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sample-09.vcf
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sample-09.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/066/348/66348164/tmp/lofreq2_call_parallelzjngpncq/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_74,Description="Minimum SNV Quality (Phred) 74">
##FILTER=<ID=min_indelqual_59,Description="Minimum Indel Quality (Phred) 59">
##FILTER=<ID=min_snvqual_81,Description="Minimum SNV Quality (Phred) 81">
##FILTER=<ID=min_indelqual_65,Description="Minimum Indel Quality (Phred) 65">
##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 22:07:59 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 22:09:18 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/jwd02f/main/066/348/66348344/outputs/dataset_b0560374-ac2b-4413-85d4-d57d00739e7d.dat NC_045512.2 /data/dnb09/galaxy_db/files/7/0/3/dataset_7035947d-df70-432a-911f-d26afe290877.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 DP=1968;AF=0.932419;SB=0;DP4=2,3,978,980
NC_045512.2 401 . C T 89.0 PASS DP=7352;AF=0.001768;SB=37;DP4=3809,3517,17,1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L46F|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L46F|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L46F|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L46F|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T)
NC_045512.2 443 . GT G 275.0 PASS DP=7947;AF=0.002643;SB=0;DP4=4073,3847,11,10;INDEL;HRUN=4;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_045512.2 443 . GTT G 76.0 PASS DP=7947;AF=0.001007;SB=0;DP4=4073,3847,4,4;INDEL;HRUN=4;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_045512.2 463 . GC G 102.0 PASS DP=9354;AF=0.001069;SB=2;DP4=4835,4513,4,6;INDEL;HRUN=3;EFF=FRAME_SHIFT(HIGH||ccc/|P67|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ccc/|P67|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ccc/|P67|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ccc/|P67|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 300.0 PASS DP=9473;AF=0.002322;SB=0;DP4=4722,4727,11,11;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 . GGTCATGTTATGGTT G 505.0 PASS DP=9469;AF=0.003591;SB=0;DP4=4721,4726,17,17;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_045512.2 518 . ATGGTT A 106.0 PASS DP=9525;AF=0.00105;SB=0;DP4=4843,4855,5,5;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_045512.2 518 . ATG A 77.0 PASS DP=9525;AF=0.00084;SB=1;DP4=4843,4855,3,5;INDEL;HRUN=1;EFF=FRAME_SHIFT(HIGH||atg/|M85|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),FRAME_SHIFT(HIGH||atg/|M85|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON),FRAME_SHIFT(HIGH||atg/|M85|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON),FRAME_SHIFT(HIGH||atg/|M85|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 578 . G A 151.0 PASS DP=8839;AF=0.002489;SB=75;DP4=4408,4393,0,26;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G105S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G105S|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G105S|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G105S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A)
NC_045512.2 685 . AAAGTCATTT A 115.0 PASS DP=7032;AF=0.001422;SB=0;DP4=3501,3553,5,5;INDEL;HRUN=3;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 1887 . C T 94.0 PASS DP=7615;AF=0.002101;SB=19;DP4=3806,3769,18,5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A541V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A541V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A361V|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A361V|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 1931 . C T 149.0 PASS DP=8151;AF=0.002331;SB=35;DP4=4245,3872,19,2;EFF=STOP_GAINED(HIGH|NONSENSE|Caa/Taa|Q556*|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),STOP_GAINED(HIGH|NONSENSE|Caa/Taa|Q556*|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),STOP_GAINED(HIGH|NONSENSE|Caa/Taa|Q376*|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),STOP_GAINED(HIGH|NONSENSE|Caa/Taa|Q376*|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 2047 . T A 121.0 PASS DP=11700;AF=0.001624;SB=56;DP4=5841,5794,5,33;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaA|N594K|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaA|N594K|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaA|N414K|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaA|N414K|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 2117 . G A 93.0 PASS DP=9958;AF=0.001506;SB=35;DP4=4852,5064,3,21;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Agc|G618S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Agc|G618S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Agc|G438S|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Agc|G438S|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 2202 . G A 85.0 PASS DP=6479;AF=0.002006;SB=47;DP4=3338,3116,0,15;EFF=STOP_GAINED(HIGH|NONSENSE|tGg/tAg|W646*|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),STOP_GAINED(HIGH|NONSENSE|tGg/tAg|W646*|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),STOP_GAINED(HIGH|NONSENSE|tGg/tAg|W466*|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),STOP_GAINED(HIGH|NONSENSE|tGg/tAg|W466*|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.04);NMD=(ORF1ab|GU280_gp01|28|0.04)
NC_045512.2 2330 . T A 129.0 PASS DP=4352;AF=0.003217;SB=2;DP4=2142,2162,13,10;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 2403 . CA C 73.0 PASS DP=4381;AF=0.00137;SB=0;DP4=2187,2188,3,3;INDEL;HRUN=3;EFF=FRAME_SHIFT(HIGH||aag/|K714|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aag/|K714|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aag/|K534|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aag/|K534|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 2477 . G A 82.0 PASS DP=2269;AF=0.003526;SB=22;DP4=1030,1229,0,9;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gaa/Aaa|E738K|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gaa/Aaa|E738K|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gaa/Aaa|E558K|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gaa/Aaa|E558K|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 2637 . T A 83.0 PASS DP=7832;AF=0.00166;SB=53;DP4=3905,3881,3,28;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTc/cAc|L791H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTc/cAc|L791H|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTc/cAc|L611H|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTc/cAc|L611H|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 2710 . CA C 112.0 PASS DP=7951;AF=0.001258;SB=0;DP4=3976,3977,5,5;INDEL;HRUN=3;EFF=FRAME_SHIFT(HIGH||aaa/|K816|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K816|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K636|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K636|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 2832 . A G 49314.0 PASS DP=4590;AF=0.930937;SB=8;DP4=1,6,2140,2433;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 3036 . TC T 85.0 PASS DP=2796;AF=0.002146;SB=0;DP4=1347,1447,3,3;INDEL;HRUN=1;EFF=FRAME_SHIFT(HIGH||ttc/|F924|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),FRAME_SHIFT(HIGH||ttc/|F924|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),FRAME_SHIFT(HIGH||ttc/|F106|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),FRAME_SHIFT(HIGH||ttc/|F106|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.14)
NC_045512.2 3037 . C T 49314.0 PASS DP=2796;AF=0.935265;SB=0;DP4=1,1,1341,1436;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 3722 . AT A 75.0 PASS DP=4484;AF=0.001561;SB=0;DP4=2140,2345,3,4;INDEL;HRUN=5;EFF=FRAME_SHIFT(HIGH||ttt/|F1154|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F1154|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F336|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F336|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 4174 . TA T 163.0 PASS DP=3443;AF=0.003485;SB=0;DP4=1715,1716,6,6;INDEL;HRUN=5;EFF=FRAME_SHIFT(HIGH||aag/|K1305|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aag/|K1305|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aag/|K487|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aag/|K487|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14)
NC_045512.2 4825 . T C 105.0 PASS DP=8193;AF=0.001831;SB=0;DP4=4087,4084,8,8;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S1520|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S1520|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S702|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S702|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 4975 . G A 91.0 PASS DP=7517;AF=0.001995;SB=60;DP4=3763,3726,0,20;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V1570|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V1570|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V752|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V752|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 5085 . TA T 101.0 PASS DP=8812;AF=0.001135;SB=0;DP4=4411,4403,5,5;INDEL;HRUN=4;EFF=FRAME_SHIFT(HIGH||aaa/|K1608|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K1608|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K790|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K790|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 5157 . CT C 100.0 PASS DP=8873;AF=0.001127;SB=0;DP4=4459,4459,5,5;INDEL;HRUN=4;EFF=FRAME_SHIFT(HIGH||ttt/|F1632|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F1632|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F814|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F814|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 5386 . T G 49314.0 PASS DP=7052;AF=0.914634;SB=0;DP4=5,4,3519,3509;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 5595 . A T 82.0 PASS DP=6966;AF=0.001723;SB=43;DP4=3426,3498,23,3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gTa|E1777V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gTa|E1777V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gTa|E959V|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gTa|E959V|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 5743 . G C 4413.0 PASS DP=9956;AF=0.027923;SB=0;DP4=4827,4814,152,152;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 4263.0 PASS DP=9950;AF=0.027437;SB=1;DP4=4805,4819,156,149;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 6148 . T C 122.0 PASS DP=3054;AF=0.005566;SB=11;DP4=1425,1600,7,18;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P1961|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P1961|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P1143|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P1143|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 6512 . AGTT A 49314.0 PASS DP=2638;AF=0.992419;SB=3;DP4=11,7,1354,1264;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 7246 . GT G 112.0 PASS DP=5407;AF=0.001849;SB=0;DP4=2720,2715,5,5;INDEL;HRUN=5;EFF=FRAME_SHIFT(HIGH||ttg/|L2329|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L2329|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L1511|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L1511|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14)
NC_045512.2 7813 . TTC T 70.0 PASS DP=5121;AF=0.001172;SB=0;DP4=2600,2520,3,3;INDEL;HRUN=2;EFF=FRAME_SHIFT(HIGH||tctcat/|SH2519|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tctcat/|SH2519|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tctcat/|SH1701|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tctcat/|SH1701|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14)
NC_045512.2 8376 . CA C 103.0 PASS DP=4699;AF=0.001915;SB=1;DP4=2567,2120,4,5;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 49314.0 PASS DP=5402;AF=0.935579;SB=1;DP4=4,2,2952,2424;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 8464 . TA T 74.0 PASS DP=7163;AF=0.001117;SB=0;DP4=3579,3576,4,4;INDEL;HRUN=5;EFF=FRAME_SHIFT(HIGH||aag/|K2735|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aag/|K2735|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aag/|K1917|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aag/|K1917|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 9166 . C T 323.0 PASS DP=3795;AF=0.007378;SB=0;DP4=1879,1880,17,16;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T2967|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T2967|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T204|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T204|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=8452;AF=0.88831;SB=9;DP4=2,7,4219,4189;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 144.0 PASS DP=7296;AF=0.002467;SB=1;DP4=3626,3629,12,9;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 10449 . C A 49314.0 PASS DP=6718;AF=0.898035;SB=35;DP4=4,23,3302,3357;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 382.0 PASS DP=5387;AF=0.006497;SB=0;DP4=2861,2476,23,20;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 341.0 PASS DP=7183;AF=0.004733;SB=13;DP4=3627,3488,22,36;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 10563 . G A 98.0 PASS DP=7572;AF=0.001849;SB=10;DP4=3771,3770,5,13;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gAa|G3433E|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gAa|G3433E|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gAa|G170E|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gAa|G170E|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 10594 . CT C 111.0 PASS DP=7640;AF=0.00144;SB=0;DP4=3821,3826,5,6;INDEL;HRUN=4;EFF=FRAME_SHIFT(HIGH||tat/|Y3445|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tat/|Y3445|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tat/|Y182|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tat/|Y182|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14)
NC_045512.2 10605 . CT C 167.0 PASS DP=7578;AF=0.001847;SB=0;DP4=3792,3798,7,7;INDEL;HRUN=4;EFF=FRAME_SHIFT(HIGH||ttt/|F3448|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F3448|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F185|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F185|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14)
NC_045512.2 10932 . CT C 67.0 PASS DP=5881;AF=0.00119;SB=1;DP4=2974,2968,3,4;INDEL;HRUN=4;EFF=FRAME_SHIFT(HIGH||ttt/|F3557|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F3557|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F294|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F294|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 11074 . C CT 546.0 PASS DP=7429;AF=0.01023;SB=0;DP4=3943,3551,40,36;INDEL;HRUN=8;EFF=FRAME_SHIFT(HIGH||ttg/ttTg|L3606F?|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|CT|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/ttTg|L3606F?|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|CT|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/ttTg|L37F?|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|CT|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/ttTg|L37F?|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|CT|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14)
NC_045512.2 11074 . CT C 5355.0 PASS DP=7429;AF=0.052093;SB=0;DP4=3775,3400,204,183;INDEL;HRUN=8;EFF=FRAME_SHIFT(HIGH||ttg/|L3606|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L3606|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L37|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L37|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14)
NC_045512.2 11082 . TG T 102.0 PASS DP=7394;AF=0.001352;SB=2;DP4=3864,3538,4,6;INDEL;HRUN=1;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 11211 . AT A 71.0 PASS DP=9814;AF=0.000815;SB=0;DP4=4897,4909,4,4;INDEL;HRUN=4;EFF=FRAME_SHIFT(HIGH||ttt/|F3650|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F3650|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F81|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F81|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14)
NC_045512.2 11282 . AGTTTGTCTG A 49314.0 PASS DP=8567;AF=0.930781;SB=8;DP4=269,323,3871,4103;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 11521 . GT G 89.0 PASS DP=9272;AF=0.001079;SB=0;DP4=4664,4667,5,5;INDEL;HRUN=5;EFF=FRAME_SHIFT(HIGH||ttg/|L3754|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L3754|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L185|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L185|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 11537 . A G 49314.0 PASS DP=9217;AF=0.932299;SB=1;DP4=2,4,4595,4599;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 11653 . CT C 85.0 PASS DP=6467;AF=0.001237;SB=0;DP4=3034,3430,4,4;INDEL;HRUN=4;EFF=FRAME_SHIFT(HIGH||tgt/|C3798|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tgt/|C3798|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tgt/|C229|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tgt/|C229|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14)
NC_045512.2 11679 . G A 110.0 PASS DP=7146;AF=0.002239;SB=35;DP4=3436,3681,1,16;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGa/aAa|R3805K|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGa/aAa|R3805K|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGa/aAa|R236K|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGa/aAa|R236K|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 12242 . C T 178.0 PASS DP=5768;AF=0.003467;SB=0;DP4=2686,3044,12,13;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R3993C|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R3993C|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R51C|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R51C|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 12410 . A G 124.0 PASS DP=7083;AF=0.002259;SB=0;DP4=3523,3522,10,9;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Gtc|I4049V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Gtc|I4049V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Gtc|I107V|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Gtc|I107V|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 13078 . T C 85.0 PASS DP=9859;AF=0.00142;SB=0;DP4=4909,4906,9,7;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A4271|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A4271|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A18|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A18|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 13123 . TG T 145.0 PASS DP=8657;AF=0.001617;SB=0;DP4=4151,4504,7,7;INDEL;HRUN=5;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 13195 . T C 49314.0 PASS DP=9555;AF=0.917739;SB=6;DP4=8,3,5025,4515;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 13282 . TA T 76.0 PASS DP=10623;AF=0.000753;SB=0;DP4=5312,5303,4,4;INDEL;HRUN=3;EFF=FRAME_SHIFT(HIGH||aaa/|K4340|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K4340|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K87|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K87|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 13459 . GT G 79.0 PASS DP=7345;AF=0.001225;SB=0;DP4=3317,4092,4,5;INDEL;HRUN=5;EFF=FRAME_SHIFT(HIGH||tta/|L4400|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tta/|L4400|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tta/|L8|12|ORF1ab|protein_coding|CODING|YP_009725312.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tta/|L8|931|ORF1ab|protein_coding|CODING|YP_009725307.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 14407 . CCTACAAG C 90.0 PASS DP=5526;AF=0.001629;SB=1;DP4=2934,2709,4,5;INDEL;HRUN=2;EFF=FRAME_SHIFT(HIGH||cctacaagt/|PTS4715|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),FRAME_SHIFT(HIGH||cctacaagt/|PTS323|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|C|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 14408 . C T 49314.0 PASS DP=5527;AF=0.945359;SB=0;DP4=2,1,2871,2636;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 14432 . GA G 148.0 PASS DP=4843;AF=0.002478;SB=0;DP4=2570,2261,6,6;INDEL;HRUN=5;EFF=FRAME_SHIFT(HIGH||ata/|I4725|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ata/|I333|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 15106 . A C 162.0 PASS DP=5069;AF=0.003551;SB=728;DP4=2566,2233,0,227;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acc/Ccc|T4948P|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acc/Ccc|T556P|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 15157 . CA C 98.0 PASS DP=5177;AF=0.001738;SB=0;DP4=2602,2566,5,4;INDEL;HRUN=5;EFF=FRAME_SHIFT(HIGH||aaa/|K4966|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K574|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 15240 . C T 49314.0 PASS DP=4662;AF=0.939296;SB=0;DP4=2,2,2217,2432;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 15521 . T A 327.0 PASS DP=328;AF=0.04878;SB=0;DP4=151,161,8,8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTt/tAt|F5086Y|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTt/tAt|F694Y|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 15579 . CA C 100.0 PASS DP=3972;AF=0.002014;SB=0;DP4=2154,1812,4,4;INDEL;HRUN=4;EFF=FRAME_SHIFT(HIGH||att/|I5107|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||att/|I715|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 15738 . C T 187.0 PASS DP=9393;AF=0.002449;SB=1;DP4=4668,4676,15,13;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F5158|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F766|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 15830 . CA C 78.0 PASS DP=7977;AF=0.001003;SB=0;DP4=3836,4195,4,4;INDEL;HRUN=4;EFF=FRAME_SHIFT(HIGH||aaa/|K5190|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K798|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 15983 . TA T 168.0 PASS DP=9569;AF=0.001672;SB=0;DP4=4954,4601,8,8;INDEL;HRUN=5;EFF=FRAME_SHIFT(HIGH||aca/|T5242|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aca/|T850|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 16215 . C T 82.0 PASS DP=14679;AF=0.001294;SB=0;DP4=7154,7469,14,13;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y5317|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y925|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 16837 . GA G 66.0 PASS DP=9291;AF=0.000861;SB=0;DP4=4794,4489,4,4;INDEL;HRUN=5;EFF=FRAME_SHIFT(HIGH||aaa/|K5526|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K202|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 17068 . T A 177.0 PASS DP=10381;AF=0.002312;SB=87;DP4=5003,5325,1,35;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tct/Act|S5602T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tct/Act|S278T|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 17079 . G A 198.0 PASS DP=9461;AF=0.002748;SB=62;DP4=4540,4873,1,26;EFF=SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q5605|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q281|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 17144 . G A 251.0 PASS DP=4667;AF=0.005142;SB=9;DP4=2336,2301,9,17;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R5627H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R303H|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 17285 . C T 27513.0 PASS DP=5402;AF=0.19104;SB=0;DP4=2113,2216,520,545;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S5674L|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S350L|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 17652 . TA T 71.0 PASS DP=6476;AF=0.001081;SB=1;DP4=3244,3234,3,4;INDEL;HRUN=4;EFF=FRAME_SHIFT(HIGH||atg/|M5798|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||atg/|M474|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 17723 . TA T 75.0 PASS DP=3621;AF=0.001657;SB=0;DP4=1844,1773,3,3;INDEL;HRUN=2;EFF=FRAME_SHIFT(HIGH||aga/|R5821|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aga/|R497|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 18163 . A G 43398.0 PASS DP=1276;AF=0.927116;SB=0;DP4=0,0,638,636;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 18687 . CT C 221.0 PASS DP=5361;AF=0.002985;SB=0;DP4=2727,2662,8,8;INDEL;HRUN=4;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 19066 . C T 108.0 PASS DP=10531;AF=0.001614;SB=28;DP4=5237,5257,19,4;EFF=STOP_GAINED(HIGH|NONSENSE|Caa/Taa|Q6268*|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),STOP_GAINED(HIGH|NONSENSE|Caa/Taa|Q343*|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 19188 . AT A 106.0 PASS DP=7679;AF=0.001302;SB=0;DP4=3680,4009,5,5;INDEL;HRUN=4;EFF=FRAME_SHIFT(HIGH||tgg/|W6310|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tgg/|W385|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2 19387 . A T 104.0 PASS DP=1733;AF=0.005193;SB=0;DP4=857,860,5,5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agt/Tgt|S6375C|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agt/Tgt|S450C|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 20360 . GT G 74.0 PASS DP=6936;AF=0.001009;SB=0;DP4=3407,3738,3,4;INDEL;HRUN=3;EFF=FRAME_SHIFT(HIGH||tta/|L6700|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tta/|L248|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 20464 . G A 107.0 PASS DP=6735;AF=0.002227;SB=35;DP4=3325,3389,1,16;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D6734N|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D282N|345|ORF1ab|protein_coding|CODING|YP_009725310.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 20625 . TG T 66.0 PASS DP=5540;AF=0.001083;SB=0;DP4=2768,2768,3,3;INDEL;HRUN=2;EFF=FRAME_SHIFT(HIGH||ggc/|G6788|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ggc/|G336|345|ORF1ab|protein_coding|CODING|YP_009725310.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME)
NC_045512.2 20930 . C T 91.0 PASS DP=4828;AF=0.002486;SB=3;DP4=2400,2407,9,6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T6889M|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T91M|297|ORF1ab|protein_coding|CODING|YP_009725311.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 21123 . GT G 96.0 PASS DP=5416;AF=0.001477;SB=0;DP4=2767,2683,4,4;INDEL;HRUN=3;EFF=FRAME_SHIFT(HIGH||ttt/|F6954|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F156|297|ORF1ab|protein_coding|CODING|YP_009725311.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.04)
NC_045512.2 21651 . A G 90.0 PASS DP=8050;AF=0.001739;SB=5;DP4=4032,3976,13,7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aGt|N30S|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512.2 21740 . TCCAATGTTACTTGGTTCCATGCTATACATGTCTCTGGGA T 633.0 PASS DP=6125;AF=0.005878;SB=0;DP4=3046,3043,18,18;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 49314.0 PASS DP=5640;AF=0.944681;SB=0;DP4=2,3,2781,2797;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A67V|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 21764 . ATACATG A 49314.0 PASS DP=5441;AF=0.990443;SB=3;DP4=26,33,2696,2693;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 21834 . AT A 66.0 PASS DP=4681;AF=0.001282;SB=0;DP4=2307,2382,3,3;INDEL;HRUN=4;EFF=FRAME_SHIFT(HIGH||ttt/|F92|1273|S|protein_coding|CODING|GU280_gp02|1|A|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00)
NC_045512.2 21846 . C T 49314.0 PASS DP=4500;AF=0.944222;SB=0;DP4=1,2,2201,2290;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T95I|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 21890 . TTA T 72.0 PASS DP=3537;AF=0.001696;SB=0;DP4=1742,1835,3,3;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 121.0 PASS DP=2979;AF=0.004028;SB=1;DP4=1548,1415,7,5;INDEL;HRUN=3;EFF=CODON_DELETION(MODERATE||ggtgtttat/|GVY142|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512.2 21986 . GGTGTTTATT G 49314.0 PASS DP=2935;AF=0.989097;SB=5;DP4=35,41,1522,1381;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 21987 . GTGTTTATTA G 82.0 PASS DP=2935;AF=0.003407;SB=0;DP4=1534,1390,5,5;INDEL;HRUN=1;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggtgtttattac/ggc|GVYY142G|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512.2 22104 . GA G 101.0 PASS DP=4004;AF=0.001998;SB=0;DP4=2044,2046,4,4;INDEL;HRUN=4;EFF=FRAME_SHIFT(HIGH||aaa/|K182|1273|S|protein_coding|CODING|GU280_gp02|1|G|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00)
NC_045512.2 22193 . AATT A 49314.0 PASS DP=3283;AF=0.911666;SB=77;DP4=465,702,1483,1510;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 49314.0 PASS DP=2765;AF=0.798192;SB=1;DP4=239,265,1069,1138;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 TGAGCCTGAA 83.0 PASS DP=2765;AF=0.00217;SB=1;DP4=239,265,2,4;INDEL;HRUN=1;EFF=CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||gat/gaGCCTGAAGAt|D215EPED|1273|S|protein_coding|CODING|GU280_gp02|1|TGAGCCTGAA|INFO_REALIGN_3_PRIME)
NC_045512.2 22204 . T TGAGCAAGAA 118.0 PASS DP=2765;AF=0.002893;SB=5;DP4=239,265,2,6;INDEL;HRUN=1;EFF=CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||gat/gaGCAAGAAGAt|D215EQED|1273|S|protein_coding|CODING|GU280_gp02|1|TGAGCAAGAA|INFO_REALIGN_3_PRIME)
NC_045512.2 22204 . T TGAGCCAGCA 81.0 PASS DP=2765;AF=0.00217;SB=0;DP4=239,265,3,3;INDEL;HRUN=1;EFF=CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||gat/gaGCCAGCAGAt|D215EPAD|1273|S|protein_coding|CODING|GU280_gp02|1|TGAGCCAGCA|INFO_REALIGN_3_PRIME)
NC_045512.2 22204 . T TGATCCAGAA 118.0 PASS DP=2765;AF=0.002893;SB=15;DP4=239,265,7,1;INDEL;HRUN=1;EFF=CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||ctc/cCAGAAGATCtc|L216PEDL|1273|S|protein_coding|CODING|GU280_gp02|1|TGATCCAGAA|INFO_REALIGN_3_PRIME)
NC_045512.2 22578 . G A 49314.0 PASS DP=4984;AF=0.95004;SB=0;DP4=2,1,2486,2484;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G339D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 22583 . GT G 85.0 PASS DP=4986;AF=0.001604;SB=0;DP4=2495,2491,4,4;INDEL;HRUN=5;EFF=FRAME_SHIFT(HIGH||ttt/|F342|1273|S|protein_coding|CODING|GU280_gp02|1|G|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00)
NC_045512.2 22661 . G T 49314.0 PASS DP=3934;AF=0.593035;SB=1;DP4=719,740,1233,1239;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Ttc|V367F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 22667 . T C 6108.0 PASS DP=3505;AF=0.079886;SB=0;DP4=1568,1637,145,153;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tat/Cat|Y369H|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512.2 22673 . T C 49314.0 PASS DP=2517;AF=0.923321;SB=1;DP4=14,16,1057,1426;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tcc/Ccc|S371P|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512.2 22674 . C T 49314.0 PASS DP=2510;AF=0.892829;SB=1;DP4=1,3,1062,1422;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S371F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 22679 . T C 49314.0 PASS DP=2660;AF=0.92782;SB=3;DP4=1,0,1142,1512;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Cca|S373P|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512.2 22686 . C T 49314.0 PASS DP=2692;AF=0.945765;SB=0;DP4=2,4,1149,1531;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S375F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 22713 . C T 3289.0 PASS DP=2252;AF=0.068384;SB=0;DP4=913,1175,68,92;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P384L|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 22992 . G A 49314.0 PASS DP=1670;AF=0.929341;SB=0;DP4=0,0,896,764;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S477N|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 22995 . C A 49314.0 PASS DP=1694;AF=0.929162;SB=9;DP4=0,3,902,783;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aAa|T478K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 23013 . A C 49314.0 PASS DP=2402;AF=0.939217;SB=0;DP4=2,2,1303,1092;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gCa|E484A|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512.2 23040 . A G 49314.0 PASS DP=3058;AF=0.942446;SB=6;DP4=0,2,1608,1445;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q493R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512.2 23048 . G A 49314.0 PASS DP=3572;AF=0.959406;SB=0;DP4=4,4,1872,1690;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G496S|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 23055 . A G 49314.0 PASS DP=3703;AF=0.923035;SB=3;DP4=0,1,1940,1755;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q498R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512.2 23063 . A T 49314.0 PASS DP=4339;AF=0.952985;SB=3;DP4=0,1,2283,2047;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Tat|N501Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 23075 . T C 49314.0 PASS DP=4435;AF=0.928523;SB=3;DP4=5,2,2313,2110;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y505H|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512.2 23143 . TA T 87.0 PASS DP=6215;AF=0.001448;SB=0;DP4=3104,3103,5,4;INDEL;HRUN=5;EFF=FRAME_SHIFT(HIGH||aag/|K529|1273|S|protein_coding|CODING|GU280_gp02|1|T|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00)
NC_045512.2 23201 . AC A 82.0 PASS DP=6121;AF=0.001307;SB=2;DP4=3058,3068,5,3;INDEL;HRUN=1;EFF=FRAME_SHIFT(HIGH||aca/|T547|1273|S|protein_coding|CODING|GU280_gp02|1|A);LOF=(S|GU280_gp02|1|1.00)
NC_045512.2 23202 . C A 49314.0 PASS DP=6121;AF=0.94527;SB=3;DP4=0,2,3043,3065;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aAa|T547K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 23230 . CA C 84.0 PASS DP=5328;AF=0.001502;SB=0;DP4=2634,2742,4,4;INDEL;HRUN=5;EFF=FRAME_SHIFT(HIGH||aag/|K558|1273|S|protein_coding|CODING|GU280_gp02|1|C|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00)
NC_045512.2 23403 . A G 49314.0 PASS DP=9967;AF=0.93027;SB=5;DP4=5,2,4961,4973;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D614G|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512.2 23525 . C T 49314.0 PASS DP=8263;AF=0.943483;SB=0;DP4=0,1,3975,4269;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H655Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 23540 . T C 93.0 PASS DP=7325;AF=0.001911;SB=3;DP4=3426,3860,10,8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tat/Cat|Y660H|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512.2 23599 . T G 49314.0 PASS DP=3513;AF=0.936806;SB=0;DP4=1,1,1624,1882;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N679K|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512.2 23604 . C A 49314.0 PASS DP=2953;AF=0.932611;SB=3;DP4=2,5,1348,1592;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cAt|P681H|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 23854 . C A 224.0 PASS DP=6;AF=1;SB=0;DP4=0,0,3,3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaC/aaA|N764K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 23948 . G T 49314.0 PASS DP=1559;AF=0.917896;SB=2;DP4=2,1,760,790;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Tat|D796Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 24130 . C A 49314.0 PASS DP=2618;AF=0.911001;SB=0;DP4=0,1,1249,1355;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaC/aaA|N856K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 24320 . CA C 126.0 PASS DP=7381;AF=0.001626;SB=0;DP4=3690,3685,6,6;INDEL;HRUN=5;EFF=FRAME_SHIFT(HIGH||aaa/|K921|1273|S|protein_coding|CODING|GU280_gp02|1|C|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00)
NC_045512.2 24424 . A T 49314.0 PASS DP=7163;AF=0.94667;SB=14;DP4=1,7,3581,3571;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caA/caT|Q954H|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 24469 . T A 49314.0 PASS DP=7536;AF=0.92768;SB=28;DP4=17,3,3741,3757;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=7699;AF=0.934407;SB=6;DP4=5,11,3746,3922;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L981F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 24530 . G A 113.0 PASS DP=7291;AF=0.002057;SB=50;DP4=3514,3754,0,18;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gaa/Aaa|E990K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 24672 . CA C 127.0 PASS DP=5402;AF=0.002036;SB=1;DP4=2695,2700,6,5;INDEL;HRUN=5;EFF=FRAME_SHIFT(HIGH||aga/|R1039|1273|S|protein_coding|CODING|GU280_gp02|1|C|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00)
NC_045512.2 24798 . C T 107.0 PASS DP=4203;AF=0.003093;SB=18;DP4=2137,2048,12,2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P1079L|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 24858 . G A 100.0 PASS DP=4472;AF=0.002683;SB=5;DP4=2287,2150,9,14;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGc/gAc|G1099D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 24878 . CA C 102.0 PASS DP=4832;AF=0.001656;SB=0;DP4=2466,2427,4,4;INDEL;HRUN=3;EFF=FRAME_SHIFT(HIGH||agg/|R1107|1273|S|protein_coding|CODING|GU280_gp02|1|C|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00)
NC_045512.2 25000 . C T 49314.0 PASS DP=4335;AF=0.928028;SB=12;DP4=0,5,2160,2161;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D1146|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 25381 . A C 85.0 PASS DP=6731;AF=0.002228;SB=2;DP4=3399,3305,10,7;EFF=SYNONYMOUS_CODING(LOW|SILENT|acA/acC|T1273|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512.2 25584 . C T 49314.0 PASS DP=6203;AF=0.90956;SB=3;DP4=2,5,3086,3088;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T64|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
NC_045512.2 25613 . C T 206.0 PASS DP=6306;AF=0.003647;SB=4;DP4=2900,3363,11,19;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S74F|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
NC_045512.2 25771 . C T 81.0 PASS DP=6266;AF=0.001915;SB=12;DP4=3250,2989,13,4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L127F|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
NC_045512.2 25797 . CA C 313.0 PASS DP=6569;AF=0.003654;SB=0;DP4=3274,3271,12,12;INDEL;HRUN=5;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 26211 . G A 100.0 PASS DP=9850;AF=0.001827;SB=54;DP4=4910,4901,0,19;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V273|275|ORF3a|protein_coding|CODING|GU280_gp03|1|A)
NC_045512.2 26270 . C T 49314.0 PASS DP=8324;AF=0.918549;SB=2;DP4=6,10,3860,4424;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T9I|75|E|protein_coding|CODING|GU280_gp04|1|T)
NC_045512.2 26325 . G A 297.0 PASS DP=6204;AF=0.004674;SB=59;DP4=2641,3519,1,30;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttG/ttA|L27|75|E|protein_coding|CODING|GU280_gp04|1|A)
NC_045512.2 26440 . A T 85.0 PASS DP=3050;AF=0.002951;SB=36;DP4=1507,1524,12,0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Tat|N66Y|75|E|protein_coding|CODING|GU280_gp04|1|T)
NC_045512.2 26461 . C T 102.0 PASS DP=2637;AF=0.003792;SB=0;DP4=1275,1349,6,6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L73F|75|E|protein_coding|CODING|GU280_gp04|1|T)
NC_045512.2 26530 . A G 49314.0 PASS DP=2720;AF=0.924265;SB=0;DP4=0,0,1319,1395;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D3G|222|M|protein_coding|CODING|GU280_gp05|1|G)
NC_045512.2 26577 . C G 39597.0 PASS DP=1149;AF=0.929504;SB=0;DP4=2,2,560,581;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q19E|222|M|protein_coding|CODING|GU280_gp05|1|G)
NC_045512.2 26709 . G A 14818.0 PASS DP=448;AF=0.895089;SB=1;DP4=2,3,227,209;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A63T|222|M|protein_coding|CODING|GU280_gp05|1|A)
NC_045512.2 26767 . T C 171.0 PASS DP=496;AF=0.020161;SB=0;DP4=245,239,5,5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTc/aCc|I82T|222|M|protein_coding|CODING|GU280_gp05|1|C)
NC_045512.2 27259 . A C 49314.0 PASS DP=5010;AF=0.938124;SB=1;DP4=2,3,2617,2385;EFF=SYNONYMOUS_CODING(LOW|SILENT|Agg/Cgg|R20|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
NC_045512.2 27384 . T C 198.0 PASS DP=6663;AF=0.003602;SB=0;DP4=3312,3312,14,13;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D61|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
NC_045512.2 27605 . TA T 104.0 PASS DP=3640;AF=0.002198;SB=0;DP4=1818,1818,4,4;INDEL;HRUN=4;EFF=FRAME_SHIFT(HIGH||aaa/|K72|121|ORF7a|protein_coding|CODING|GU280_gp07|1|T|INFO_REALIGN_3_PRIME);LOF=(ORF7a|GU280_gp07|1|1.00)
NC_045512.2 27807 . C T 49314.0 PASS DP=7410;AF=0.94251;SB=3;DP4=2,4,3695,3683;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L18|43|ORF7b|protein_coding|CODING|GU280_gp08|1|T)
NC_045512.2 27984 . T C 98.0 PASS DP=5560;AF=0.002338;SB=3;DP4=2551,2976,7,12;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tat/Cat|Y31H|121|ORF8|protein_coding|CODING|GU280_gp09|1|C)
NC_045512.2 28001 . G A 92.0 PASS DP=4726;AF=0.002539;SB=0;DP4=2151,2552,6,9;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P36|121|ORF8|protein_coding|CODING|GU280_gp09|1|A)
NC_045512.2 28250 . T TG 2905.0 PASS DP=8012;AF=0.024713;SB=3;DP4=4125,4003,106,92;INDEL;HRUN=3;EFF=FRAME_SHIFT(HIGH||ttc/Gttc|F120V?|121|ORF8|protein_coding|CODING|GU280_gp09|1|TG)
NC_045512.2 28251 . T G 9019.0 PASS DP=8013;AF=0.061525;SB=2;DP4=3794,3643,271,277;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttc/Gtc|F120V|121|ORF8|protein_coding|CODING|GU280_gp09|1|G)
NC_045512.2 28253 . CA C 2970.0 PASS DP=8033;AF=0.025022;SB=3;DP4=3963,3875,107,94;INDEL;HRUN=1;EFF=FRAME_SHIFT(HIGH||atc/|I121|121|ORF8|protein_coding|CODING|GU280_gp09|1|C)
NC_045512.2 28253 . C T 9090.0 PASS DP=8039;AF=0.06145;SB=1;DP4=3789,3687,272,276;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F120|121|ORF8|protein_coding|CODING|GU280_gp09|1|T)
NC_045512.2 28254 . A C 10854.0 PASS DP=8054;AF=0.062702;SB=4;DP4=3686,3593,271,286;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Ctc|I121L|121|ORF8|protein_coding|CODING|GU280_gp09|1|C)
NC_045512.2 28271 . A T 49314.0 PASS DP=9205;AF=0.948723;SB=16;DP4=1,9,4592,4591
NC_045512.2 28311 . C T 49314.0 PASS DP=9355;AF=0.878033;SB=27;DP4=5,22,4543,4741;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=8154;AF=0.841182;SB=3;DP4=611,693,3292,3567;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 496.0 PASS DP=6970;AF=0.00703;SB=72;DP4=3333,3606,42,7;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 28720 . C T 110.0 PASS DP=6341;AF=0.002366;SB=0;DP4=3158,3156,11,10;EFF=SYNONYMOUS_CODING(LOW|SILENT|cgC/cgT|R149|419|N|protein_coding|CODING|GU280_gp10|1|T)
NC_045512.2 28881 . G A 49314.0 PASS DP=3638;AF=0.917262;SB=0;DP4=3,2,1833,1786;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aAg|R203K|419|N|protein_coding|CODING|GU280_gp10|1|A)
NC_045512.2 28882 . G A 49314.0 PASS DP=3628;AF=0.888093;SB=4;DP4=4,7,1829,1759;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R203|419|N|protein_coding|CODING|GU280_gp10|1|A)
NC_045512.2 28883 . G C 49314.0 PASS DP=3630;AF=0.934435;SB=0;DP4=3,3,1828,1789;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gga/Cga|G204R|419|N|protein_coding|CODING|GU280_gp10|1|C)
NC_045512.2 28936 . G T 100.0 PASS DP=4155;AF=0.002647;SB=748;DP4=1885,2014,248,0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttT|L221F|419|N|protein_coding|CODING|GU280_gp10|1|T)
NC_045512.2 28981 . T G 94.0 PASS DP=5123;AF=0.002342;SB=994;DP4=2196,2574,323,2;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggT/ggG|G236|419|N|protein_coding|CODING|GU280_gp10|1|G)
NC_045512.2 28987 . CCAA C 115.0 PASS DP=5117;AF=0.001759;SB=0;DP4=2575,2627,4,5;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 29127 . AT A 118.0 PASS DP=3849;AF=0.002338;SB=0;DP4=1842,2003,4,5;INDEL;HRUN=4;EFF=FRAME_SHIFT(HIGH||ttt/|F286|419|N|protein_coding|CODING|GU280_gp10|1|A|INFO_REALIGN_3_PRIME);LOF=(N|GU280_gp10|1|1.00)
NC_045512.2 29494 . G A 121.0 PASS DP=3419;AF=0.004095;SB=45;DP4=1574,1820,0,17;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttG/ttA|L407|419|N|protein_coding|CODING|GU280_gp10|1|A)
NC_045512.2 29675 . C A 100.0 PASS DP=1264;AF=0.006329;SB=2;DP4=625,628,6,4