Variants Table
Use the Variants Table to view, sort, filter, and export a subset of the data provided in the VCF files.
|
Statistic |
Definition |
|---|---|
|
Chromosome (Chr) |
Name of reference chromosome. |
|
Position (Pos) |
Position within reference chromosome. |
|
Reference Allele (Ref) |
The reference allele. |
|
Variant Allele (Alt) |
The alt allele. |
|
Variant Type (Type) |
Type of variant, including single nucleotide variant (SNV), insertion, and deletion. |
|
Sequence Context (Context) |
Location of the variant based on annotations of the reference genome. |
|
Consequence |
Predicted transcript consequence as described at uswest.ensembl.org/info/genome/variation/predicted_data.html#consequences. |
|
dbSNP ID (dbSNP) |
Identifier in the Single Nucleotide Polymorphism Database (dbSNP), a free public archive for genetic variation within and across different species developed and hosted by the National Center for Biotechnology Information (NCBI). |
|
COSMIC ID (COSMIC) |
The numeric identifier for the variant in the Catalogue of Somatic Mutations in Cancer (COSMIC) database. |
|
ClinVar |
Clinical significance based on the freely accessible, public archive of reports of the relationships among human variations and phenotypes |
|
Variant Quality (Qual) |
Phred-scaled quality score indicating how confident we are in this asserted haplotype. |
|
Variant Frequency (Alt Freq) |
Proportion of the variant allele among all alleles being considered. |
|
Total Depth |
Number of reads aligned at this position. |
|
Reference Allele Depth (Ref Depth) |
Number of reads containing the reference allele. |
|
Variant Allele Depth (Alt Depth) |
Number of reads containing the variant allele. |
|
Strand Bias |
Strand bias is a type of sequencing bias in which one DNA strand is favored over the other. This bias can result in incorrect evaluation of the amount of evidence observed for one allele versus the other. |