test.nextprot.vcf

##fileformat=VCFv4.1
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">
##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
##contig=<ID=6,length=171115067,assembly=hg19>
##SnpEffVersion="4.1g (build 2015-05-17), by Pablo Cingolani"
##SnpEffCmd="SnpEff  GRCh37.75 -formatEff -classic /tmp/test.nextprot.vcf "
##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_Number [ | 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	FORMAT	1094PC0005
6	34950531	.	G	A	.	PASS	EFF=SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T245|1134|ANKS1A|protein_coding|CODING|ENST00000360359|5|A),SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T245|320|ANKS1A|protein_coding|CODING|ENST00000535627|5|A)	GT:AD:BQ:DP:FREQ:SS	0/1:38,34:36:72:0.472:2
6	170862300	.	G	C	.	PASS	EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Gct|P11A|241|PSMB1|protein_coding|CODING|ENST00000262193|1|C),NEXT_PROT[maturation_peptide](LOW||||241|PSMB1|protein_coding|CODING|||C),UPSTREAM(MODIFIER||1167||339|TBP|protein_coding|CODING|ENST00000230354||C),UPSTREAM(MODIFIER||2771|||PSMB1|processed_transcript|CODING|ENST00000462957||C),UPSTREAM(MODIFIER||1090||207|TBP|protein_coding|CODING|ENST00000421512||C|WARNING_TRANSCRIPT_INCOMPLETE),UPSTREAM(MODIFIER||1121||339|TBP|protein_coding|CODING|ENST00000392092||C),UPSTREAM(MODIFIER||1121||319|TBP|protein_coding|CODING|ENST00000540980||C),UPSTREAM(MODIFIER||1393||149|TBP|protein_coding|CODING|ENST00000423353||C|WARNING_TRANSCRIPT_INCOMPLETE)	GT:AD:DP:GQ:PL	1/1:0,108:108:99:3610,324,0