Detailed Information for Outputted Files from Somatic Mutation Annotators（annovar 注释文件条目详细解释）

• CONTENTS
• *_annoTable.txt (ANNOVAR)
• *_annoTable.txt (SnpEff)
• *_genelist.txt (ANNOVAR & SnpEff)
• dbNSFP Information

We provide here detailed Description about the files outputted from the somatic mutation annotators via ANNOVAR and SnpEff.

• *_annoTable.txt from the annotator via ANNOVAR

Column Names	Description
Chr	Chromosome number
Start	Start position
End	End position
Ref	Reference base(s)
Alt	Alternate non-reference alleles called on at least one of the samples
COSMIC ID	COSMIC ID
Func.refGene	Regions (e.g., exonic, intronic, non-coding RNA)) that one variant hits; please click here for details.
Gene.refGene	Gene name associated with one variant
ExonicFunc.refGene	Exonic variant function, e.g., nonsynonymous, synonymous, frameshift insertion.please click here for details.
AAChange.refGene	Amino acid change. For example, SAMD11:NM_152486:exon10:c.T1027C:p.W343R stands for gene name, Known RefSeq accession, region, cDNA level change, protein level change.
SIFT_score	SIFT score. See the dbNSFP information table for details.
SIFT_pred	SIFT prediction. See the dbNSFP information table for details.
Polyphen2_HDIV_score	Pholyphen2 score based on HDIV. See the dbNSFP information table for details.
Polyphen2_HDIV_pred	Pholyphen2 prediction based on HDIV. See the dbNSFP information table for details.
Polyphen2_HVAR_score	Polyphen2 score based on HVAR. See the dbNSFP information table for details.
Polyphen2_HVAR_pred	Polyphen2 prediction based on HVAR. See the dbNSFP information table for details.
LRT_score	LRT score. See the dbNSFP information table for details.
LRT_pred	LRT prediction. See the dbNSFP information table for details.
MutationTaster_score	MutationTaster score. See the dbNSFP information table for details.
MutationTaster_pred	MutationTaster prediction. See the dbNSFP information table for details.
MutationAssessor_score	MutationTaster score. See the dbNSFP information table for details.
MutationAssessor_pred	MutationTaster prediction. See the dbNSFP information table for details.
FATHMM_score	FATHMM score. See the dbNSFP information table for details.
FATHMM_pred	FATHMM prediction. See the dbNSFP information table for details.
PROVEAN_score	PROVEAN score<. See the dbNSFP information table for details./td>
PROVEAN_pred	PROVEAN prediction. See the dbNSFP information table for details.
VEST3_score	VEST V3 score. See the dbNSFP information table for details.
CADD_raw	CADD raw score. See the dbNSFP information table for details.
CADD_phred	CADD phred-like score. See the dbNSFP information table for details.
DANN_score	DANN score. See the dbNSFP information table for details.
fathmm-MKL_coding_score	fathmm-MKL score for one coding variant. See the dbNSFP information table for details.
fathmm-MKL_coding_pred	fathmm-MKL prediction for one coding variant. See the dbNSFP information table for details.
MetaSVM_score	MetaSVM score. See the dbNSFP information table for details.
MetaSVM_pred	MetaSVM prediction. See the dbNSFP information table for details.
MetaLR_score	MetaLR score. See the dbNSFP information table for details.
MetaLR_pred	MetaLR prediction. See the dbNSFP information table for details.
integrated_fitCons_score	fitCons score<. See the dbNSFP information table for details./td>
integrated_confidence_value	confidence level. See the dbNSFP information table for details.
GERP++_RS	GREP++ "rejected substitutions" (RS) score. See the dbNSFP information table for details.
phyloP7way_vertebrate	Phylogenetic p-values for 7 vertebrate species. See the dbNSFP information table for details.
phyloP20way_mammalian	Phylogenetic p-values for 20 mammalian species. See the dbNSFP information table for details.
phastCons7way_vertebrate	PhastCons score for 7 vertebrate species. See the dbNSFP information table for details.
phastCons20way_mammalian	phastCons p-values for 20 mammalian species. See the dbNSFP information table for details.
SiPhy_29way_logOdds	SiPhy log odds score for 29 species. See the dbNSFP information table for details.

• *_annoTable.txt from the annotator via SnpEff

Column Names	Description
CHROM	Chromosome number
POS	Position
ID	semi-colon separated list of unique identifiers where available. If this is a dbSNP variant it is encouraged to use the rs number(s).
REF	Reference base(s)
ALT	Alternate non-reference alleles called on at least one of the samples
EFFECT	Functional consequences of one variant, e.g., missense_variant, synonymous_variant. please clickhere for details.
REGION	Regions (e.g., exonic, intronic) that one variant hits
IMPACT	Putative impact of the variant (e.g. HIGH, MODERATE or LOW impact).
GENE	Gene name (usually HUGO)
GENEID	Gene ID)
FEATURE	The type of feature is in the next field (e.g. transcript, motif, miRNA, etc.)
FEATUREID	Transcript ID (preferably using version number), Motif ID, miRNA, ChipSeq peak, Histone mark, depending on the annotation.
BIOTYPE	Description on whether the transcript is {“Coding”, “Noncoding”}. Whenever possible, use ENSEMBL biotypes. .
HGVS_C	Variant using HGVS notation (DNA level). For example, c.352A>G stands for A to G substitution of nucleotide 352. Click here for details.
HGVS_P	Coding variant using HGVS notation (Protein level). For example, p.Ile118Val stands for Isoleucine at position number 66 substitution to Valine. p.Ile118Val can be also be represented by p.I118V using the 1-letter symbol here. Click here for details.
SIFT_score	SIFT score. See the dbNSFP information table for details.
SIFT_pred	SIFT prediction. See the dbNSFP information table for details.
Polyphen2_HDIV_score	Pholyphen2 score based on HDIV. See the dbNSFP information table for details.
Polyphen2_HDIV_pred	Pholyphen2 prediction based on HDIV. See the dbNSFP information table for details.
Polyphen2_HVAR_score	Polyphen2 score based on HVAR. See the dbNSFP information table for details.
Polyphen2_HVAR_pred	Polyphen2 prediction based on HVAR. See the dbNSFP information table for details.
LRT_score	LRT score. See the dbNSFP information table for details.
LRT_pred	LRT prediction. See the dbNSFP information table for details.
MutationTaster_score	MutationTaster score. See the dbNSFP information table for details.
MutationTaster_pred	MutationTaster prediction. See the dbNSFP information table for details.
MutationAssessor_score	MutationAssessor score. See the dbNSFP information table for details.
MutationAssessor_pred	MutationAssessor prediction. See the dbNSFP information table for details.
FATHMM_score	FATHMM score. See the dbNSFP information table for details.
FATHMM_pred	FATHMM prediction. See the dbNSFP information table for details.
PROVEAN_score	PROVEAN score<. See the dbNSFP information table for details./td>
PROVEAN_pred	PROVEAN prediction. See the dbNSFP information table for details.
VEST3_score	VEST V3 score. See the dbNSFP information table for details.
CADD_raw	CADD raw score. See the dbNSFP information table for details.
CADD_phred	CADD phred-like score. See the dbNSFP information table for details.
MetaSVM_score	MetaSVM score. See the dbNSFP information table for details.
MetaSVM_pred	MetaSVM prediction. See the dbNSFP information table for details.
MetaLR_score	MetaLR score. See the dbNSFP information table for details.
MetaLR_pred	MetaLR prediction. See the dbNSFP information table for details.
GERP++_NR	GREP++ conservation score. See the dbNSFP information table for details.
GERP++_RS	GREP++ "rejected substitutions" (RS) score. See the dbNSFP information table for details.
phyloP100way_vertebrate	Phylogenetic p-values for 100 vertebrate species. See the dbNSFP information table for details.
phastCons100way_vertebrate	PhastCons score for 7 vertebrate species. See the dbNSFP information table for details.
SiPhy_29way_logOdds	SiPhy log odds score for 29 species. See the dbNSFP information table for details.

• *_genelist.txt from the annotators via ANNOVAR and SnpEff

Column Names	Description
Gene	Gene name associated with each variant; one gene name may correspond to several variants.
Mutations	Amino acid change information. For example, SAMD11:NM_152486:exon10:c.T1027C:p.W343R stands for gene name, Known RefSeq accession, region, cDNA level change, protein level change..

• dbNSFP Information

Columns of Annotations from dbNSFP Database	Pediction Algorithm/Conservation Score	Description	Method	Categorical Prediction	Author(s)
SIFT_pred  SIFT_score	SIFT	Sort intolerated from tolerated	P(An amino acid at a position is tolerated | The most frequentest amino acid being tolerated)	D: Deleterious (sift<=0.05); T: tolerated (sift>0.05)	Pauline Ng, Fred Hutchinson  Cancer Research Center, Seattle, Washington
Polyphen2_HDIV_pred  Polyphen2_HDIV_score	Polyphen v2	Polymorphism phenotyping v2	D: Probably damaging (>=0.957),  P: possibly damaging (0.453<=pp2_hdiv<=0.956),  B: benign (pp2_hdiv<=0.452)	Probablistic Classifier Training sets: HumDiv	Havard Medical School/td>
Polyphen2_HVAR_pred Polyphen2_HVAR_score	Polyphen v2	Polymorphism phenotyping v2	Machine learning Training sets: HumVar	D: Probably damaging (>=0.957),  P: possibly damaging (0.453<=pp2_hdiv<=0.956); B: benign (pp2_hdiv<=0.452)	Shamil Sunyaev Havard Medical School
LRT_pred  LRT_score	LRT	Likelihood ratio test	LRT of H0: each codon evolves neutrally vs H1: the codon evovles under negative selection	D: Deleterious;  N: Neutral; U: Unknown Lower scores are more deleterious	Sung Chung, Justin Fay Washington University
MutationTaster_pred  MutationTaster_score	MutationTaster	Bayes Classifier	A: (""disease_causing_automatic"");  D: (""disease_causing"");  N: (""polymorphism [probably harmless]"");  P: (""polymorphism_automatic[known to be harmless]" higher values are more deleterious"		Markus Schuelke the Charité - Universitätsmedizin Berlin
MutationAssessor_pred  MutationAssessor_score	MutationAssessor	Entropy of multiple sequence alighnment	H: high;  M: medium;  L: low;  N: neutral.  H/M means functional and L/N means non-functional higher values are more deleterious		Reva Boris Computation Biology Center Memorial Sloan Kettering Cancer Center
FATHMM_pred  FATHMM_score	FATHMM	HMM	Functional analysis through hidden markov model HMM	D: Deleterious;  T: Tolerated; lower values are more deleterious	Shihab Hashem University of Bristol, UK
PROVEAN_pred  PROVEAN_score		Protein Variation Effect Analyzer	Clustering of homologus sequences	D: Deleterious;  N: Neutral higher values are more deleterious	Choi Y J. Craig Venter Institute
VEST3_score	VEST V3	Variant effect scoring tool	Random forest classifier	higher values are more deleterious	Rachel Karchin John Hopkins University
CADD_raw CADD_phred	CADD Combined annotation dependent depletion	Linear kernel SVM	higher values are more deleterious		Jay Shendure, Xiaohui Xie University of California - Irvine
DANN_score	DANN	Deleterious Annotation of genetic variants using Neural Networks	Neural network	higher values are more deleterious	Jay Shendure, Xiaohui Xie University of California - Irvine
fathmm-MKL_coding_pred	FATHMM-MKL	predicting the effects of both coding and non-coding variants using nucleotide-based HMMs	Classifier based on multiple kernel learning	D: Deleterious;  T: Tolerated Score >= 0.5: D;  Score < 0.5: T	Shihab Hashem University of Bristol, UK
MetaSVM_pred  MetaSVM_score	MetaSVM	Support vector machine	D: Deleterious; T: Tolerated; higher scores are more deleterious		Coco Dong USC Biostatiscs Department
MetaLR_pred  MetaLR_score	MetaLR	Logistic regression	D: Deleterious;  T: Tolerated;  higher scores are more deleterious		Coco Dong  USC Biostatiscs Department
integrated_fitCons_score  integrated_confidence_value	FitCons	Fitness consequences of functional annotation	Integrate functional assays like ChIP-Seq with conservation measure of transcription factor binding sites	higher scores are more deleterious	Abriza Cold Spring Harbor Lab
GERP++_RS GERP++_NR	Genome Evolutionary Rate Profiling ++	maximum likelihood estimation procedure	higher scores are more deleterious		Eugne Davydov Stanford University, CS Department
phyloP7way_vertebrate	PhyloP	Phylogentic p-values	Phylogentic p-values calculated from a LRT, score-based test, GERP test Use 7 species	higher scores are more deleterious	Adam Siepel  UCSC
phyloP20way_mammalian	PhyloP	Phylogentic p-values	a phylogenetic hidden Markov model (phylo-HMM) Use 20 species	higher scores are more deleterious	Adam Siepel UCSC
phastCons7way_vertebrate	phastCons	A phylogenetic hidden Markov model (phylo-HMM) Use 7 species	higher scores are more deleterious		Adam Siepel UCSC
phastCons20way_mammalian	phastCons	a phylogenetic hidden Markov model (phylo-HMM) Use 20 species	higher scores are more deleterious		Adam Siepel UCSC
SiPhy_29_way	SiPhy	Probablistic framework, HMM Use 29 species	higher scores are more deleterious		Manual Garber Broad Institute of MIT & Harvard

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Questions? Kindly contact arraytools [at] emmes.com using the subject heading detailed information for outputted files from somatic mutation annotators.

原文链接地址：https://brb.nci.nih.gov/seqtools/colexpanno.html