##fileformat=VCFv4.0
##FILTER=<ID=PASS,Description="All filters passed">
##fileDate=20211019
##source=lofreq call --min-bq 20 --min-alt-bq 20 --min-mq 20 --ref /home/priesgo/src/github/covigator-ngs-pipeline/reference/Sars_cov_2.ASM985889v3.dna.toplevel.fa --call-indels /dev/fd/63 
##reference=/home/priesgo/src/github/covigator-ngs-pipeline/reference/Sars_cov_2.ASM985889v3.dna.toplevel.fa
##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth">
##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias at this position">
##INFO=<ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">
##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position">
##FILTER=<ID=min_dp_10,Description="Minimum Coverage 10">
##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000">
##FILTER=<ID=min_snvqual_62,Description="Minimum SNV Quality (Phred) 62">
##FILTER=<ID=min_indelqual_46,Description="Minimum Indel Quality (Phred) 46">
##contig=<ID=MN908947.3>
##bcftools_viewVersion=1.12+htslib-1.12
##bcftools_viewCommand=view -Ob ERR4145453.lofreq.vcf.gz; Date=Tue Oct 19 20:45:35 2021
##FILTER=<ID=LOW_FREQUENCY,Description="Set if true: INFO/AF < 0.2">
##bcftools_filterVersion=1.12+htslib-1.12
##bcftools_filterCommand=filter --exclude 'INFO/AF < 0.2' --soft-filter LOW_FREQUENCY -; Date=Tue Oct 19 20:45:35 2021
##FILTER=<ID=SUBCLONAL,Description="Set if true: INFO/AF >= 0.2 && INFO/AF < 0.8">
##bcftools_filterCommand=filter --exclude 'INFO/AF >= 0.2 && INFO/AF < 0.8' --soft-filter SUBCLONAL -; Date=Tue Oct 19 20:45:35 2021
##INFO=<ID=OLD_CLUMPED,Number=1,Type=String,Description="Original variant. Format: CHR|POS|REF|ALT|USED_ALT_IDX">
##bcftools_normVersion=1.12+htslib-1.12
##bcftools_normCommand=norm --multiallelics -any --check-ref e --fasta-ref /home/priesgo/src/github/covigator-ngs-pipeline/reference/Sars_cov_2.ASM985889v3.dna.toplevel.fa --old-rec-tag OLD_CLUMPED -; Date=Tue Oct 19 20:45:37 2021
##FORMAT=<ID=PS,Number=1,Type=Integer,Description="ID for set of phased genotypes">
##bcftools_normCommand=norm --rm-dup exact -o ERR4145453.lofreq.normalized.vcf -; Date=Tue Oct 19 20:45:37 2021
##SnpEffVersion="5.0e (build 2021-03-09 06:01), by Pablo Cingolani"
##SnpEffCmd="SnpEff  -noStats -no-downstream -no-upstream -no-intergenic -no-intron -noShiftHgvs Sars_cov_2.ASM985889v3.101 ERR4145453.lofreq.normalized.vcf "
##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO'">
##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'">
##INFO=<ID=CONS_HMM_SARS_COV_2,Number=1,Type=Float,Description="Mutation depletion score track based on significant enrichment/depletion of nonsingleton SARS-CoV-2 mutations (https://github.com/ernstlab/ConsHMM_CoV)">
##bcftools_annotateVersion=1.12+htslib-1.12
##bcftools_annotateCommand=annotate --annotations /home/priesgo/src/github/covigator-ngs-pipeline/reference/wuhCor1.mutDepletionConsHMM.bed.gz --header-lines /home/priesgo/src/github/covigator-ngs-pipeline/reference/wuhCor1.mutDepletionConsHMM.header.txt -c CHROM,FROM,TO,CONS_HMM_SARS_COV_2 --output-type z -; Date=Tue Oct 19 20:45:43 2021
##INFO=<ID=CONS_HMM_SARBECOVIRUS,Number=1,Type=Float,Description="30 ConsHMM conservation states learned from the Sarbecovirus sequence alignment (https://github.com/ernstlab/ConsHMM_CoV)">
##bcftools_annotateCommand=annotate --annotations /home/priesgo/src/github/covigator-ngs-pipeline/reference/wuhCor1.mutDepletionSarbecovirusConsHMM.bed.gz --header-lines /home/priesgo/src/github/covigator-ngs-pipeline/reference/wuhCor1.mutDepletionSarbecovirusConsHMM.header.txt -c CHROM,FROM,TO,CONS_HMM_SARBECOVIRUS --output-type z -; Date=Tue Oct 19 20:45:43 2021
##INFO=<ID=CONS_HMM_VERTEBRATE_COV,Number=1,Type=Float,Description="30 ConsHMM conservation states learned from the vertebrate CoV sequence alignment (https://github.com/ernstlab/ConsHMM_CoV)">
##bcftools_annotateCommand=annotate --annotations /home/priesgo/src/github/covigator-ngs-pipeline/reference/wuhCor1.mutDepletionVertebrateCoVConsHMM.bed.gz --header-lines /home/priesgo/src/github/covigator-ngs-pipeline/reference/wuhCor1.mutDepletionVertebrateCoVConsHMM.header.txt -c CHROM,FROM,TO,CONS_HMM_VERTEBRATE_COV --output-type z -; Date=Tue Oct 19 20:45:43 2021
##INFO=<ID=PFAM_NAME,Number=.,Type=String,Description="Pfam domain name as reported in Ensembl annotations">
##bcftools_annotateCommand=annotate --annotations /home/priesgo/src/github/covigator-ngs-pipeline/reference/pfam_names.bed.gz --header-lines /home/priesgo/src/github/covigator-ngs-pipeline/reference/pfam_names.header.txt -c CHROM,FROM,TO,PFAM_NAME --output-type z -; Date=Tue Oct 19 20:45:43 2021
##INFO=<ID=PFAM_DESCRIPTION,Number=.,Type=String,Description="Pfam domain description as reported in Ensembl annotations">
##bcftools_annotateCommand=annotate --annotations /home/priesgo/src/github/covigator-ngs-pipeline/reference/pfam_descriptions.bed.gz --header-lines /home/priesgo/src/github/covigator-ngs-pipeline/reference/pfam_descriptions.header.txt -c CHROM,FROM,TO,PFAM_DESCRIPTION --output-type z -; Date=Tue Oct 19 20:45:43 2021
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
MN908947.3	401	.	C	T	118	LOW_FREQUENCY	DP=53;AF=0.09434;SB=0;DP4=26,22,3,2;ANN=T|missense_variant|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.136C>T|p.L46F|136/21290|136/21290|46/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=-0.35633;CONS_HMM_SARBECOVIRUS=-0.35633;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=NSP1_bCoV;PFAM_DESCRIPTION=Non-structural protein NSP1, betacoronavirus
MN908947.3	559	.	T	C	79	LOW_FREQUENCY	DP=59;AF=0.067797;SB=0;DP4=32,23,2,2;ANN=C|synonymous_variant|LOW|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.294T>C|p.G98G|294/21290|294/21290|98/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=0.57215;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=NSP1_bCoV;PFAM_DESCRIPTION=Non-structural protein NSP1, betacoronavirus
MN908947.3	673	.	C	G	141	LOW_FREQUENCY	DP=136;AF=0.051471;SB=6;DP4=73,56,6,1;ANN=G|stop_gained|HIGH|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.408C>G|p.Y136*|408/21290|408/21290|136/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=-0.85561;CONS_HMM_SARBECOVIRUS=-0.85561;CONS_HMM_VERTEBRATE_COV=-0.72927;PFAM_NAME=NSP1_bCoV;PFAM_DESCRIPTION=Non-structural protein NSP1, betacoronavirus
MN908947.3	829	.	C	T	261	LOW_FREQUENCY	DP=181;AF=0.066298;SB=2;DP4=86,83,5,7;ANN=T|synonymous_variant|LOW|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.564C>T|p.N188N|564/21290|564/21290|188/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=0;CONS_HMM_SARBECOVIRUS=0;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=CoV_NSP2_N;PFAM_DESCRIPTION=Coronavirus replicase NSP2, N-terminal
MN908947.3	847	.	T	C	106	LOW_FREQUENCY	DP=177;AF=0.033898;SB=0;DP4=89,82,3,3;ANN=C|synonymous_variant|LOW|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.582T>C|p.D194D|582/21290|582/21290|194/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=0;CONS_HMM_SARBECOVIRUS=0;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=CoV_NSP2_N;PFAM_DESCRIPTION=Coronavirus replicase NSP2, N-terminal
MN908947.3	1070	.	G	A	73	LOW_FREQUENCY	DP=157;AF=0.038217;SB=19;DP4=82,69,0,6;ANN=A|missense_variant|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.805G>A|p.E269K|805/21290|805/21290|269/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=0.57215;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=CoV_NSP2_N;PFAM_DESCRIPTION=Coronavirus replicase NSP2, N-terminal
MN908947.3	1415	.	C	T	135	LOW_FREQUENCY	DP=141;AF=0.049645;SB=1;DP4=68,63,3,4;ANN=T|missense_variant|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.1150C>T|p.L384F|1150/21290|1150/21290|384/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=-0.72927;CONS_HMM_SARBECOVIRUS=0;CONS_HMM_VERTEBRATE_COV=-0.72927;PFAM_NAME=CoV_NSP2_N;PFAM_DESCRIPTION=Coronavirus replicase NSP2, N-terminal
MN908947.3	1468	.	T	A	119	LOW_FREQUENCY	DP=188;AF=0.037234;SB=1;DP4=88,93,4,3;ANN=A|synonymous_variant|LOW|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.1203T>A|p.G401G|1203/21290|1203/21290|401/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=0.57215;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=CoV_NSP2_N;PFAM_DESCRIPTION=Coronavirus replicase NSP2, N-terminal
MN908947.3	1691	.	AT	A	55	LOW_FREQUENCY	DP=263;AF=0.011407;SB=0;DP4=131,130,2,1;INDEL;HRUN=4;ANN=A|frameshift_variant|HIGH|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.1427delT|p.L477fs|1427/21290|1427/21290|476/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(ORF1ab|gene-GU280_gp01|1|1.00);CONS_HMM_SARS_COV_2=-0.35633;CONS_HMM_SARBECOVIRUS=-0.35633;CONS_HMM_VERTEBRATE_COV=0
MN908947.3	1761	.	T	C	85	LOW_FREQUENCY	DP=245;AF=0.020408;SB=0;DP4=113,127,2,3;ANN=C|missense_variant|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.1496T>C|p.F499S|1496/21290|1496/21290|499/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=0.57215;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=0
MN908947.3	1777	.	A	G	93	LOW_FREQUENCY	DP=248;AF=0.024194;SB=0;DP4=111,131,3,3;ANN=G|synonymous_variant|LOW|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.1512A>G|p.E504E|1512/21290|1512/21290|504/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=0;CONS_HMM_SARBECOVIRUS=0;CONS_HMM_VERTEBRATE_COV=0
MN908947.3	2113	.	CT	C	94	LOW_FREQUENCY	DP=156;AF=0.025641;SB=0;DP4=89,64,2,2;INDEL;HRUN=3;ANN=C|frameshift_variant|HIGH|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.1849delT|p.F617fs|1849/21290|1849/21290|617/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(ORF1ab|gene-GU280_gp01|1|1.00);CONS_HMM_SARS_COV_2=-0.72927;CONS_HMM_SARBECOVIRUS=0;CONS_HMM_VERTEBRATE_COV=-0.72927
MN908947.3	2177	.	GGT	G	73	LOW_FREQUENCY	DP=161;AF=0.018634;SB=2;DP4=89,69,1,2;INDEL;HRUN=2;ANN=G|frameshift_variant|HIGH|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.1913_1914delGT|p.V639fs|1913/21290|1913/21290|638/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(ORF1ab|gene-GU280_gp01|1|1.00);CONS_HMM_SARS_COV_2=0.57215;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=0
MN908947.3	2452	.	A	T	79	LOW_FREQUENCY	DP=137;AF=0.036496;SB=0;DP4=70,61,3,3;ANN=T|synonymous_variant|LOW|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.2187A>T|p.L729L|2187/21290|2187/21290|729/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=-0.35633;CONS_HMM_SARBECOVIRUS=-0.35633;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=CoV_NSP2_C;PFAM_DESCRIPTION=Coronavirus replicase NSP2, C-terminal
MN908947.3	2453	.	C	A	66	LOW_FREQUENCY	DP=138;AF=0.028986;SB=2;DP4=71,63,3,1;ANN=A|missense_variant|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.2188C>A|p.L730I|2188/21290|2188/21290|730/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=-0.35633;CONS_HMM_SARBECOVIRUS=-0.35633;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=CoV_NSP2_C;PFAM_DESCRIPTION=Coronavirus replicase NSP2, C-terminal
MN908947.3	2458	.	G	C	121	LOW_FREQUENCY	DP=137;AF=0.043796;SB=1;DP4=69,62,4,2;ANN=C|missense_variant|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.2193G>C|p.M731I|2193/21290|2193/21290|731/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=0.57215;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=CoV_NSP2_C;PFAM_DESCRIPTION=Coronavirus replicase NSP2, C-terminal
MN908947.3	2706	.	C	T	66	LOW_FREQUENCY	DP=223;AF=0.017937;SB=4;DP4=113,106,1,3;ANN=T|missense_variant|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.2441C>T|p.T814I|2441/21290|2441/21290|814/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=0;CONS_HMM_SARBECOVIRUS=0;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=CoV_NSP2_C;PFAM_DESCRIPTION=Coronavirus replicase NSP2, C-terminal
MN908947.3	2917	.	A	AC	47	LOW_FREQUENCY	DP=143;AF=0.013986;SB=0;DP4=64,80,1,1;INDEL;HRUN=2;ANN=AC|frameshift_variant|HIGH|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.2652_2653insC|p.V886fs|2653/21290|2653/21290|885/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(ORF1ab|gene-GU280_gp01|1|1.00);CONS_HMM_SARS_COV_2=0;CONS_HMM_SARBECOVIRUS=0;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=NSP3_N_bCoV;PFAM_DESCRIPTION=Non-structural protein NSP3, N-terminal, betacoronavirus
MN908947.3	2956	.	A	C	65	LOW_FREQUENCY	DP=142;AF=0.028169;SB=2;DP4=65,73,1,3;ANN=C|missense_variant|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.2691A>C|p.L897F|2691/21290|2691/21290|897/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=0;CONS_HMM_SARBECOVIRUS=0;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=NSP3_N_bCoV;PFAM_DESCRIPTION=Non-structural protein NSP3, N-terminal, betacoronavirus
MN908947.3	3037	.	C	T	6329	PASS	DP=181;AF=0.977901;SB=0;DP4=0,0,91,89;ANN=T|synonymous_variant|LOW|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.2772C>T|p.F924F|2772/21290|2772/21290|924/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=0;CONS_HMM_SARBECOVIRUS=0;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=NSP3_N_bCoV;PFAM_DESCRIPTION=Non-structural protein NSP3, N-terminal, betacoronavirus
MN908947.3	3055	.	TG	T	56	LOW_FREQUENCY	DP=182;AF=0.016484;SB=6;DP4=95,84,3,0;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.2791delG|p.E931fs|2791/21290|2791/21290|931/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(ORF1ab|gene-GU280_gp01|1|1.00);CONS_HMM_SARS_COV_2=-1.04511;CONS_HMM_SARBECOVIRUS=-1.04511;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=NSP3_N_bCoV;PFAM_DESCRIPTION=Non-structural protein NSP3, N-terminal, betacoronavirus
MN908947.3	3378	.	T	C	138	LOW_FREQUENCY	DP=274;AF=0.029197;SB=1;DP4=133,133,5,3;ANN=C|missense_variant|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.3113T>C|p.V1038A|3113/21290|3113/21290|1038/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=0.57215;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=NSP3_N_bCoV;PFAM_DESCRIPTION=Non-structural protein NSP3, N-terminal, betacoronavirus
MN908947.3	3650	.	C	T	90	LOW_FREQUENCY	DP=197;AF=0.025381;SB=0;DP4=105,86,3,3;ANN=T|stop_gained|HIGH|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.3385C>T|p.Q1129*|3385/21290|3385/21290|1129/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=-0.59191;CONS_HMM_SARBECOVIRUS=-0.35633;CONS_HMM_VERTEBRATE_COV=-0.59191;PFAM_NAME=Macro_dom;PFAM_DESCRIPTION=Macro domain
MN908947.3	3679	.	T	TA	112	LOW_FREQUENCY	DP=203;AF=0.024631;SB=0;DP4=107,92,3,2;INDEL;HRUN=2;ANN=TA|frameshift_variant|HIGH|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.3414_3415insA|p.N1139fs|3415/21290|3415/21290|1139/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(ORF1ab|gene-GU280_gp01|1|1.00);CONS_HMM_SARS_COV_2=-0.85561;CONS_HMM_SARBECOVIRUS=-0.85561;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=Macro_dom;PFAM_DESCRIPTION=Macro domain
MN908947.3	3721	.	T	TA	69	LOW_FREQUENCY	DP=196;AF=0.015306;SB=2;DP4=105,91,1,2;INDEL;HRUN=1;ANN=TA|frameshift_variant|HIGH|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.3456_3457insA|p.I1153fs|3457/21290|3457/21290|1153/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(ORF1ab|gene-GU280_gp01|1|1.00);CONS_HMM_SARS_COV_2=0;CONS_HMM_SARBECOVIRUS=0;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=Macro_dom;PFAM_DESCRIPTION=Macro domain
MN908947.3	3968	.	T	G	67	LOW_FREQUENCY	DP=174;AF=0.022989;SB=4;DP4=73,97,3,1;ANN=G|missense_variant|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.3703T>G|p.C1235G|3703/21290|3703/21290|1235/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=-1.27455;CONS_HMM_SARBECOVIRUS=-1.27455;CONS_HMM_VERTEBRATE_COV=0
MN908947.3	4141	.	A	ACACAAGCTTT	48	LOW_FREQUENCY	DP=110;AF=0.018182;SB=0;DP4=51,57,1,1;INDEL;HRUN=1;ANN=ACACAAGCTTT|frameshift_variant&stop_gained|HIGH|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.3876_3877insCACAAGCTTT|p.E1293fs|3877/21290|3877/21290|1293/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(ORF1ab|gene-GU280_gp01|1|1.00);CONS_HMM_SARS_COV_2=-0.72927;CONS_HMM_SARBECOVIRUS=0;CONS_HMM_VERTEBRATE_COV=-0.72927
MN908947.3	4143	.	AGGGTG	A	49	LOW_FREQUENCY	DP=110;AF=0.018182;SB=0;DP4=52,56,1,1;INDEL;HRUN=3;ANN=A|frameshift_variant|HIGH|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.3879_3883delGGGTG|p.E1293fs|3879/21290|3879/21290|1293/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(ORF1ab|gene-GU280_gp01|1|1.00);CONS_HMM_SARS_COV_2=-0.72927;CONS_HMM_SARBECOVIRUS=0;CONS_HMM_VERTEBRATE_COV=-0.72927
MN908947.3	4295	.	A	T	83	LOW_FREQUENCY	DP=88;AF=0.045455;SB=0;DP4=34,50,2,2;ANN=T|missense_variant|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.4030A>T|p.T1344S|4030/21290|4030/21290|1344/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=-0.35633;CONS_HMM_SARBECOVIRUS=-0.35633;CONS_HMM_VERTEBRATE_COV=0
MN908947.3	4376	.	G	A	211	LOW_FREQUENCY	DP=157;AF=0.063694;SB=2;DP4=72,75,6,4;ANN=A|missense_variant|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.4111G>A|p.V1371I|4111/21290|4111/21290|1371/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=0.57215;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=NSP3_bCoV;PFAM_DESCRIPTION=Non-structural protein NSP3, single-stranded poly(A) binding domain, betacoronavirus
MN908947.3	4450	.	T	TA	410	LOW_FREQUENCY	DP=166;AF=0.084337;SB=0;DP4=81,72,7,7;INDEL;HRUN=3;ANN=TA|frameshift_variant|HIGH|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.4185_4186insA|p.A1397fs|4186/21290|4186/21290|1396/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(ORF1ab|gene-GU280_gp01|1|1.00);CONS_HMM_SARS_COV_2=0;CONS_HMM_SARBECOVIRUS=0;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=NSP3_bCoV;PFAM_DESCRIPTION=Non-structural protein NSP3, single-stranded poly(A) binding domain, betacoronavirus
MN908947.3	4618	.	C	T	173	LOW_FREQUENCY	DP=172;AF=0.052326;SB=3;DP4=79,84,3,6;ANN=T|synonymous_variant|LOW|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.4353C>T|p.G1451G|4353/21290|4353/21290|1451/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=-1.04511;CONS_HMM_SARBECOVIRUS=-1.04511;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=NSP3_bCoV;PFAM_DESCRIPTION=Non-structural protein NSP3, single-stranded poly(A) binding domain, betacoronavirus
MN908947.3	4779	.	T	C	75	LOW_FREQUENCY	DP=121;AF=0.033058;SB=0;DP4=52,65,2,2;ANN=C|missense_variant|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.4514T>C|p.I1505T|4514/21290|4514/21290|1505/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=0;CONS_HMM_SARBECOVIRUS=0;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=DPUP_SUD_C_bCoV;PFAM_DESCRIPTION=DPUP/SUD, C-terminal, betacoronavirus
MN908947.3	4886	.	C	T	140	LOW_FREQUENCY	DP=82;AF=0.085366;SB=3;DP4=38,37,2,5;ANN=T|missense_variant|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.4621C>T|p.P1541S|4621/21290|4621/21290|1541/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=-0.35633;CONS_HMM_SARBECOVIRUS=-0.35633;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=DPUP_SUD_C_bCoV;PFAM_DESCRIPTION=DPUP/SUD, C-terminal, betacoronavirus
MN908947.3	4998	.	A	T	84	LOW_FREQUENCY	DP=49;AF=0.081633;SB=2;DP4=22,23,1,3;ANN=T|missense_variant|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.4733A>T|p.N1578I|4733/21290|4733/21290|1578/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=0.57215;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=Peptidase_C16_CoV;PFAM_DESCRIPTION=Peptidase C16, coronavirus
MN908947.3	5084	.	AT	A	50	LOW_FREQUENCY	DP=70;AF=0.028571;SB=0;DP4=33,35,1,1;INDEL;HRUN=1;ANN=A|frameshift_variant|HIGH|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.4820delT|p.I1607fs|4820/21290|4820/21290|1607/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(ORF1ab|gene-GU280_gp01|1|1.00);CONS_HMM_SARS_COV_2=0;CONS_HMM_SARBECOVIRUS=0;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=Peptidase_C16_CoV;PFAM_DESCRIPTION=Peptidase C16, coronavirus
MN908947.3	5324	.	G	A	122	LOW_FREQUENCY	DP=124;AF=0.048387;SB=0;DP4=73,45,4,2;ANN=A|missense_variant|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.5059G>A|p.E1687K|5059/21290|5059/21290|1687/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=0.57215;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=Peptidase_C16_CoV;PFAM_DESCRIPTION=Peptidase C16, coronavirus
MN908947.3	7309	.	A	G	356	LOW_FREQUENCY	DP=223;AF=0.076233;SB=0;DP4=101,105,9,8;ANN=G|synonymous_variant|LOW|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.7044A>G|p.Q2348Q|7044/21290|7044/21290|2348/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=0;CONS_HMM_SARBECOVIRUS=0;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=CoV_NSP3_C;PFAM_DESCRIPTION=Coronavirus replicase NSP3, C-terminal
MN908947.3	7471	.	CG	C	181	LOW_FREQUENCY	DP=197;AF=0.035533;SB=1;DP4=102,89,3,4;INDEL;HRUN=2;ANN=C|frameshift_variant|HIGH|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.7207delG|p.G2403fs|7207/21290|7207/21290|2403/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(ORF1ab|gene-GU280_gp01|1|1.00);CONS_HMM_SARS_COV_2=-1.04511;CONS_HMM_SARBECOVIRUS=-1.04511;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=CoV_NSP3_C;PFAM_DESCRIPTION=Coronavirus replicase NSP3, C-terminal
MN908947.3	7709	.	A	T	66	LOW_FREQUENCY	DP=111;AF=0.036036;SB=4;DP4=57,50,1,3;ANN=T|missense_variant|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.7444A>T|p.N2482Y|7444/21290|7444/21290|2482/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=0.57215;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=CoV_NSP3_C;PFAM_DESCRIPTION=Coronavirus replicase NSP3, C-terminal
MN908947.3	8017	.	G	GC	46	LOW_FREQUENCY	DP=152;AF=0.013158;SB=2;DP4=83,67,2,0;INDEL;HRUN=2;ANN=GC|frameshift_variant|HIGH|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.7752_7753insC|p.E2585fs|7753/21290|7753/21290|2585/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(ORF1ab|gene-GU280_gp01|1|1.00);CONS_HMM_SARS_COV_2=-1.04511;CONS_HMM_SARBECOVIRUS=-1.04511;CONS_HMM_VERTEBRATE_COV=-0.59191;PFAM_NAME=CoV_NSP3_C;PFAM_DESCRIPTION=Coronavirus replicase NSP3, C-terminal
MN908947.3	8350	.	TG	T	99	LOW_FREQUENCY	DP=167;AF=0.023952;SB=4;DP4=86,78,1,3;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.8086delG|p.A2696fs|8086/21290|8086/21290|2696/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(ORF1ab|gene-GU280_gp01|1|1.00);CONS_HMM_SARS_COV_2=0.57215;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=CoV_NSP3_C;PFAM_DESCRIPTION=Coronavirus replicase NSP3, C-terminal
MN908947.3	8488	.	G	A	139	LOW_FREQUENCY	DP=161;AF=0.049689;SB=14;DP4=73,80,7,1;ANN=A|synonymous_variant|LOW|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.8223G>A|p.K2741K|8223/21290|8223/21290|2741/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=-0.85561;CONS_HMM_SARBECOVIRUS=-0.85561;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=CoV_NSP3_C;PFAM_DESCRIPTION=Coronavirus replicase NSP3, C-terminal
MN908947.3	8785	.	G	A	95	LOW_FREQUENCY	DP=162;AF=0.037037;SB=3;DP4=84,72,2,4;ANN=A|synonymous_variant|LOW|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.8520G>A|p.Q2840Q|8520/21290|8520/21290|2840/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=-0.35633;CONS_HMM_SARBECOVIRUS=-0.35633;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=CoV_NSP4_N;PFAM_DESCRIPTION=Coronavirus replicase NSP4, N-terminal
MN908947.3	8815	.	T	C	66	LOW_FREQUENCY	DP=163;AF=0.030675;SB=7;DP4=88,70,1,4;ANN=C|synonymous_variant|LOW|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.8550T>C|p.A2850A|8550/21290|8550/21290|2850/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=0;CONS_HMM_SARBECOVIRUS=0;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=CoV_NSP4_N;PFAM_DESCRIPTION=Coronavirus replicase NSP4, N-terminal
MN908947.3	9969	.	CA	C	99	LOW_FREQUENCY	DP=166;AF=0.024096;SB=9;DP4=80,82,4,0;INDEL;HRUN=3;ANN=C|frameshift_variant|HIGH|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.9705delA|p.K3236fs|9705/21290|9705/21290|3235/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(ORF1ab|gene-GU280_gp01|1|1.00);CONS_HMM_SARS_COV_2=1.1685;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=1.1685;PFAM_NAME=NSP4_C_CoV;PFAM_DESCRIPTION=Non-structural protein NSP4, C-terminal, coronavirus
MN908947.3	10140	.	G	A	89	LOW_FREQUENCY	DP=201;AF=0.024876;SB=12;DP4=100,96,5,0;ANN=A|missense_variant|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.9875G>A|p.G3292D|9875/21290|9875/21290|3292/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=2.17352;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=2.17352
MN908947.3	10241	.	A	G	139	LOW_FREQUENCY	DP=233;AF=0.034335;SB=1;DP4=122,103,5,3;ANN=G|missense_variant|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.9976A>G|p.N3326D|9976/21290|9976/21290|3326/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=0;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=-0.59191;PFAM_NAME=Peptidase_C30_CoV;PFAM_DESCRIPTION=Peptidase C30, coronavirus
MN908947.3	10386	.	CT	C	475	LOW_FREQUENCY	DP=233;AF=0.081545;SB=12;DP4=108,107,5,14;INDEL;HRUN=5;ANN=C|frameshift_variant|HIGH|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.10122delT|p.S3376fs|10122/21290|10122/21290|3374/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(ORF1ab|gene-GU280_gp01|1|1.00);CONS_HMM_SARS_COV_2=0.57215;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=Peptidase_C30_CoV;PFAM_DESCRIPTION=Peptidase C30, coronavirus
MN908947.3	10612	.	T	C	102	LOW_FREQUENCY	DP=242;AF=0.024793;SB=1;DP4=118,118,2,4;ANN=C|synonymous_variant|LOW|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.10347T>C|p.V3449V|10347/21290|10347/21290|3449/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=-0.72839;CONS_HMM_SARBECOVIRUS=0;CONS_HMM_VERTEBRATE_COV=-0.72839;PFAM_NAME=Peptidase_C30_CoV;PFAM_DESCRIPTION=Peptidase C30, coronavirus
MN908947.3	10832	.	GC	G	70	LOW_FREQUENCY	DP=187;AF=0.016043;SB=0;DP4=93,93,1,2;INDEL;HRUN=2;ANN=G|frameshift_variant|HIGH|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.10568delC|p.V3524fs|10568/21290|10568/21290|3523/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(ORF1ab|gene-GU280_gp01|1|1.00);CONS_HMM_SARS_COV_2=0.57215;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=Peptidase_C30_CoV;PFAM_DESCRIPTION=Peptidase C30, coronavirus
MN908947.3	10932	.	C	T	84	LOW_FREQUENCY	DP=188;AF=0.026596;SB=1;DP4=97,86,2,3;ANN=T|missense_variant|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.10667C>T|p.P3556L|10667/21290|10667/21290|3556/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=1.1685;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=1.1685;PFAM_NAME=Peptidase_C30_CoV;PFAM_DESCRIPTION=Peptidase C30, coronavirus
MN908947.3	11074	.	CT	C	286	LOW_FREQUENCY	DP=194;AF=0.087629;SB=3;DP4=83,95,10,7;INDEL;HRUN=8;ANN=C|frameshift_variant|HIGH|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.10810delT|p.L3606fs|10810/21290|10810/21290|3604/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(ORF1ab|gene-GU280_gp01|1|1.00);CONS_HMM_SARS_COV_2=0.57215;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=CoV_NSP6;PFAM_DESCRIPTION=Coronavirus replicase NSP6
MN908947.3	11567	.	AT	A	115	LOW_FREQUENCY	DP=239;AF=0.020921;SB=6;DP4=120,114,1,4;INDEL;HRUN=4;ANN=A|frameshift_variant|HIGH|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.11303delT|p.F3769fs|11303/21290|11303/21290|3768/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(ORF1ab|gene-GU280_gp01|1|1.00);CONS_HMM_SARS_COV_2=0;CONS_HMM_SARBECOVIRUS=0;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=CoV_NSP6;PFAM_DESCRIPTION=Coronavirus replicase NSP6
MN908947.3	11650	.	C	G	77	LOW_FREQUENCY	DP=254;AF=0.023622;SB=9;DP4=119,125,5,1;ANN=G|synonymous_variant|LOW|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.11385C>G|p.G3795G|11385/21290|11385/21290|3795/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=-1.27455;CONS_HMM_SARBECOVIRUS=-1.27455;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=CoV_NSP6;PFAM_DESCRIPTION=Coronavirus replicase NSP6
MN908947.3	11859	.	T	A	63	LOW_FREQUENCY	DP=281;AF=0.014235;SB=2;DP4=142,135,3,1;ANN=A|missense_variant|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.11594T>A|p.V3865E|11594/21290|11594/21290|3865/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=0.57215;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=NSP7_CoV;PFAM_DESCRIPTION=Non-structural protein NSP7, coronavirus
MN908947.3	11944	.	GT	G	143	LOW_FREQUENCY	DP=286;AF=0.020979;SB=0;DP4=139,142,3,3;INDEL;HRUN=2;ANN=G|frameshift_variant|HIGH|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.11680delT|p.L3894fs|11680/21290|11680/21290|3894/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(ORF1ab|gene-GU280_gp01|1|1.00);CONS_HMM_SARS_COV_2=-1.04511;CONS_HMM_SARBECOVIRUS=-1.04511;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=NSP7_CoV;PFAM_DESCRIPTION=Non-structural protein NSP7, coronavirus
MN908947.3	11962	.	C	G	63	LOW_FREQUENCY	DP=284;AF=0.014085;SB=0;DP4=137,142,2,2;ANN=G|synonymous_variant|LOW|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.11697C>G|p.L3899L|11697/21290|11697/21290|3899/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=-1.04511;CONS_HMM_SARBECOVIRUS=-1.04511;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=NSP7_CoV;PFAM_DESCRIPTION=Non-structural protein NSP7, coronavirus
MN908947.3	12014	.	GT	G	112	LOW_FREQUENCY	DP=276;AF=0.018116;SB=7;DP4=129,143,4,1;INDEL;HRUN=4;ANN=G|frameshift_variant|HIGH|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.11750delT|p.L3918fs|11750/21290|11750/21290|3917/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(ORF1ab|gene-GU280_gp01|1|1.00);CONS_HMM_SARS_COV_2=0.57215;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=NSP7_CoV;PFAM_DESCRIPTION=Non-structural protein NSP7, coronavirus
MN908947.3	12020	.	CTT	C	62	LOW_FREQUENCY	DP=272;AF=0.011029;SB=2;DP4=129,142,2,1;INDEL;HRUN=3;ANN=C|frameshift_variant|HIGH|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.11756_11757delTT|p.S3920fs|11756/21290|11756/21290|3919/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(ORF1ab|gene-GU280_gp01|1|1.00);CONS_HMM_SARS_COV_2=0.57215;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=NSP7_CoV;PFAM_DESCRIPTION=Non-structural protein NSP7, coronavirus
MN908947.3	12087	.	T	C	104	LOW_FREQUENCY	DP=264;AF=0.022727;SB=9;DP4=134,124,1,5;ANN=C|missense_variant|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.11822T>C|p.L3941S|11822/21290|11822/21290|3941/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=2.31892;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=2.31892;PFAM_NAME=NSP7_CoV;PFAM_DESCRIPTION=Non-structural protein NSP7, coronavirus
MN908947.3	12319	.	T	G	77	LOW_FREQUENCY	DP=224;AF=0.022321;SB=7;DP4=100,119,4,1;ANN=G|synonymous_variant|LOW|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.12054T>G|p.S4018S|12054/21290|12054/21290|4018/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=0.67226;CONS_HMM_SARBECOVIRUS=0.67226;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=NSP8_CoV-like;PFAM_DESCRIPTION=Non-structural protein NSP8, coronavirus-like
MN908947.3	12334	.	A	C	100	LOW_FREQUENCY	DP=241;AF=0.029046;SB=1;DP4=108,121,4,3;ANN=C|synonymous_variant|LOW|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.12069A>C|p.A4023A|12069/21290|12069/21290|4023/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=-0.35633;CONS_HMM_SARBECOVIRUS=-0.35633;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=NSP8_CoV-like;PFAM_DESCRIPTION=Non-structural protein NSP8, coronavirus-like
MN908947.3	12354	.	A	G	79	LOW_FREQUENCY	DP=243;AF=0.020576;SB=0;DP4=107,129,3,3;ANN=G|missense_variant|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.12089A>G|p.Q4030R|12089/21290|12089/21290|4030/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=2.31892;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=2.31892;PFAM_NAME=NSP8_CoV-like;PFAM_DESCRIPTION=Non-structural protein NSP8, coronavirus-like
MN908947.3	12663	.	C	T	80	LOW_FREQUENCY	DP=284;AF=0.017606;SB=4;DP4=136,143,1,4;ANN=T|missense_variant|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.12398C>T|p.A4133V|12398/21290|12398/21290|4133/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=0.57215;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=NSP8_CoV-like;PFAM_DESCRIPTION=Non-structural protein NSP8, coronavirus-like
MN908947.3	12683	.	C	T	76	LOW_FREQUENCY	DP=279;AF=0.017921;SB=4;DP4=131,143,1,4;ANN=T|stop_gained|HIGH|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.12418C>T|p.Q4140*|12418/21290|12418/21290|4140/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=2.31892;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=2.31892
MN908947.3	12751	.	T	C	63	LOW_FREQUENCY	DP=263;AF=0.015209;SB=9;DP4=125,134,0,4;ANN=C|synonymous_variant|LOW|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.12486T>C|p.A4162A|12486/21290|12486/21290|4162/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=0.57215;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=NSP9_CoV;PFAM_DESCRIPTION=Non-structural protein NSP9, coronavirus
MN908947.3	12808	.	A	G	62	LOW_FREQUENCY	DP=263;AF=0.015209;SB=0;DP4=129,130,2,2;ANN=G|synonymous_variant|LOW|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.12543A>G|p.V4181V|12543/21290|12543/21290|4181/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=-1.04511;CONS_HMM_SARBECOVIRUS=-1.04511;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=NSP9_CoV;PFAM_DESCRIPTION=Non-structural protein NSP9, coronavirus
MN908947.3	12895	.	AC	A	65	LOW_FREQUENCY	DP=275;AF=0.010909;SB=6;DP4=142,132,3,0;INDEL;HRUN=2;ANN=A|frameshift_variant|HIGH|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.12631delC|p.P4211fs|12631/21290|12631/21290|4211/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(ORF1ab|gene-GU280_gp01|1|1.00);CONS_HMM_SARS_COV_2=1.1685;CONS_HMM_SARBECOVIRUS=0.67226;CONS_HMM_VERTEBRATE_COV=1.1685;PFAM_NAME=NSP9_CoV;PFAM_DESCRIPTION=Non-structural protein NSP9, coronavirus
MN908947.3	13129	.	A	G	86	LOW_FREQUENCY	DP=264;AF=0.026515;SB=3;DP4=134,123,5,2;ANN=G|synonymous_variant|LOW|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.12864A>G|p.G4288G|12864/21290|12864/21290|4288/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=0.67226;CONS_HMM_SARBECOVIRUS=0.67226;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=RNA_synth_NSP10_CoV;PFAM_DESCRIPTION=RNA synthesis protein NSP10, coronavirus
MN908947.3	13156	.	G	A	64	LOW_FREQUENCY	DP=265;AF=0.015094;SB=4;DP4=134,127,1,3;ANN=A|missense_variant|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.12891G>A|p.M4297I|12891/21290|12891/21290|4297/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=2.31892;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=2.31892;PFAM_NAME=RNA_synth_NSP10_CoV;PFAM_DESCRIPTION=RNA synthesis protein NSP10, coronavirus
MN908947.3	13489	.	G	A	134	LOW_FREQUENCY	DP=133;AF=0.052632;SB=6;DP4=53,73,1,6;ANN=A|synonymous_variant|LOW|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.13224G>A|p.Q4408Q|13224/21290|13224/21290|4408/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=2.17352;CONS_HMM_SARBECOVIRUS=0.67226;CONS_HMM_VERTEBRATE_COV=2.17352;PFAM_NAME=RNA_pol_N_coronovir;PFAM_DESCRIPTION=RNA polymerase, N-terminal, coronaviral
MN908947.3	13701	.	TA	T	49	LOW_FREQUENCY	DP=115;AF=0.017391;SB=3;DP4=57,56,0,2;INDEL;HRUN=2;ANN=T|frameshift_variant|HIGH|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.13437delA|p.I4480fs|13437/21290|13437/21290|4479/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(ORF1ab|gene-GU280_gp01|1|1.00);CONS_HMM_SARS_COV_2=0;CONS_HMM_SARBECOVIRUS=0;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=RNA_pol_N_coronovir;PFAM_DESCRIPTION=RNA polymerase, N-terminal, coronaviral
MN908947.3	13759	.	G	A	66	LOW_FREQUENCY	DP=145;AF=0.027586;SB=9;DP4=73,68,4,0;ANN=A|stop_retained_variant|LOW|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.13494G>A|p.*4498*|13494/21290|13494/21290|4498/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=2.31892;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=2.31892;PFAM_NAME=RNA_pol_N_coronovir;PFAM_DESCRIPTION=RNA polymerase, N-terminal, coronaviral
MN908947.3	13761	.	CG	C	102	LOW_FREQUENCY	DP=146;AF=0.027397;SB=13;DP4=77,65,0,4;INDEL;HRUN=2;ANN=C|frameshift_variant|HIGH|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.13497delG|p.V4500fs|13497/21290|13497/21290|4499/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(ORF1ab|gene-GU280_gp01|1|1.00);CONS_HMM_SARS_COV_2=-1.04511;CONS_HMM_SARBECOVIRUS=-1.04511;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=RNA_pol_N_coronovir;PFAM_DESCRIPTION=RNA polymerase, N-terminal, coronaviral
MN908947.3	13862	.	C	T	75	LOW_FREQUENCY	DP=133;AF=0.030075;SB=9;DP4=66,63,4,0;ANN=T|missense_variant|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.13597C>T|p.H4533Y|13597/21290|13597/21290|4533/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=-0.35633;CONS_HMM_SARBECOVIRUS=-0.35633;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=RNA_pol_N_coronovir;PFAM_DESCRIPTION=RNA polymerase, N-terminal, coronaviral
MN908947.3	14351	.	A	G	147	LOW_FREQUENCY	DP=112;AF=0.0625;SB=9;DP4=65,40,2,5;ANN=G|missense_variant|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.14086A>G|p.T4696A|14086/21290|14086/21290|4696/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=2.17352;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=2.17352;PFAM_NAME=RNA_pol_N_coronovir;PFAM_DESCRIPTION=RNA polymerase, N-terminal, coronaviral
MN908947.3	14408	.	C	T	4066	PASS	DP=112;AF=1;SB=0;DP4=0,0,61,51;ANN=T|synonymous_variant|LOW|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.14143C>T|p.L4715L|14143/21290|14143/21290|4715/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=0;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=-0.72839;PFAM_NAME=RNA_pol_N_coronovir;PFAM_DESCRIPTION=RNA polymerase, N-terminal, coronaviral
MN908947.3	14446	.	G	A	78	LOW_FREQUENCY	DP=134;AF=0.037313;SB=12;DP4=68,61,5,0;ANN=A|synonymous_variant|LOW|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.14181G>A|p.L4727L|14181/21290|14181/21290|4727/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=2.17352;CONS_HMM_SARBECOVIRUS=0.67226;CONS_HMM_VERTEBRATE_COV=2.17352;PFAM_NAME=RNA_pol_N_coronovir;PFAM_DESCRIPTION=RNA polymerase, N-terminal, coronaviral
MN908947.3	14632	.	G	T	122	LOW_FREQUENCY	DP=131;AF=0.045802;SB=1;DP4=63,62,2,4;ANN=T|missense_variant|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.14367G>T|p.Q4789H|14367/21290|14367/21290|4789/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=0.57215;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=0
MN908947.3	15016	.	G	A	266	LOW_FREQUENCY	DP=143;AF=0.083916;SB=1;DP4=62,68,5,7;ANN=A|missense_variant|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.14751G>A|p.M4917I|14751/21290|14751/21290|4917/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=0.67226;CONS_HMM_SARBECOVIRUS=0.67226;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=RNA-dir_pol_C;PFAM_DESCRIPTION=RNA-directed RNA polymerase,  C-terminal domain
MN908947.3	15018	.	A	C	72	LOW_FREQUENCY	DP=143;AF=0.027972;SB=4;DP4=64,74,3,1;ANN=C|missense_variant|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.14753A>C|p.H4918P|14753/21290|14753/21290|4918/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=-0.35633;CONS_HMM_SARBECOVIRUS=-0.35633;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=RNA-dir_pol_C;PFAM_DESCRIPTION=RNA-directed RNA polymerase,  C-terminal domain
MN908947.3	15160	.	A	G	75	LOW_FREQUENCY	DP=136;AF=0.029412;SB=0;DP4=65,66,2,2;ANN=G|synonymous_variant|LOW|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.14895A>G|p.K4965K|14895/21290|14895/21290|4965/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=2.17352;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=2.17352;PFAM_NAME=RNA-dir_pol_C;PFAM_DESCRIPTION=RNA-directed RNA polymerase,  C-terminal domain
MN908947.3	15243	.	G	A	133	LOW_FREQUENCY	DP=182;AF=0.038462;SB=3;DP4=88,87,5,2;ANN=A|missense_variant|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.14978G>A|p.C4993Y|14978/21290|14978/21290|4993/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=2.17352;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=2.17352;PFAM_NAME=RNA-dir_pol_C;PFAM_DESCRIPTION=RNA-directed RNA polymerase,  C-terminal domain
MN908947.3	15482	.	C	T	480	LOW_FREQUENCY	DP=226;AF=0.097345;SB=5;DP4=105,99,8,14;ANN=T|missense_variant|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.15217C>T|p.H5073Y|15217/21290|15217/21290|5073/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=0.57215;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=RNA-dir_pol_C;PFAM_DESCRIPTION=RNA-directed RNA polymerase,  C-terminal domain
MN908947.3	15490	.	G	T	63	LOW_FREQUENCY	DP=222;AF=0.018018;SB=4;DP4=107,111,3,1;ANN=T|missense_variant|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.15225G>T|p.E5075D|15225/21290|15225/21290|5075/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=2.17352;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=2.17352;PFAM_NAME=RNA-dir_pol_C;PFAM_DESCRIPTION=RNA-directed RNA polymerase,  C-terminal domain
MN908947.3	15530	.	G	A	106	LOW_FREQUENCY	DP=214;AF=0.028037;SB=1;DP4=107,99,3,4;ANN=A|missense_variant|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.15265G>A|p.V5089I|15265/21290|15265/21290|5089/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=0.67226;CONS_HMM_SARBECOVIRUS=0.67226;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=RNA-dir_pol_C;PFAM_DESCRIPTION=RNA-directed RNA polymerase,  C-terminal domain
MN908947.3	15572	.	A	G	88	LOW_FREQUENCY	DP=202;AF=0.024752;SB=4;DP4=101,96,4,1;ANN=G|missense_variant|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.15307A>G|p.M5103V|15307/21290|15307/21290|5103/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=0.57215;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=RNA-dir_pol_C;PFAM_DESCRIPTION=RNA-directed RNA polymerase,  C-terminal domain
MN908947.3	15854	.	T	C	93	LOW_FREQUENCY	DP=178;AF=0.02809;SB=12;DP4=84,89,0,5;ANN=C|synonymous_variant|LOW|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.15589T>C|p.L5197L|15589/21290|15589/21290|5197/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=2.17352;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=2.17352;PFAM_NAME=RNA-dir_pol_C;PFAM_DESCRIPTION=RNA-directed RNA polymerase,  C-terminal domain
MN908947.3	16152	.	T	C	103	LOW_FREQUENCY	DP=239;AF=0.029289;SB=3;DP4=116,116,2,5;ANN=C|missense_variant|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.15887T>C|p.L5296P|15887/21290|15887/21290|5296/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=1.1685;CONS_HMM_SARBECOVIRUS=0;CONS_HMM_VERTEBRATE_COV=1.1685
MN908947.3	16363	.	T	C	135	LOW_FREQUENCY	DP=195;AF=0.035897;SB=18;DP4=91,97,0,7;ANN=C|synonymous_variant|LOW|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.16098T>C|p.S5366S|16098/21290|16098/21290|5366/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=0;CONS_HMM_SARBECOVIRUS=0;CONS_HMM_VERTEBRATE_COV=0
MN908947.3	16379	.	A	C	130	LOW_FREQUENCY	DP=182;AF=0.038462;SB=18;DP4=89,86,0,7;ANN=C|missense_variant|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.16114A>C|p.M5372L|16114/21290|16114/21290|5372/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=2.17352;CONS_HMM_SARBECOVIRUS=0.67226;CONS_HMM_VERTEBRATE_COV=2.17352
MN908947.3	16546	.	A	G	69	LOW_FREQUENCY	DP=165;AF=0.024242;SB=2;DP4=82,79,3,1;ANN=G|synonymous_variant|LOW|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.16281A>G|p.L5427L|16281/21290|16281/21290|5427/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=-0.72839;CONS_HMM_SARBECOVIRUS=-0.35633;CONS_HMM_VERTEBRATE_COV=-0.72839
MN908947.3	16707	.	G	C	355	LOW_FREQUENCY	DP=170;AF=0.094118;SB=0;DP4=81,73,8,8;ANN=C|missense_variant|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.16442G>C|p.C5481S|16442/21290|16442/21290|5481/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=-1.04511;CONS_HMM_SARBECOVIRUS=-1.04511;CONS_HMM_VERTEBRATE_COV=0
MN908947.3	17004	.	CA	C	94	LOW_FREQUENCY	DP=222;AF=0.018018;SB=4;DP4=107,113,3,1;INDEL;HRUN=2;ANN=C|frameshift_variant|HIGH|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.16740delA|p.I5581fs|16740/21290|16740/21290|5580/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(ORF1ab|gene-GU280_gp01|1|1.00);CONS_HMM_SARS_COV_2=-1.27455;CONS_HMM_SARBECOVIRUS=-1.27455;CONS_HMM_VERTEBRATE_COV=0
MN908947.3	17005	.	AAT	A	94	LOW_FREQUENCY	DP=222;AF=0.018018;SB=4;DP4=108,112,3,1;INDEL;HRUN=2;ANN=A|frameshift_variant|HIGH|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.16741_16742delAT|p.Q5583fs|16741/21290|16741/21290|5581/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(ORF1ab|gene-GU280_gp01|1|1.00);CONS_HMM_SARS_COV_2=2.31892;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=2.31892
MN908947.3	17036	.	C	G	65	LOW_FREQUENCY	DP=249;AF=0.016064;SB=9;DP4=121,124,4,0;ANN=G|missense_variant|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.16771C>G|p.Q5591E|16771/21290|16771/21290|5591/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=0.67226;CONS_HMM_SARBECOVIRUS=0.67226;CONS_HMM_VERTEBRATE_COV=0
MN908947.3	17076	.	C	A	82	LOW_FREQUENCY	DP=264;AF=0.018939;SB=6;DP4=134,125,1,4;ANN=A|missense_variant|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.16811C>A|p.S5604Y|16811/21290|16811/21290|5604/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=0;CONS_HMM_SARBECOVIRUS=0;CONS_HMM_VERTEBRATE_COV=0
MN908947.3	17354	.	TTGA	T	66	LOW_FREQUENCY	DP=274;AF=0.010949;SB=0;DP4=132,141,1,2;INDEL;HRUN=3;ANN=T|conservative_inframe_deletion|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.17090_17092delTGA|p.M5698del|17090/21290|17090/21290|5697/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=2.17352;CONS_HMM_SARBECOVIRUS=0.67226;CONS_HMM_VERTEBRATE_COV=2.17352;PFAM_NAME=(+)RNA_virus_helicase_core_dom;PFAM_DESCRIPTION=(+) RNA virus helicase core domain
MN908947.3	17404	.	A	G	63	LOW_FREQUENCY	DP=246;AF=0.01626;SB=0;DP4=128,113,2,2;ANN=G|synonymous_variant|LOW|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.17139A>G|p.P5713P|17139/21290|17139/21290|5713/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=0;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=-0.72839;PFAM_NAME=(+)RNA_virus_helicase_core_dom;PFAM_DESCRIPTION=(+) RNA virus helicase core domain
MN908947.3	17588	.	CTG	C	118	LOW_FREQUENCY	DP=251;AF=0.01992;SB=0;DP4=126,121,3,2;INDEL;HRUN=1;ANN=C|frameshift_variant|HIGH|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.17324_17325delTG|p.*5776fs|17324/21290|17324/21290|5775/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(ORF1ab|gene-GU280_gp01|1|1.00);CONS_HMM_SARS_COV_2=2.17352;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=2.17352;PFAM_NAME=(+)RNA_virus_helicase_core_dom;PFAM_DESCRIPTION=(+) RNA virus helicase core domain
MN908947.3	17721	.	GGT	G	92	LOW_FREQUENCY	DP=253;AF=0.01581;SB=4;DP4=122,127,3,1;INDEL;HRUN=2;ANN=G|frameshift_variant&stop_lost|HIGH|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.17457_17458delGT|p.W5819fs|17457/21290|17457/21290|5819/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(ORF1ab|gene-GU280_gp01|1|1.00);CONS_HMM_SARS_COV_2=-1.04511;CONS_HMM_SARBECOVIRUS=-1.04511;CONS_HMM_VERTEBRATE_COV=-0.72839;PFAM_NAME=(+)RNA_virus_helicase_core_dom;PFAM_DESCRIPTION=(+) RNA virus helicase core domain
MN908947.3	17753	.	GGA	G	173	LOW_FREQUENCY	DP=264;AF=0.026515;SB=22;DP4=123,135,7,0;INDEL;HRUN=2;ANN=G|frameshift_variant|HIGH|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.17489_17490delGA|p.E5831fs|17489/21290|17489/21290|5830/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(ORF1ab|gene-GU280_gp01|1|1.00);CONS_HMM_SARS_COV_2=2.17352;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=2.17352;PFAM_NAME=(+)RNA_virus_helicase_core_dom;PFAM_DESCRIPTION=(+) RNA virus helicase core domain
MN908947.3	18032	.	CT	C	121	LOW_FREQUENCY	DP=219;AF=0.022831;SB=11;DP4=105,118,0,5;INDEL;HRUN=3;ANN=C|frameshift_variant|HIGH|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.17768delT|p.Y5924fs|17768/21290|17768/21290|5923/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(ORF1ab|gene-GU280_gp01|1|1.00);CONS_HMM_SARS_COV_2=-0.35633;CONS_HMM_SARBECOVIRUS=-0.35633;CONS_HMM_VERTEBRATE_COV=0
MN908947.3	18187	.	AC	A	119	LOW_FREQUENCY	DP=208;AF=0.024038;SB=4;DP4=102,101,1,4;INDEL;HRUN=2;ANN=A|frameshift_variant|HIGH|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.17923delC|p.P5975fs|17923/21290|17923/21290|5975/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(ORF1ab|gene-GU280_gp01|1|1.00);CONS_HMM_SARS_COV_2=0.67226;CONS_HMM_SARBECOVIRUS=0.67226;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=NSP15_CoV;PFAM_DESCRIPTION=Non-structural protein NSP15, coronavirus
MN908947.3	19038	.	T	C	154	LOW_FREQUENCY	DP=210;AF=0.038095;SB=1;DP4=98,104,3,5;ANN=C|missense_variant|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.18773T>C|p.V6258A|18773/21290|18773/21290|6258/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=-1.04511;CONS_HMM_SARBECOVIRUS=-1.04511;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=NSP15_CoV;PFAM_DESCRIPTION=Non-structural protein NSP15, coronavirus
MN908947.3	19102	.	C	A	235	LOW_FREQUENCY	DP=181;AF=0.082873;SB=9;DP4=81,85,4,11;ANN=A|missense_variant|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.18837C>A|p.S6279R|18837/21290|18837/21290|6279/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=2.31892;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=2.31892;PFAM_NAME=NSP15_CoV;PFAM_DESCRIPTION=Non-structural protein NSP15, coronavirus
MN908947.3	19210	.	A	AT	163	LOW_FREQUENCY	DP=115;AF=0.052174;SB=15;DP4=58,54,0,6;INDEL;HRUN=1;ANN=AT|frameshift_variant&stop_gained|HIGH|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.18945_18946insT|p.D6316fs|18946/21290|18946/21290|6316/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(ORF1ab|gene-GU280_gp01|1|1.00);CONS_HMM_SARS_COV_2=-1.04511;CONS_HMM_SARBECOVIRUS=-1.04511;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=NSP15_CoV;PFAM_DESCRIPTION=Non-structural protein NSP15, coronavirus
MN908947.3	19215	.	TC	T	134	LOW_FREQUENCY	DP=120;AF=0.041667;SB=4;DP4=59,57,4,1;INDEL;HRUN=2;ANN=T|frameshift_variant|HIGH|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.18951delC|p.L6318fs|18951/21290|18951/21290|6317/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(ORF1ab|gene-GU280_gp01|1|1.00);CONS_HMM_SARS_COV_2=-1.04511;CONS_HMM_SARBECOVIRUS=-1.04511;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=NSP15_CoV;PFAM_DESCRIPTION=Non-structural protein NSP15, coronavirus
MN908947.3	19216	.	C	T	71	LOW_FREQUENCY	DP=120;AF=0.033333;SB=2;DP4=56,55,3,1;ANN=T|synonymous_variant|LOW|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.18951C>T|p.I6317I|18951/21290|18951/21290|6317/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=2.17352;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=2.17352;PFAM_NAME=NSP15_CoV;PFAM_DESCRIPTION=Non-structural protein NSP15, coronavirus
MN908947.3	19248	.	T	G	80	LOW_FREQUENCY	DP=105;AF=0.038095;SB=13;DP4=56,44,0,4;ANN=G|missense_variant|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.18983T>G|p.L6328R|18983/21290|18983/21290|6328/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=0;CONS_HMM_SARBECOVIRUS=0;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=NSP15_CoV;PFAM_DESCRIPTION=Non-structural protein NSP15, coronavirus
MN908947.3	19679	.	G	C	90	LOW_FREQUENCY	DP=179;AF=0.03352;SB=0;DP4=88,85,3,3;ANN=C|missense_variant|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.19414G>C|p.V6472L|19414/21290|19414/21290|6472/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=0.57215;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=CoV_NSP15_N;PFAM_DESCRIPTION=Coronavirus replicase NSP15, N-terminal oligomerisation
MN908947.3	19722	.	A	G	81	LOW_FREQUENCY	DP=196;AF=0.02551;SB=4;DP4=94,97,4,1;ANN=G|missense_variant|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.19457A>G|p.K6486R|19457/21290|19457/21290|6486/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=0;CONS_HMM_SARBECOVIRUS=0;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=CoV_NSP15_N;PFAM_DESCRIPTION=Coronavirus replicase NSP15, N-terminal oligomerisation
MN908947.3	19736	.	A	C	106	LOW_FREQUENCY	DP=214;AF=0.028037;SB=6;DP4=105,101,5,1;ANN=C|missense_variant|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.19471A>C|p.M6491L|19471/21290|19471/21290|6491/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=0.57215;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=CoV_NSP15_N;PFAM_DESCRIPTION=Coronavirus replicase NSP15, N-terminal oligomerisation
MN908947.3	19782	.	AT	A	68	LOW_FREQUENCY	DP=236;AF=0.012712;SB=2;DP4=123,110,1,2;INDEL;HRUN=3;ANN=A|frameshift_variant|HIGH|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.19518delT|p.L6507fs|19518/21290|19518/21290|6506/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(ORF1ab|gene-GU280_gp01|1|1.00);CONS_HMM_SARS_COV_2=0;CONS_HMM_SARBECOVIRUS=0;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=CoV_NSP15_N;PFAM_DESCRIPTION=Coronavirus replicase NSP15, N-terminal oligomerisation
MN908947.3	19838	.	A	T	72	LOW_FREQUENCY	DP=235;AF=0.025532;SB=3;DP4=115,112,2,5;ANN=T|missense_variant|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.19573A>T|p.I6525L|19573/21290|19573/21290|6525/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=0.57215;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=CoV_NSP15_M;PFAM_DESCRIPTION=Coronavirus replicase NSP15, middle domain
MN908947.3	20343	.	T	C	95	LOW_FREQUENCY	DP=124;AF=0.040323;SB=4;DP4=61,58,4,1;ANN=C|missense_variant|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.20078T>C|p.V6693A|20078/21290|20078/21290|6693/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=-0.72839;CONS_HMM_SARBECOVIRUS=-0.35633;CONS_HMM_VERTEBRATE_COV=-0.72839;PFAM_NAME=CoV_NSP15_C;PFAM_DESCRIPTION=Coronavirus replicase NSP15, uridylate-specific endoribonuclease
MN908947.3	20497	.	T	A	71	LOW_FREQUENCY	DP=151;AF=0.02649;SB=0;DP4=78,69,2,2;ANN=A|synonymous_variant|LOW|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.20232T>A|p.V6744V|20232/21290|20232/21290|6744/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=0;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=-0.72839;PFAM_NAME=CoV_NSP15_C;PFAM_DESCRIPTION=Coronavirus replicase NSP15, uridylate-specific endoribonuclease
MN908947.3	20648	.	C	CA	224	LOW_FREQUENCY	DP=104;AF=0.076923;SB=11;DP4=47,53,1,7;INDEL;HRUN=4;ANN=CA|frameshift_variant|HIGH|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.20383_20384insA|p.N6796fs|20384/21290|20384/21290|6795/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=2.17352;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=2.17352;PFAM_NAME=CoV_NSP15_C;PFAM_DESCRIPTION=Coronavirus replicase NSP15, uridylate-specific endoribonuclease
MN908947.3	20679	.	G	T	78	LOW_FREQUENCY	DP=114;AF=0.035088;SB=2;DP4=52,57,1,3;ANN=T|missense_variant|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.20414G>T|p.R6805L|20414/21290|20414/21290|6805/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=-0.72839;CONS_HMM_SARBECOVIRUS=0;CONS_HMM_VERTEBRATE_COV=-0.72839;PFAM_NAME=NSP16_CoV-like;PFAM_DESCRIPTION=Non-structural protein NSP16, coronavirus-like
MN908947.3	21133	.	C	CA	48	LOW_FREQUENCY	DP=54;AF=0.037037;SB=2;DP4=32,21,2,0;INDEL;HRUN=4;ANN=CA|frameshift_variant|HIGH|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.20868_20869insA|p.S6958fs|20869/21290|20869/21290|6957/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=0;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=-0.72839;PFAM_NAME=NSP16_CoV-like;PFAM_DESCRIPTION=Non-structural protein NSP16, coronavirus-like
MN908947.3	21230	.	C	T	77	LOW_FREQUENCY	DP=126;AF=0.031746;SB=0;DP4=69,52,2,2;ANN=T|stop_gained|HIGH|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.20965C>T|p.Q6989*|20965/21290|20965/21290|6989/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=2.17352;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=2.17352;PFAM_NAME=NSP16_CoV-like;PFAM_DESCRIPTION=Non-structural protein NSP16, coronavirus-like
MN908947.3	21363	.	T	G	79	LOW_FREQUENCY	DP=241;AF=0.020747;SB=4;DP4=131,103,4,1;ANN=G|missense_variant|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.21098T>G|p.I7033S|21098/21290|21098/21290|7033/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=1.1685;CONS_HMM_SARBECOVIRUS=0;CONS_HMM_VERTEBRATE_COV=1.1685;PFAM_NAME=NSP16_CoV-like;PFAM_DESCRIPTION=Non-structural protein NSP16, coronavirus-like
MN908947.3	21575	.	C	T	71	LOW_FREQUENCY	DP=250;AF=0.02;SB=4;DP4=120,125,1,4;ANN=T|missense_variant|MODERATE|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.13C>T|p.L5F|13/3822|13/3822|5/1273||
MN908947.3	21759	.	A	G	376	LOW_FREQUENCY	DP=139;AF=0.115108;SB=0;DP4=58,65,8,8;ANN=G|missense_variant|MODERATE|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.197A>G|p.H66R|197/3822|197/3822|66/1273||;CONS_HMM_SARS_COV_2=0;CONS_HMM_SARBECOVIRUS=0;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=bCoV_S1_N;PFAM_DESCRIPTION=Betacoronavirus-like spike glycoprotein S1, N-terminal
MN908947.3	21764	.	ATACATG	A	923	SUBCLONAL	DP=144;AF=0.222222;SB=0;DP4=53,56,16,16;INDEL;HRUN=1;ANN=A|disruptive_inframe_deletion|MODERATE|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.203_208delTACATG|p.H69_V70del|203/3822|203/3822|68/1273||;CONS_HMM_SARS_COV_2=-1.04511;CONS_HMM_SARBECOVIRUS=-1.04511;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=bCoV_S1_N;PFAM_DESCRIPTION=Betacoronavirus-like spike glycoprotein S1, N-terminal
MN908947.3	21764	.	ATACATGTCTCTGGGACCAATG	A	103	LOW_FREQUENCY	DP=144;AF=0.027778;SB=2;DP4=53,56,1,3;INDEL;HRUN=1;ANN=A|disruptive_inframe_deletion|MODERATE|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.203_223delTACATGTCTCTGGGACCAATG|p.I68_G75delinsS|203/3822|203/3822|68/1273||;CONS_HMM_SARS_COV_2=-1.04511;CONS_HMM_SARBECOVIRUS=-1.04511;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=bCoV_S1_N;PFAM_DESCRIPTION=Betacoronavirus-like spike glycoprotein S1, N-terminal
MN908947.3	21781	.	C	T	334	LOW_FREQUENCY	DP=133;AF=0.105263;SB=1;DP4=53,62,7,7;ANN=T|synonymous_variant|LOW|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.219C>T|p.T73T|219/3822|219/3822|73/1273||;CONS_HMM_SARS_COV_2=-0.80744;CONS_HMM_SARBECOVIRUS=0;CONS_HMM_VERTEBRATE_COV=-0.80744;PFAM_NAME=bCoV_S1_N;PFAM_DESCRIPTION=Betacoronavirus-like spike glycoprotein S1, N-terminal
MN908947.3	21784	.	T	G	4505	PASS	DP=137;AF=0.934307;SB=10;DP4=3,0,59,71;ANN=G|missense_variant|MODERATE|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.222T>G|p.N74K|222/3822|222/3822|74/1273||;CONS_HMM_SARS_COV_2=-0.80744;CONS_HMM_SARBECOVIRUS=0;CONS_HMM_VERTEBRATE_COV=-0.80744;PFAM_NAME=bCoV_S1_N;PFAM_DESCRIPTION=Betacoronavirus-like spike glycoprotein S1, N-terminal
MN908947.3	21846	.	C	T	1763	SUBCLONAL	DP=109;AF=0.513761;SB=0;DP4=24,28,26,31;ANN=T|missense_variant|MODERATE|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.284C>T|p.T95I|284/3822|284/3822|95/1273||;CONS_HMM_SARS_COV_2=0;CONS_HMM_SARBECOVIRUS=0;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=bCoV_S1_N;PFAM_DESCRIPTION=Betacoronavirus-like spike glycoprotein S1, N-terminal
MN908947.3	22060	.	C	G	68	LOW_FREQUENCY	DP=42;AF=0.071429;SB=5;DP4=17,22,0,3;ANN=G|missense_variant|MODERATE|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.498C>G|p.C166W|498/3822|498/3822|166/1273||;CONS_HMM_SARS_COV_2=0;CONS_HMM_SARBECOVIRUS=0;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=bCoV_S1_N;PFAM_DESCRIPTION=Betacoronavirus-like spike glycoprotein S1, N-terminal
MN908947.3	22155	.	A	T	63	LOW_FREQUENCY	DP=63;AF=0.047619;SB=2;DP4=26,34,2,1;ANN=T|missense_variant|MODERATE|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.593A>T|p.D198V|593/3822|593/3822|198/1273||;CONS_HMM_SARS_COV_2=0.57215;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=bCoV_S1_N;PFAM_DESCRIPTION=Betacoronavirus-like spike glycoprotein S1, N-terminal
M