTSLSGF3668|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),FRAME_SHIFT(HIGH||gatatggttgatactagtttgtctggtttt/|DMVDTSLSGF3668|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),FRAME_SHIFT(HIGH||gatatggttgatactagtttgtctggtttt/|DMVDTSLSGF99|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),FRAME_SHIFT(HIGH||gatatggttgatactagtttgtctggtttt/|DMVDTSLSGF99|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.14)
NC_045512.2 11282 . AGTTTGTCTG A 47790.0 PASS DP=1422;AF=0.901547;SB=9;DP4=68,59,591,691;INDEL;HRUN=1;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ttgtctggtttt/ttt|LSGF3674F|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ttgtctggtttt/ttt|LSGF3674F|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ttgtctggtttt/ttt|LSGF105F|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ttgtctggtttt/ttt|LSGF105F|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME)
NC_045512.2 11282 . AGTTTGTCTGGTTT A 269.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1422;AF=0.009845;SB=2;DP4=68,59,6,8;INDEL;HRUN=1;EFF=FRAME_SHIFT(HIGH||agtttgtctggtttt/|SLSGF3673|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),FRAME_SHIFT(HIGH||agtttgtctggtttt/|SLSGF3673|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),FRAME_SHIFT(HIGH||agtttgtctggtttt/|SLSGF104|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),FRAME_SHIFT(HIGH||agtttgtctggtttt/|SLSGF104|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.14)
NC_045512.2 11483 . GTTACTTCTAACTACTCAGGTGTAGTTACAACTGTCATGTTT G 454.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=3012;AF=0.007968;SB=0;DP4=1485,1505,12,12;INDEL;HRUN=2;EFF=FRAME_SHIFT(HIGH||acttctaactactcaggtgtagttacaactgtcatgtttttg/|TSNYSGVVTTVMFL3741|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||acttctaactactcaggtgtagttacaactgtcatgtttttg/|TSNYSGVVTTVMFL3741|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||acttctaactactcaggtgtagttacaactgtcatgtttttg/|TSNYSGVVTTVMFL172|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||acttctaactactcaggtgtagttacaactgtcatgtttttg/|TSNYSGVVTTVMFL172|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 11486 . ACTTCTAACTACTCAGGTGTAGTTACAACTGTCATG A 117.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=3002;AF=0.002665;SB=0;DP4=1491,1511,4,4;INDEL;HRUN=1;EFF=FRAME_SHIFT(HIGH||acttctaactactcaggtgtagttacaactgtcatg/|TSNYSGVVTTVM3741|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),FRAME_SHIFT(HIGH||acttctaactactcaggtgtagttacaactgtcatg/|TSNYSGVVTTVM3741|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),FRAME_SHIFT(HIGH||acttctaactactcaggtgtagttacaactgtcatg/|TSNYSGVVTTVM172|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),FRAME_SHIFT(HIGH||acttctaactactcaggtgtagttacaactgtcatg/|TSNYSGVVTTVM172|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.14)
NC_045512.2 11486 . ACTT A 80.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=3002;AF=0.001999;SB=0;DP4=1491,1511,3,3;INDEL;HRUN=1;EFF=CODON_DELETION(MODERATE||tct/|S3742|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A|INFO_REALIGN_3_PRIME),CODON_DELETION(MODERATE||tct/|S3742|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A|INFO_REALIGN_3_PRIME),CODON_DELETION(MODERATE||tct/|S173|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),CODON_DELETION(MODERATE||tct/|S173|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME)
NC_045512.2 11534 . G A 136.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2849;AF=0.004914;SB=5;DP4=1387,1434,8,14;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G3757S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G3757S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G188S|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G188S|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 11537 . A G 49314.0 PASS DP=2822;AF=0.890149;SB=0;DP4=2,2,1379,1431;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Gtt|I3758V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Gtt|I3758V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Gtt|I189V|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Gtt|I189V|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 11630 . TTTTGTACTTG T 114.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1722;AF=0.004065;SB=0;DP4=784,933,3,4;INDEL;HRUN=5;EFF=FRAME_SHIFT(HIGH||tgtacttgttac/|CTCY3790|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tgtacttgttac/|CTCY3790|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tgtacttgttac/|CTCY221|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tgtacttgttac/|CTCY221|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14)
NC_045512.2 11654 . T C 132.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1654;AF=0.006651;SB=3;DP4=751,884,8,6;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 12137 . G A 76.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1636;AF=0.004279;SB=0;DP4=811,805,5,5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A3958T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A3958T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A16T|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A16T|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 12748 . T G 104.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1439;AF=0.006254;SB=1;DP4=712,707,7,5;EFF=SYNONYMOUS_CODING(LOW|SILENT|acT/acG|T4161|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),SYNONYMOUS_CODING(LOW|SILENT|acT/acG|T4161|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),SYNONYMOUS_CODING(LOW|SILENT|acT/acG|T21|112|ORF1ab|protein_coding|CODING|YP_009725305.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|acT/acG|T21|112|ORF1ab|protein_coding|CODING|YP_009742616.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 12756 . CTGA C 142.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1416;AF=0.00565;SB=0;DP4=728,728,4,4;INDEL;HRUN=1;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gatgac/gac|DD4165D|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gatgac/gac|DD4165D|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gatgac/gac|DD25D|112|ORF1ab|protein_coding|CODING|YP_009725305.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gatgac/gac|DD25D|112|ORF1ab|protein_coding|CODING|YP_009742616.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME)
NC_045512.2 12866 . G A 118.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1783;AF=0.005609;SB=2;DP4=891,879,7,4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gga/Aga|G4201R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gga/Aga|G4201R|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gga/Aga|G61R|112|ORF1ab|protein_coding|CODING|YP_009725305.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gga/Aga|G61R|112|ORF1ab|protein_coding|CODING|YP_009742616.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 13162 . TAC T 227.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2946;AF=0.004752;SB=0;DP4=1433,1506,7,7;INDEL;HRUN=1;EFF=FRAME_SHIFT(HIGH||act/|T4302|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||act/|T4302|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||act/|T49|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||act/|T49|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 13195 . T C 49314.0 PASS DP=3110;AF=0.914791;SB=0;DP4=2,2,1639,1462;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtT/gtC|V4310|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|gtT/gtC|V4310|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|gtT/gtC|V57|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|gtT/gtC|V57|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 13339 . T A 103.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=3420;AF=0.003216;SB=0;DP4=1689,1703,7,7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaA|N4358K|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaA|N4358K|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaA|N105K|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaA|N105K|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 13358 . C T 191.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=3401;AF=0.004999;SB=0;DP4=1674,1695,12,11;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L4365F|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L4365F|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L112F|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L112F|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 13791 . A C 225.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=908;AF=0.01652;SB=4;DP4=480,410,7,10;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caA/caC|Q4509H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caA/caC|Q117H|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 13820 . T C 199.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1149;AF=0.012185;SB=0;DP4=611,519,8,7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTc/cCc|L4519P|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTc/cCc|L127P|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 13962 . A G 83.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1486;AF=0.005384;SB=0;DP4=736,731,5,5;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V4566|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V174|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 13994 . CT C 63.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1358;AF=0.002946;SB=0;DP4=685,677,2,2;INDEL;HRUN=3;EFF=FRAME_SHIFT(HIGH||ttg/|L4578|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L186|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 14001 . A T 94.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1410;AF=0.005674;SB=1;DP4=702,694,5,6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttA/ttT|L4579F|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttA/ttT|L187F|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 14009 . T C 124.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1460;AF=0.006849;SB=9;DP4=711,720,16,8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTa/gCa|V4582A|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTa/gCa|V190A|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 14408 . C T 49193.0 PASS DP=1454;AF=0.917469;SB=0;DP4=4,3,738,700;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 14412 . AAGTT A 61.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1431;AF=0.002795;SB=0;DP4=733,694,2,2;INDEL;HRUN=2;EFF=FRAME_SHIFT(HIGH||agtttt/|SF4717|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),FRAME_SHIFT(HIGH||agtttt/|SF325|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 14574 . TGCTA T 298.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1570;AF=0.009554;SB=0;DP4=774,781,8,7;INDEL;HRUN=1;EFF=FRAME_SHIFT(HIGH||gctatg/|AM4771|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),FRAME_SHIFT(HIGH||gctatg/|AM379|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 14864 . TTG T 113.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=945;AF=0.006349;SB=0;DP4=472,471,3,3;INDEL;HRUN=2;EFF=FRAME_SHIFT(HIGH||gtt/|V4868|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||gtt/|V476|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 15157 . C A 121.0 sb_fdr;min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1194;AF=0.007538;SB=471;DP4=617,435,1,141;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Aaa|Q4965K|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Aaa|Q573K|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 15240 . C T 39303.0 PASS DP=1116;AF=0.932796;SB=0;DP4=0,0,530,584;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N4992|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N600|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 15266 . T C 142.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1015;AF=0.009852;SB=1;DP4=468,528,7,6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTa/gCa|V5001A|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTa/gCa|V609A|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 15636 . T C 194.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1993;AF=0.007526;SB=0;DP4=1044,927,8,8;EFF=SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y5124|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y732|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 15690 . T C 210.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2551;AF=0.007056;SB=3;DP4=1216,1278,14,10;EFF=SYNONYMOUS_CODING(LOW|SILENT|cgT/cgC|R5142|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),SYNONYMOUS_CODING(LOW|SILENT|cgT/cgC|R750|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 15726 . T C 324.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2702;AF=0.009993;SB=2;DP4=1322,1344,16,20;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A5154|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A762|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 15819 . T G 83.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2384;AF=0.003775;SB=9;DP4=1125,1237,5,13;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttT/ttG|F5185L|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttT/ttG|F793L|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 15917 . ATG A 125.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1347;AF=0.005939;SB=0;DP4=1219,1210,4,4;INDEL;HRUN=1;EFF=FRAME_SHIFT(HIGH||gtgtac/|VY5219|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||gtgtac/|VY827|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 16276 . T C 86.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1910;AF=0.004188;SB=0;DP4=937,959,5,5;EFF=SYNONYMOUS_CODING(LOW|SILENT|Tta/Cta|L5338|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),SYNONYMOUS_CODING(LOW|SILENT|Tta/Cta|L14|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 16907 . AT A 82.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2421;AF=0.002478;SB=0;DP4=1207,1208,3,3;INDEL;HRUN=4;EFF=FRAME_SHIFT(HIGH||ttt/|F5549|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F225|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 17030 . ATGT A 173.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=3145;AF=0.003498;SB=0;DP4=1535,1605,5,6;INDEL;HRUN=1;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gttgca/gca|VA5590A|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gttgca/gca|VA266A|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME)
NC_045512.2 17148 . AGTGTATACAGCTTGCTCTCATGCCGCT A 67.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1148;AF=0.003484;SB=0;DP4=576,571,2,2;INDEL;HRUN=1;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gtgtatacagcttgctctcatgccgctgtt/gtt|VYTACSHAAV5629V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gtgtatacagcttgctctcatgccgctgtt/gtt|VYTACSHAAV305V|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME)
NC_045512.2 17408 . TA T 124.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1305;AF=0.00613;SB=0;DP4=661,638,4,4;INDEL;HRUN=1;EFF=FRAME_SHIFT(HIGH||tta/|L5715|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),FRAME_SHIFT(HIGH||tta/|L391|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 17539 . G A 78.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2605;AF=0.003455;SB=2;DP4=1293,1284,10,7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gac/Aac|D5759N|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gac/Aac|D435N|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 17580 . T C 261.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2306;AF=0.008673;SB=1;DP4=1135,1142,12,15;EFF=SYNONYMOUS_CODING(LOW|SILENT|atT/atC|I5772|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),SYNONYMOUS_CODING(LOW|SILENT|atT/atC|I448|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 17918 . T G 89.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=635;AF=0.009449;SB=1;DP4=298,330,2,4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTt/tGt|F5885C|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTt/tGt|F561C|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 18163 . A G 1218.0 PASS DP=41;AF=0.804878;SB=0;DP4=0,0,21,20;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I5967V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I42V|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 18391 . G A 94.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=857;AF=0.008168;SB=0;DP4=427,414,4,3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V6043I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V118I|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 18474 . A AT 111.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=916;AF=0.00655;SB=0;DP4=454,456,3,3;INDEL;HRUN=3;EFF=FRAME_SHIFT+STOP_GAINED(HIGH||aaa/Taaa|K6072*?|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|AT|INFO_REALIGN_3_PRIME),FRAME_SHIFT+STOP_GAINED(HIGH||aaa/Taaa|K147*?|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|AT|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 18735 . AT A 97.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1640;AF=0.003659;SB=0;DP4=823,811,3,3;INDEL;HRUN=3;EFF=FRAME_SHIFT(HIGH||ttt/|F6158|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F233|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 18739 . GATT G 135.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1634;AF=0.004896;SB=0;DP4=820,807,4,4;INDEL;HRUN=1;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gattac/gac|DY6159D|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gattac/gac|DY234D|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME)
NC_045512.2 18788 . C T 137.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1678;AF=0.006555;SB=0;DP4=829,834,6,6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T6175I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T250I|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 18965 . G T 140.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1846;AF=0.006501;SB=12;DP4=954,868,17,6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tTt|C6234F|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tTt|C309F|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 19053 . T C 116.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2503;AF=0.004395;SB=3;DP4=1244,1234,6,9;EFF=SYNONYMOUS_CODING(LOW|SILENT|atT/atC|I6263|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),SYNONYMOUS_CODING(LOW|SILENT|atT/atC|I338|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 19239 . AT A 147.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1249;AF=0.006405;SB=1;DP4=589,691,3,5;INDEL;HRUN=3;EFF=FRAME_SHIFT(HIGH||ttt/|F6326|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F401|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 19517 . TGTA T 75.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=669;AF=0.005979;SB=0;DP4=358,313,2,2;INDEL;HRUN=1;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ttgtat/ttt|LY6418F|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ttgtat/ttt|LY493F|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 19567 . G GT 72.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=798;AF=0.005013;SB=0;DP4=425,369,2,2;INDEL;HRUN=3;EFF=FRAME_SHIFT(HIGH||tac/tTac|Y6436L?|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|GT|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tac/tTac|Y511L?|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|GT|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.04)
NC_045512.2 19983 . C T 170.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1638;AF=0.008547;SB=6;DP4=813,783,8,14;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtC/gtT|V6573|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),SYNONYMOUS_CODING(LOW|SILENT|gtC/gtT|V121|345|ORF1ab|protein_coding|CODING|YP_009725310.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 20091 . C CA 67.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1108;AF=0.00361;SB=0;DP4=560,550,2,2;INDEL;HRUN=3;EFF=FRAME_SHIFT(HIGH||caa/Acaa|Q6611T?|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|CA|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||caa/Acaa|Q159T?|345|ORF1ab|protein_coding|CODING|YP_009725310.1|1|CA|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 20102 . GTC G 150.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1019;AF=0.007851;SB=2;DP4=503,511,5,3;INDEL;HRUN=1;EFF=FRAME_SHIFT(HIGH||ctt/|L6614|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ctt/|L162|345|ORF1ab|protein_coding|CODING|YP_009725310.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 20308 . T C 169.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1635;AF=0.007951;SB=0;DP4=801,814,7,8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tat/Cat|Y6682H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tat/Cat|Y230H|345|ORF1ab|protein_coding|CODING|YP_009725310.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 20313 . C T 175.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1679;AF=0.008338;SB=3;DP4=810,835,10,7;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A6683|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A231|345|ORF1ab|protein_coding|CODING|YP_009725310.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 20701 . T C 90.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1044;AF=0.006705;SB=1;DP4=513,520,3,5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y6813H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y15H|297|ORF1ab|protein_coding|CODING|YP_009725311.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 21740 . TCCAATGTTACTTGGTTCCATGCTATACATGTCTCTGGGA T 741.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1514;AF=0.021136;SB=2;DP4=739,744,14,18;INDEL;HRUN=2;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gttacttggttccatgctatacatgtctctgggaccaatggt/ggt|VTWFHAIHVSGTNG62G|1273|S|protein_coding|CODING|GU280_gp02|1|T|INFO_REALIGN_3_PRIME)
NC_045512.2 21762 . C T 39876.0 PASS DP=1279;AF=0.892103;SB=12;DP4=4,0,600,634;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A67V|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 21764 . ATACATG A 40467.0 PASS DP=1221;AF=0.964783;SB=0;DP4=21,24,576,602;INDEL;HRUN=1;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||atacatgtc/atc|IHV68I|1273|S|protein_coding|CODING|GU280_gp02|1|A|INFO_REALIGN_3_PRIME)
NC_045512.2 21846 . C T 43411.0 PASS DP=1194;AF=0.956449;SB=0;DP4=0,1,568,624;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T95I|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 21890 . TTA T 77.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=984;AF=0.005081;SB=0;DP4=459,530,2,3;INDEL;HRUN=3;EFF=FRAME_SHIFT(HIGH||tta/|L110|1273|S|protein_coding|CODING|GU280_gp02|1|T);LOF=(S|GU280_gp02|1|1.00)
NC_045512.2 21985 . GGGTGTTTAT G 109.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=706;AF=0.011331;SB=0;DP4=360,338,4,4;INDEL;HRUN=3;EFF=CODON_DELETION(MODERATE||ggtgtttat/|GVY142|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512.2 21986 . GGTGTTTATT G 22042.0 PASS DP=693;AF=0.982684;SB=1;DP4=14,11,350,331;INDEL;HRUN=3;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggtgtttattac/gac|GVYY142D|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512.2 22157 . GGTT G 70.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=866;AF=0.004619;SB=0;DP4=428,436,2,2;INDEL;HRUN=2;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggttat/gat|GY199D|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512.2 22163 . TTTA T 71.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=842;AF=0.004751;SB=0;DP4=410,429,2,2;INDEL;HRUN=4;EFF=STOP_GAINED+CODON_CHANGE_PLUS_CODON_DELETION(HIGH||tttaaa/taa|FK201*|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 22193 . AATT A 15712.0 PASS DP=537;AF=0.927374;SB=14;DP4=92,148,233,265;INDEL;HRUN=2;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aattta/ata|NL211I|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 22204 . T TGAGCCAGAA 11832.0 PASS DP=464;AF=0.778017;SB=0;DP4=40,49,162,199;INDEL;HRUN=1;EFF=CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||gat/gaGCCAGAAGAt|D215EPED|1273|S|protein_coding|CODING|GU280_gp02|1|TGAGCCAGAA|INFO_REALIGN_3_PRIME)
NC_045512.2 22204 . T TGAGCCAGTA 68.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=464;AF=0.008621;SB=13;DP4=40,49,4,0;INDEL;HRUN=1;EFF=CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||gat/gaGCCAGTAGAt|D215EPVD|1273|S|protein_coding|CODING|GU280_gp02|1|TGAGCCAGTA|INFO_REALIGN_3_PRIME)
NC_045512.2 22527 . C CT 83.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1007;AF=0.004965;SB=0;DP4=521,485,3,2;INDEL;HRUN=2;EFF=FRAME_SHIFT(HIGH||cca/ccTa|P322P?|1273|S|protein_coding|CODING|GU280_gp02|1|CT);LOF=(S|GU280_gp02|1|1.00)
NC_045512.2 22578 . G A 36552.0 PASS DP=1018;AF=0.956778;SB=0;DP4=1,0,515,502;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G339D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 22673 . T C 16406.0 PASS DP=508;AF=0.866142;SB=20;DP4=7,1,202,296;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tcc/Ccc|S371P|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512.2 22674 . C T 16092.0 PASS DP=507;AF=0.859961;SB=0;DP4=1,2,206,294;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S371F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 22679 . T C 17282.0 PASS DP=538;AF=0.862454;SB=10;DP4=5,1,218,311;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Cca|S373P|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512.2 22686 . C T 18527.0 PASS DP=540;AF=0.911111;SB=2;DP4=2,1,220,316;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S375F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 22992 . G A 11096.0 PASS DP=344;AF=0.906977;SB=0;DP4=0,0,180,162;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S477N|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 22995 . C A 11189.0 PASS DP=345;AF=0.884058;SB=2;DP4=1,2,180,162;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aAa|T478K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 23013 . A C 16818.0 PASS DP=484;AF=0.917355;SB=5;DP4=3,0,256,224;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gCa|E484A|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512.2 23040 . A G 19461.0 PASS DP=580;AF=0.9;SB=3;DP4=0,1,298,278;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q493R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512.2 23048 . G A 24975.0 PASS DP=688;AF=0.953488;SB=0;DP4=0,0,358,330;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G496S|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 23055 . A G 22450.0 PASS DP=711;AF=0.857947;SB=0;DP4=0,0,367,342;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q498R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512.2 23063 . A T 30725.0 PASS DP=852;AF=0.965962;SB=0;DP4=0,0,446,406;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Tat|N501Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 23075 . T C 27264.0 PASS DP=854;AF=0.877049;SB=17;DP4=7,0,439,404;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y505H|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512.2 23202 . C A 44060.0 PASS DP=1267;AF=0.923441;SB=3;DP4=1,0,623,639;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aAa|T547K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 23267 . A G 87.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1634;AF=0.004896;SB=0;DP4=816,807,5,5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Gtt|I569V|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512.2 23403 . A G 49314.0 PASS DP=2451;AF=0.871889;SB=33;DP4=11,0,1208,1223;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D614G|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512.2 23517 . G A 119.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2138;AF=0.005145;SB=0;DP4=984,1104,6,6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGg/gAg|G652E|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 23525 . C T 49314.0 PASS DP=2152;AF=0.930762;SB=0;DP4=0,0,1022,1125;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H655Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 23568 . GTA G 62.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1434;AF=0.002789;SB=0;DP4=667,769,2,2;INDEL;HRUN=1;EFF=FRAME_SHIFT(HIGH||atatgc/|IC670|1273|S|protein_coding|CODING|GU280_gp02|1|G|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00)
NC_045512.2 23599 . T G 31844.0 PASS DP=946;AF=0.914376;SB=0;DP4=0,0,425,520;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N679K|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512.2 23604 . C A 27971.0 PASS DP=805;AF=0.934161;SB=2;DP4=0,2,361,440;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cAt|P681H|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 23948 . G T 21096.0 PASS DP=619;AF=0.898223;SB=0;DP4=1,0,326,285;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Tat|D796Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 24130 . C A 19310.0 PASS DP=581;AF=0.886403;SB=2;DP4=0,2,258,318;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaC/aaA|N856K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 24358 . C A 81.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1436;AF=0.004875;SB=15;DP4=721,695,4,13;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggC/ggA|G932|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 24424 . A T 49314.0 PASS DP=1483;AF=0.942684;SB=0;DP4=0,0,738,742;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caA/caT|Q954H|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 24435 . C CT 65.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1231;AF=0.003249;SB=0;DP4=602,640,2,2;INDEL;HRUN=3;EFF=FRAME_SHIFT(HIGH||tta/ttTa|L959F?|1273|S|protein_coding|CODING|GU280_gp02|1|CT|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00)
NC_045512.2 24442 . C T 95.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1181;AF=0.006774;SB=1;DP4=555,608,4,6;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N960|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 24469 . T A 49314.0 PASS DP=2035;AF=0.932678;SB=3;DP4=5,2,1013,1013;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaA|N969K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 24503 . C T 49314.0 PASS DP=2064;AF=0.935078;SB=0;DP4=2,2,995,1055;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L981F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 24594 . A AC 96.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1513;AF=0.003966;SB=0;DP4=755,752,3,3;INDEL;HRUN=2;EFF=FRAME_SHIFT(HIGH||caa/caCa|Q1011H?|1273|S|protein_coding|CODING|GU280_gp02|1|AC);LOF=(S|GU280_gp02|1|1.00)
NC_045512.2 24842 . G A 90.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=850;AF=0.008235;SB=0;DP4=443,398,4,4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V1094I|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 24858 . G A 101.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=930;AF=0.008602;SB=11;DP4=479,434,4,11;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGc/gAc|G1099D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 25000 . C T 21478.0 PASS DP=674;AF=0.881306;SB=9;DP4=0,4,334,330;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D1146|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 25531 . ATTG A 66.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1201;AF=0.003331;SB=0;DP4=594,603,2,2;INDEL;HRUN=2;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gttggc/ggc|VG48G|275|ORF3a|protein_coding|CODING|GU280_gp03|1|A|INFO_REALIGN_3_PRIME)
NC_045512.2 25533 . TG T 65.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1203;AF=0.003325;SB=0;DP4=595,604,2,2;INDEL;HRUN=1;EFF=FRAME_SHIFT(HIGH||gtt/|V48|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T);LOF=(ORF3a|GU280_gp03|1|1.00)
NC_045512.2 25584 . C T 39037.0 PASS DP=1141;AF=0.912358;SB=0;DP4=0,1,562,575;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T64|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
NC_045512.2 25650 . GTT G 134.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=924;AF=0.007576;SB=0;DP4=449,501,3,4;INDEL;HRUN=3;EFF=FRAME_SHIFT(HIGH||ttt/|F87|275|ORF3a|protein_coding|CODING|GU280_gp03|1|G|INFO_REALIGN_3_PRIME);LOF=(ORF3a|GU280_gp03|1|1.00)
NC_045512.2 25797 . C CA 110.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1398;AF=0.005007;SB=1;DP4=698,693,3,4;INDEL;HRUN=5;EFF=FRAME_SHIFT(HIGH||aac/aaAc|N137K?|275|ORF3a|protein_coding|CODING|GU280_gp03|1|CA|INFO_REALIGN_3_PRIME);LOF=(ORF3a|GU280_gp03|1|1.00)
NC_045512.2 26070 . A T 82.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2257;AF=0.003545;SB=28;DP4=1236,979,28,6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaA/gaT|E226D|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
NC_045512.2 26155 . GTTGTTAATCCAGTAATGGAACCAA G 83.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2865;AF=0.002094;SB=0;DP4=1438,1453,3,3;INDEL;HRUN=2;EFF=CODON_DELETION(MODERATE||gttaatccagtaatggaaccaatt/|VNPVMEPI256|275|ORF3a|protein_coding|CODING|GU280_gp03|1|G|INFO_REALIGN_3_PRIME)
NC_045512.2 26270 . C T 49314.0 PASS DP=2570;AF=0.922179;SB=3;DP4=1,0,1205,1359;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T9I|75|E|protein_coding|CODING|GU280_gp04|1|T)
NC_045512.2 26281 . ATAGT A 85.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=2571;AF=0.002334;SB=1;DP4=1217,1369,2,4;INDEL;HRUN=1;EFF=FRAME_SHIFT(HIGH||gttaat/|VN14|75|E|protein_coding|CODING|GU280_gp04|1|A|INFO_REALIGN_3_PRIME);LOF=(E|GU280_gp04|1|1.00)
NC_045512.2 26467 . G C 76.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=216;AF=0.027778;SB=0;DP4=105,101,3,3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Ctc|V75L|75|E|protein_coding|CODING|GU280_gp04|1|C)
NC_045512.2 26486 . TATA T 68.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=406;AF=0.019704;SB=0;DP4=200,198,4,4;INDEL;HRUN=1
NC_045512.2 26490 . T TC 67.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=406;AF=0.019704;SB=0;DP4=200,198,4,4;INDEL;HRUN=2
NC_045512.2 26530 . A G 13253.0 PASS DP=394;AF=0.916244;SB=0;DP4=0,0,194,197;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D3G|222|M|protein_coding|CODING|GU280_gp05|1|G)
NC_045512.2 26577 . C G 4011.0 PASS DP=136;AF=0.838235;SB=0;DP4=6,6,62,61;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q19E|222|M|protein_coding|CODING|GU280_gp05|1|G)
NC_045512.2 26709 . G A 13373.0 PASS DP=427;AF=0.847775;SB=0;DP4=2,2,197,224;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A63T|222|M|protein_coding|CODING|GU280_gp05|1|A)
NC_045512.2 26774 . GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT G 235.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=468;AF=0.021368;SB=1;DP4=222,243,4,6;INDEL;HRUN=2;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 26778 . TGTCTTGTA T 283.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=468;AF=0.025641;SB=1;DP4=218,240,5,7;INDEL;HRUN=1;EFF=FRAME_SHIFT(HIGH||tgtcttgtaggc/|CLVG86|222|M|protein_coding|CODING|GU280_gp05|1|T|INFO_REALIGN_3_PRIME);LOF=(M|GU280_gp05|1|1.00)
NC_045512.2 27259 . A C 38032.0 PASS DP=1159;AF=0.88956;SB=0;DP4=2,1,612,537;EFF=SYNONYMOUS_CODING(LOW|SILENT|Agg/Cgg|R20|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
NC_045512.2 27481 . C T 98.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1960;AF=0.004592;SB=2;DP4=953,991,4,7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L30F|121|ORF7a|protein_coding|CODING|GU280_gp07|1|T)
NC_045512.2 27807 . C T 49314.0 PASS DP=1697;AF=0.925162;SB=6;DP4=4,1,830,853;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L18|43|ORF7b|protein_coding|CODING|GU280_gp08|1|T)
NC_045512.2 28214 . C CT 91.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1382;AF=0.004342;SB=0;DP4=685,702,3,3;INDEL;HRUN=5;EFF=FRAME_SHIFT(HIGH||tta/ttTa|L109F?|121|ORF8|protein_coding|CODING|GU280_gp09|1|CT|INFO_REALIGN_3_PRIME);LOF=(ORF8|GU280_gp09|1|1.00)
NC_045512.2 28271 . A T 49314.0 PASS DP=2424;AF=0.909653;SB=4;DP4=1,3,1205,1198
NC_045512.2 28311 . C T 49314.0 PASS DP=2555;AF=0.789041;SB=26;DP4=8,28,1187,1286;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cTc|P13L|419|N|protein_coding|CODING|GU280_gp10|1|T)
NC_045512.2 28361 . GGAGAACGCA G 49314.0 PASS DP=2305;AF=0.802169;SB=2;DP4=229,238,876,973;INDEL;HRUN=2;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggagaacgcagt/ggt|GERS30G|419|N|protein_coding|CODING|GU280_gp10|1|G|INFO_REALIGN_3_PRIME)
NC_045512.2 28363 . AGAACGCAGT A 486.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1910;AF=0.017801;SB=57;DP4=900,990,30,4;INDEL;HRUN=1;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gaacgcagtggg/ggg|ERSG31G|419|N|protein_coding|CODING|GU280_gp10|1|A|INFO_REALIGN_3_PRIME)
NC_045512.2 28881 . G A 33203.0 PASS DP=948;AF=0.925106;SB=6;DP4=0,2,490,453;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aAg|R203K|419|N|protein_coding|CODING|GU280_gp10|1|A)
NC_045512.2 28882 . G A 31137.0 PASS DP=946;AF=0.884778;SB=19;DP4=0,6,487,440;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R203|419|N|protein_coding|CODING|GU280_gp10|1|A)
NC_045512.2 28883 . G C 32607.0 PASS DP=948;AF=0.920886;SB=6;DP4=3,0,486,458;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gga/Cga|G204R|419|N|protein_coding|CODING|GU280_gp10|1|C)
NC_045512.2 28987 . CCAA C 88.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=951;AF=0.005258;SB=0;DP4=483,488,2,3;INDEL;HRUN=2;EFF=CODON_DELETION(MODERATE||caa/|Q242|419|N|protein_coding|CODING|GU280_gp10|1|C|INFO_REALIGN_3_PRIME)
NC_045512.2 29081 . GTA G 140.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1105;AF=0.00724;SB=0;DP4=546,557,4,4;INDEL;HRUN=1;EFF=FRAME_SHIFT(HIGH||gta/|V270|419|N|protein_coding|CODING|GU280_gp10|1|G);LOF=(N|GU280_gp10|1|1.00)
NC_045512.2 29313 . AAGATCAAGTCATTTTGCTGAATAAGCAT A 105.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1312;AF=0.004573;SB=0;DP4=659,647,3,3;INDEL;HRUN=3;EFF=FRAME_SHIFT(HIGH||gatcaagtcattttgctgaataagcatatt/|DQVILLNKHI348|419|N|protein_coding|CODING|GU280_gp10|1|A|INFO_REALIGN_3_PRIME);LOF=(N|GU280_gp10|1|1.00)
NC_045512.2 29363 . CCA C 75.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1422;AF=0.003516;SB=0;DP4=710,711,3,2;INDEL;HRUN=3;EFF=FRAME_SHIFT(HIGH||ccacca/|PP364|419|N|protein_coding|CODING|GU280_gp10|1|C|INFO_REALIGN_3_PRIME);LOF=(N|GU280_gp10|1|1.00)
NC_045512.2 29386 . C CA 91.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1414;AF=0.004243;SB=0;DP4=701,707,3,3;INDEL;HRUN=5;EFF=FRAME_SHIFT(HIGH||aag/aaAg|K373K?|419|N|protein_coding|CODING|GU280_gp10|1|CA|INFO_REALIGN_3_PRIME);LOF=(N|GU280_gp10|1|1.00)
NC_045512.2 29426 . A G 77.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1350;AF=0.005185;SB=0;DP4=647,694,4,5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aga/Gga|R385G|419|N|protein_coding|CODING|GU280_gp10|1|G)
NC_045512.2 29580 . CT C 97.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1147;AF=0.005231;SB=0;DP4=591,556,3,3;INDEL;HRUN=4;EFF=FRAME_SHIFT(HIGH||ttt/|F9|38|ORF10|protein_coding|CODING|GU280_gp11|1|C|INFO_REALIGN_3_PRIME);LOF=(ORF10|GU280_gp11|1|1.00)
NC_045512.2 29660 . T C 200.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1373;AF=0.010197;SB=0;DP4=674,675,8,8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttt/Ctt|F35L|38|ORF10|protein_coding|CODING|GU280_gp11|1|C)
NC_045512.2 29687 . AGT A 170.0 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 DP=1282;AF=0.00702;SB=1;DP4=633,640,5,4;INDEL;HRUN=1