mutation fields

The mutation endpoint contains data from TCGA about genes and mutations

Column names that have a . between words denote that the term after the . is a nested field. Nesting structure can be more easily browsed in the mutation JSON schema

column_name description data_type
AA_MAF Non-reference allele and frequency of existing variant in NHLBI-ESP African American population STRING
AFR_MAF Non-reference allele and frequency of existing variant in 1000 Genomes combined African population FLOAT
ALLELE_NUM Allele number from input; 0 is reference, 1 is first alternate etc. STRING
AMR_MAF Non-reference allele and frequency of existing variant in 1000 Genomes combined American population FLOAT
Allele The variant allele used to calculate the consequence STRING
Amino_acids Amino acid substitution caused by the mutation. Only given if the variation affects the protein-coding sequence STRING
BIOTYPE Biotype of transcript STRING
CANONICAL A flag (YES) indicating that the VEP-based canonical transcript, the longest translation, was used for this gene. If not, the value is null STRING
CCDS The CCDS identifier for this transcript, where applicable STRING
CDS_position Relative position of base pair in coding sequence. A - symbol is displayed as the numerator if the variant does not appear in coding sequence STRING
CLIN_SIG Clinical significance of variant from dbSNP STRING
CONTEXT The reference allele per VCF specs, and its five flanking base pairs STRING
COSMIC Overlapping COSMIC variants STRING
Center One or more genome sequencing center reporting the variant STRING
Chromosome Chromosome, possible values: chr1-22, and chrX STRING
Codons The alternative codons with the variant base in upper case STRING
Consequence Consequence type of this variant; sequence ontology terms STRING
DISTANCE Shortest distance from the variant to transcript INTEGER
DOMAINS The source and identifier of any overlapping protein domains STRING
EAS_MAF Non-reference allele and frequency of existing variant in 1000 Genomes combined East Asian population FLOAT
EA_MAF Non-reference allele and frequency of existing variant in NHLBI-ESP European American population STRING
ENSP The Ensembl protein identifier of the affected transcript STRING
EUR_MAF Non-reference allele and frequency of existing variant in 1000 Genomes combined European population FLOAT
EXON The exon number (out of total number) STRING
End_Position Highest numeric genomic position of the reported variant on the genomic reference sequence. Mutation end coordinate INTEGER
Entrez_Gene_Id Entrez gene ID (an integer). 0 is used for regions that do not correspond to a gene region or Ensembl ID INTEGER
ExAC_AF Global Allele Frequency from ExAC STRING
ExAC_AF_AFR African/African American Allele Frequency from ExAC STRING
ExAC_AF_AMR American Allele Frequency from ExAC STRING
ExAC_AF_Adj Adjusted Global Allele Frequency from ExAC STRING
ExAC_AF_EAS East Asian Allele Frequency from ExAC STRING
ExAC_AF_FIN Finnish Allele Frequency from ExAC STRING
ExAC_AF_NFE Non-Finnish European Allele Frequency from ExAC STRING
ExAC_AF_OTH Other Allele Frequency from ExAC STRING
ExAC_AF_SAS South Asian Allele Frequency from ExAC STRING
Existing_variation Known identifier of existing variation STRING
Exon_Number The exon number (out of total number) STRING
FILTER Copied from input VCF. This includes filters implemented directly by the variant caller and other external software used in the DNA-Seq pipeline. See below for additional details. STRING
Feature Stable Ensembl ID of feature (transcript, regulatory, motif) STRING
Feature_type Type of feature. Currently one of Transcript, RegulatoryFeature, MotifFeature (or blank) STRING
GDC_FILTER GDC filters applied universally across all MAFs STRING
GDC_Validation_Status GDC implementation of validation checks. See notes section (#5) below for details STRING
GMAF Non-reference allele and frequency of existing variant in 1000 Genomes FLOAT
Gene The gene symbol. In this table, gene symbol is gene name e.g. ACADVL STRING
HGNC_ID Gene identifier from the HUGO Gene Nomenclature Committee if applicable STRING
HGVS_OFFSET Indicates by how many bases the HGVS notations for this variant have been shifted INTEGER
HGVSc The coding sequence of the variant in HGVS recommended format STRING
HGVSp The protein sequence of the variant in HGVS recommended format. p.= signifies no change in the protein STRING
HGVSp_Short Same as the HGVSp column, but using 1-letter amino-acid codes STRING
Hugo_Symbol HUGO symbol for the gene (HUGO symbols are always in all caps). Unknown is used for regions that do not correspond to a gene STRING
IMPACT The impact modifier for the consequence type STRING
INTRON The intron number (out of total number) STRING
MC3_Overlap Indicates whether this region overlaps with an MC3 variant for the same sample pair STRING
MINIMISED Alleles in this variant have been converted to minimal representation before consequence calculation (1 or null) STRING
Matched_Norm_Sample_UUID Unique GDC identifier for normal aliquot (10189 unique) STRING
Mutation_Status An assessment of the mutation as somatic, germline, LOH, post transcriptional modification, unknown, or none. The values allowed in this field are constrained by the value in the Validation_Status field STRING
NCBI_Build The reference genome used for the alignment (GRCh38) STRING
One_Consequence The single consequence of the canonical transcript in sequence ontology terms, eg missense_variant STRING
PHENO Indicates if existing variant is associated with a phenotype, disease or trait (0, 1, or null) STRING
PICK Indicates if this block of consequence data was picked by VEP's pick feature (1 or null) STRING
PUBMED Pubmed ID(s) of publications that cite existing variant STRING
PolyPhen The PolyPhen prediction and/or score STRING
Protein_position Relative position of affected amino acid in protein. A - symbol is displayed as the numerator if the variant does not appear in coding sequence STRING
RefSeq RefSeq identifier for this transcript STRING
Reference_Allele The plus strand reference allele at this position. Includes the deleted sequence for a deletion or - for an insertion STRING
SAS_MAF Non-reference allele and frequency of existing variant in 1000 Genomes combined South Asian population FLOAT
SIFT The SIFT prediction and/or score, with both given as prediction (score) STRING
SOMATIC Somatic status of each ID reported under Existing_variation (0, 1, or null) STRING
SWISSPROT UniProtKB/Swiss-Prot accession STRING
SYMBOL Eg TP53, LRP1B, etc (same as Hugo_Symbol field except blank instead of Unknown STRING
SYMBOL_SOURCE The source of the gene symbol, usually HGNC, rarely blank, other sources include Uniprot_gn, EntrezGene, etc STRING
Sequencer Instrument used to produce primary sequence data STRING
Start_Position Lowest numeric position of the reported variant on the genomic reference sequence. Mutation start coordinate INTEGER
Strand Either + or - to denote whether read mapped to the sense (+) or anti-sense (-) strand STRING
TRANSCRIPT_STRAND The DNA strand (1 or -1) on which the transcript/feature lies INTEGER
TREMBL UniProtKB/TrEMBL identifier of protein product STRING
TSL Transcript support level, which is based on independent RNA analyses INTEGER
Transcript_ID Ensembl ID of the transcript affected by the variant STRING
Tumor_Sample_UUID Unique GDC identifier for tumor aliquot (10189 unique) STRING
Tumor_Seq_Allele1 Primary data genotype for tumor sequencing (discovery) allele 1. A - symbol for a deletion represents a variant. A - symbol for an insertion represents wild-type allele. Novel inserted sequence for insertion does not include flanking reference bases STRING
Tumor_Seq_Allele2 Primary data genotype for tumor sequencing (discovery) allele 2. A - symbol for a deletion represents a variant. A - symbol for an insertion represents wild-type allele. Novel inserted sequence for insertion does not include flanking reference bases STRING
Tumor_Validation_Allele1 Secondary data from orthogonal technology. Tumor genotyping (validation) for allele 1. A - symbol for a deletion represents a variant. A - symbol for an insertion represents wild-type allele. Novel inserted sequence for insertion does not include flanking reference bases STRING
Tumor_Validation_Allele2 Secondary data from orthogonal technology. Tumor genotyping (validation) for allele 2 STRING
UNIPARC UniParc identifier of protein product STRING
VARIANT_CLASS Sequence Ontology variant class STRING
Validation_Method The assay platforms used for the validation call STRING
Variant_Classification Translational effect of variant allele STRING
Variant_Type Type of mutation. TNP (tri-nucleotide polymorphism) is analogous to DNP (di-nucleotide polymorphism) but for three consecutive nucleotides. ONP (oligo-nucleotide polymorphism) is analogous to TNP but for consecutive runs of four or more (SNP, DNP, TNP, ONP, INS, DEL, or Consolidated) STRING
aliquot_barcode_normal TCGA aliquot barcode for the normal control, eg TCGA-12-1089-01A-01D-0517-01 STRING
aliquot_barcode_tumor TCGA aliquot barcode for the tumor, eg TCGA-12-1089-01A-01D-0517-01 STRING
all_effects A semicolon delimited list of all possible variant effects, sorted by priority ([Symbol,Consequence,HGVSp_Short,Transcript_ID,RefSeq,HGVSc,Impact,Canonical,Sift,PolyPhen,Strand]) STRING
cDNA_position Relative position of base pair in the cDNA sequence as a fraction. A - symbol is displayed as the numerator if the variant does not appear in cDNA STRING
callerName -delimited list of mutation caller(s) that agreed on this particular call, always in alphabetical order: muse, mutect, somaticsniper, varscan
case_barcode Original TCGA case barcode, eg TCGA-DX-A8BN STRING
case_id Unique GDC identifier for the underlying case STRING
dbSNP_RS The rs-IDs from the dbSNP database, novel if not found in any database used, or null if there is no dbSNP record, but it is found in other databases STRING
dbSNP_Val_Status The dbSNP validation status is reported as a semicolon-separated list of statuses. The union of all rs-IDs is taken when there are multiple STRING
fileName -delimited list of name of underlying MAF file
fileUUID -delimited list of unique GDC identifiers for underlying MAF file
n_depth Read depth across this locus in normal BAM STRING
normal_bam_uuid Unique GDC identifier for the underlying normal bam file STRING
project_short_name Project name abbreviation; the program name appended with a project name abbreviation; eg. TCGA-OV, etc. STRING
sample_barcode_normal TCGA sample barcode for the normal control, eg TCGA-12-1089-01A. One sample may have multiple sets of CN segmentations corresponding to multiple aliquots; use GROUP BY appropriately in queries STRING
sample_barcode_tumor TCGA sample barcode for the tumor, eg TCGA-12-1089-01A. One sample may have multiple sets of CN segmentations corresponding to multiple aliquots; use GROUP BY appropriately in queries STRING
src_vcf_id -delimited list of GDC VCF file identifiers
t_alt_count Read depth supporting the variant allele in tumor BAM STRING
t_depth Read depth across this locus in tumor BAM STRING
t_ref_count Read depth supporting the reference allele in tumor BAM STRING
tumor_bam_uuid Unique GDC identifier for the underlying bam file STRING
Last update: 2022-09-28
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