ANNOVAR人类各个数据库变异注释结果表格说明
ANNOVAR人类各个数据库变异注释结果表格说明，SnpEff
- ANNOVAR注释结果中各列的表头说明：
| ID | 详解 |
| Chr | 染色体 |
| Start | 变异位点在染色体上的起始位置 |
| End | 变异位点在染色体上的结束位置 |
| Ref | 参考基因组碱基型 |
| Alt | 变异碱基型 |
| Func.refGene | 对变异位点所在的区域进行注释（exonic, splicing, UTR5, UTR3, intronic, ncRNA_exonic, ncRNA_intronic, ncRNA_UTR3, ncRNA_UTR5, ncRNA _splicing, upstream, downstream, intergenic） |
| Gene.refGene | 列出该变异位点相关的转录本（只有功能符合 Func 列的转录本才列出）。如果 Func 为intergenic，此处列出两侧的基因名 |
| GeneDetail.refGene | 描述 UTR、splicing、ncRNA_splicing 或 intergenic 区域的变异情况。当 Func 列的值为exonic、ncRNA_exonic、intronic、ncRNA_intronic、upstream、downstream、upstream;downstream、ncRNA_UTR3、ncRNA_UTR5 时，该列为空；当 Func 列的值为 intergenic 时，该列格式为dist=1366;dist=22344，表示该变异位点距离两侧基因的距离 |
| ExonicFunc.refGene | 外显子区的 SNV or InDel 变异类型（SNV 的变异类型包括 synonymous_SNV, missense_SNV, stopgain_SNV, stopgloss_SNV 和 unknown；Indel 的变异类型包括 frameshift insertion, frameshift deletion, stopgain, stoploss, nonframeshift insertion, nonframeshift deletion 和 unknown） |
| AAChange.refGene | 氨基酸改变，只有当 Func 列为 exonic 或 exonic;splicing 时，该列才有结果。按照每个转录本进行注释（例如，NADK:NM_001198995:exon10:c.1240_1241insAGG:p.G414delinsEG，其中，NADK 表示该变异所在的基因名称，NM_001198995 表示该变异所在的转录本 ID，exon10 表示该变异位于转录本的第 10 个外显子上，c.1240_1241insAGG 表示该变异引起 cDNA 在第 1240 和 1241 位之间插入 AGG，p.G414delinsEG 表示该变异引起蛋白序列在第 414 位上的氨基酸由 Gly 变为 Gly-Glu。再如， FMN2:NM_020066:exon1:c.160_162del:p.54_54del，表示该变异引起 cDNA 的第 160 到 162 位发生删除，p.54_54del 表示该变异引起蛋白序列在第 54 位上的氨基酸删除） |
| cytoBand | 该变异位点所处的染色体区段（利用 Giemas 染色观察得到的） |
| genomicSuperDups | 基因组中的重复片段 |
| nci60 | NCI-60 human tumor cell line panel exome sequencing allele frequency data |
| esp6500siv2_all | 国家心肺和血液研究所外显子组测序计划（NHLBI-ESP project，esp6500si_all 数据库中包含SNP 变异、Indel 变异和Y 染色体上的变异）的所有个体中，突变碱基的等位基因频率（alternative allele frequency）。 |
| ALL.sites.2015_08 | 给出千人基因组计划数据（2015 年 8 月公布的版本）的所有人群中，该变异位点上突变碱基的等位基因频率 |
| EAS.sites.2015_08 | 给出千人基因组计划数据（2015 年 8 月公布的版本）的亚洲人群中，该变异位点上突变碱基的等位基因频率 |
| SAS.sites.2015_08 | 给出千人基因组计划数据（2015 年 8 月公布的版本）的南亚洲人群中，该变异位点上突变碱基的等位基因频率 |
| avsnp150 | 该变异在 dbSNP中的 ID |
| SIFT_score | SIFT 分值，表示该变异对蛋白序列的影响，SIFT 分值越小越“有害”，表明该 SNP 导致蛋白结构或功能改变的可能性大； |
| SIFT_pred | D: Deleterious (sift<=0.05); T: tolerated (sift>0.05)） |
| Polyphen2_HDIV_score | 利用 PolyPhen2 基于 HumanDiv 数据库预测该变异对蛋白序列的影响，用于复杂疾病，数值越大越“有害”，表明该 SNP 导致蛋白结构或功能改变的可能性大；damaging (0.453<=pp2_hdiv<=0.956); B: benign (pp2_hdiv<=0.452)） |
| Polyphen2_HDIV_pred | D 或 P 或 B（D: Probably damaging (>=0.957), P: possibly |
| Polyphen2_HVAR_score | 利用 PolyPhen2 基于 HumanVar 数据库预测该变异对蛋白序列的影响，用于单基因遗传病。数值越大越“有害”，表明该 SNP 导致蛋白结构或功能改变的可能性大； |
| Polyphen2_HVAR_pred | D 或 P 或 B（D: Probably damaging (>=0.909), P: possibly damaging (0.447<=pp2_hvar<=0.909); B: benign (pp2_hvar<=0.446)） |
| LRT_score | LRT 分值，表示该变异对蛋白序列的影响，值越大越“有害”，表明该 SNP 导致蛋白结构或功能改变的可能性大。 |
| LRT_pred | D、N 或者 U(D: Deleterious; N: Neutral; U: Unknown)。 |
| MutationTaster_score | MutationTaster 分值，表示该变异对蛋白序列的影响，值越大越“有害”，表明该 SNP 导致蛋白结构或功能改变的可能性大。("polymorphism_automatic" |
| MutationTaster_pred | A ("disease_causing_automatic"); "D" ("disease_causing");"N" ("polymorphism"); "P" |
| MutationAssessor_score | MutationAssessor预测的致病得分 |
| MutationAssessor_pred | MutationAssessor根据阈值判断得到的预测分类：H为较高可信度的致病位点，M为中等可信的致病位点，L为低可信度的致病位点，N为无害位点 |
| FATHMM_score | FATHMM软件预测的致病性得分 |
| FATHMM_pred | FATHMM根据阈值得到的分类：D为较高可信度的致病位点，P为可信度一般的致病位点 |
| RadialSVM_score | higher score denoting more deleterious variants |
| RadialSVM_pred | D: Deleterious; T: Tolerated |
| LR_score | higher score denoting more deleterious variants |
| LR_pred | D: Deleterious; T: Tolerated |
| VEST3_score | Variant effect scoring tool；Random forest classifier， higher values are more deleterious |
| CADD_raw | CADD raw score |
| CADD_phred | CADD phred-like score，higher values are more deleterious |
| GERP++_RS | GREP++ "rejected substitutions" (RS) score，higher scores are more deleterious |
| phyloP46way_placental | higher scores are more deleterious |
| phyloP100way_vertebrate | higher scores are more deleterious |
| SiPhy_29way_logOdds | higher scores are more deleterious |
| dgvMerged | 人类结构变异注释结果：http://dgv.tcag.ca/dgv/app/home |
| phastConsElements100way | 由 phastCons 程序基于脊椎动物全基因组比对预测得到的保守区域，100way 是指使用的物种数目为 100 个 |
| omim_201806 | 孟德尔遗传病数据库注释 |
| cosmic70 | 人类癌症体细胞突变影响的数据库，COSM开头为ID可到网站查询https://cancer.sanger.ac.uk/cosmic |
| CLNALLELEID | the ClinVar Allele ID |
| CLNDN | ClinVar's preferred disease name for the concept specified by disease identifiers in CLNDISDB |
| CLNDISDB | Tag-value pairs of disease database name and identifier, e.g. OMIM:NNNNNN |
| CLNREVSTAT | ClinVar review status for the Variation ID |
| CLNSIG | Clinical significance for this single variant |
| gwasCatalog | 检测变异位点是否在以往的 GWAS 研究中被报导，表示该变异位点与哪些疾病相关联，“.”表示没有 GWAS 报导 |
| HGMD | HGMD注释结果 |
| Allele_frequency | 样品变异碱基的等位基因频率 |
| QUAL | 变异的质量值 |
| FORMAT | 通常为：GT:AD:DP:GQ:PL，标记样品列属性 |
| sample | 样品信息列详情见：https://www.omicsclass.com/article/6 |
当然关于人类的变异信息ANNOVAR注释的数据库很多，这里只列举了部分内容，下面是网上摘录了一个信息：https://brb.nci.nih.gov/seqtools/colexpanno.html
We provide here detailed Description about the files outputted from the mutation annotators via ANNOVAR and SnpEff.
| 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 tablefor 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 tablefor 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 tablefor details. |
- SnpEff 注释结果各表头说明
| 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 click here 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 tablefor 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 tablefor 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 tablefor details. |
详细说明 Information
| 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 |
更多生物信息课程： https://study.omicsclass.com/index
- 发表于 2018-09-28 20:06
- 阅读 ( 27612 )
- 分类：临床医学
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