##fileformat=VCFv4.0
##FILTER=<ID=PASS,Description="All filters passed">
##contig=<ID=MN908947.3>
##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 20:49:43 2021
##FORMAT=<ID=PS,Number=1,Type=Integer,Description="ID for set of phased genotypes">
##bcftools_normCommand=norm --rm-dup exact -o hCoV-19_NTXX.assembly.normalized.vcf -; Date=Tue Oct 19 20:49:43 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 hCoV-19_NTXX.assembly.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 20:49:48 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 20:49:48 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 20:49:48 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 20:49:48 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 20:49:48 2021
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
MN908947.3	241	.	C	T	.	PASS	CONS_HMM_SARS_COV_2=-1.25436;CONS_HMM_SARBECOVIRUS=-1.25436;CONS_HMM_VERTEBRATE_COV=0
MN908947.3	2669	.	C	T	.	PASS	ANN=T|missense_variant|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.2404C>T|p.L802F|2404/21290|2404/21290|802/7095||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	3037	.	C	T	.	PASS	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	3905	.	T	G	.	PASS	ANN=G|missense_variant|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.3640T>G|p.F1214V|3640/21290|3640/21290|1214/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=-1.04511;CONS_HMM_SARBECOVIRUS=-1.04511;CONS_HMM_VERTEBRATE_COV=0
MN908947.3	7533	.	G	A	.	PASS	ANN=A|missense_variant|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.7268G>A|p.C2423Y|7268/21290|7268/21290|2423/7095||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	9489	.	G	A	.	PASS	ANN=A|missense_variant|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.9224G>A|p.S3075N|9224/21290|9224/21290|3075/7095||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	14408	.	C	T	.	PASS	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	15324	.	C	T	.	PASS	ANN=T|missense_variant|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.15059C>T|p.T5020I|15059/21290|15059/21290|5020/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=0;CONS_HMM_SARBECOVIRUS=0;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=RNA-dir_pol_C;PFAM_DESCRIPTION=RNA-directed RNA polymerase,  C-terminal domain
MN908947.3	20468	.	C	T	.	PASS	ANN=T|missense_variant|MODERATE|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.20203C>T|p.R6735C|20203/21290|20203/21290|6735/7095||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_C;PFAM_DESCRIPTION=Coronavirus replicase NSP15, uridylate-specific endoribonuclease
MN908947.3	23403	.	A	G	.	PASS	ANN=G|missense_variant|MODERATE|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.1841A>G|p.D614G|1841/3822|1841/3822|614/1273||;CONS_HMM_SARS_COV_2=0.57215;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=0
MN908947.3	23746	.	A	C	.	PASS	ANN=C|synonymous_variant|LOW|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.2184A>C|p.P728P|2184/3822|2184/3822|728/1273||;CONS_HMM_SARS_COV_2=0;CONS_HMM_SARBECOVIRUS=0;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=Spike_S2_CoV;PFAM_DESCRIPTION=Spike glycoprotein S2, coronavirus
MN908947.3	28667	.	T	G	.	PASS	ANN=G|missense_variant|MODERATE|N|gene-GU280_gp10|transcript|TRANSCRIPT_gene-GU280_gp10|protein_coding|1/1|c.394T>G|p.W132G|394/1260|394/1260|132/419||;CONS_HMM_SARS_COV_2=2.31892;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=2.31892;PFAM_NAME=Nucleocap_CoV;PFAM_DESCRIPTION=Nucleocapsid protein, coronavirus
MN908947.3	29852	.	AGCTTCTTAGGAGAATGAC	A	.	PASS	.