reported on 2013/02/13
Reads information
Experiment ID: test-nomonma-0103 Sample Name: NA12156_exome_1 SRX005923/SRR017931
Organism: human Sequencer: Genome Analyzer IIx
Library Layout: SINGLE


Variation Call (GATK-1.4)

*Total Number of Variations


*dbSNP (dbSNP135)

Novel:variations not registered in dbSNP, Known:variations registered in dbSNP, dbSNP%: % of variations registered in dbSNP, Ti/Tv:Transition/Transversion ration


Variation Annotation Summary ( Annovar-2011Jun18)

*Hit On

exonic:variations overlap a coding exon, splicing:variations are within 2-bp of a splicing junction, exonic,splicing:variations are within exon but close to exon/intron boundary, ncRNA:variations overlap a transcript without coding annotation in the gene definition, UTR5:variations overlap a 5' untranslated region, UTR3:variations overlap a 3' untranslated region, UTR5,UTR3:variations are located in both 5' UTR and 3' UTR region, intronic:variations overlap an intron, upstream:variations overlap 1-kb region upstream of transcription start site, downstream:variations overlap 1-kb region downtream of transcription end site, upstream,downstream:variations are located in both downstream and upstream region, intergenic:variations are in intergenic region (others) invalid:regareded as invalid data by annovar. See also Annovar gene-based annotation site

*Variation Kinds

frameshift ins.:insertions of one or more nucleotides that cause frameshift changes in protein coding sequence, frameshift del.:deletions of one or more nucleotides that cause frameshift changes in protein coding sequence, frameshift block sub.:block substitutions of one or more nucleotides that cause frameshift changes in protein coding sequence, stopgain:nonsynonymous SNV, frameshift insertion/deletion, nonframeshift insertion/deletion or block substitution that lead to the immediate creation of stop codon at the variant site. For frameshift mutations, the creation of stop codon downstream of the variant will not be counted as "stopgain", stoploss:nonsynonymous SNV, frameshift insertion/deletion, nonframeshift insertion/deletion or block substitution that lead to the immediate elimination of stop codon at the variant site, nonframeshift ins.:an insertion of 3 or multiples of 3 nucleotides that do not cause frameshift changes in protein coding sequence, nonframeshift del.:deletions of 3 or mutliples of 3 nucleotides that do not cause frameshift changes in protein coding sequence, nonframeshift block sub.:block substitutions of one or more nucleotides that do not cause frameshift changes in protein coding sequence, nonsynonymous SNV:a single nucleotide changes that cause an amino acid change, synonymous SNV:a single nucleotide changes that cause an amino acid change, unknown:unknown function (due to various errors in the gene structure definition in the database file) See also Annovar filter-based annotation site


*Variation Information and Download Files

DOWNLOAD FILE FORMAT:tab-delimited with following data; 1.chromosome 2.position 3.dbSNP ID 4.reference base(s) 5.alternate non-reference alleles 6.quality score 7.filter 8.additional information 9.hit region 10.gene or two neighboring genes 11.amino acid changes 12.gene name, transcript identifier and sequence change 13.SIFT filtering score 14.Polyphen2 filtering score 15.LRT filtering score 16.Mutation Taster filtering score 17.PhyloP filtering score (1~8 are generated by GATK, 9~12 by annovar gene-based annotation, 13~17 by annovar filter-based annotation)