Analysis Output | Sample Analysis Reports | Variants Table

Variants Table

Use the Variants Table to view, sort, filter, and export a subset of the data provided in the VCF files.

Note

The Variants table is provided on the Sample Analysis Reports page, and not in the TruSeq Amplicon Sequencing Report.

Table 7   Variants Table

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 1 DNA strand is favored over the other, which can result in incorrect evaluation of the amount of evidence observed for one allele versus the other.