Small Variants Summary
|
Statistic |
Description |
|---|---|
|
Total Passing |
The total number of variants present in the data set that passed the variant quality filters. |
|
Percent Found in dbSNP |
100*(number of variants in dbSNP/Number of variants) |
|
Het/Hom Ratio |
Number of heterozygous variants/Number of homozygous variants. |
|
Ts/Tv Ratio |
Transition rate of SNVs that pass the quality filters divided by the transversion rate of SNVs that pass the quality filters. Transitions are interchanges of purines (A, G) or of pyrimidines (C, T). Transversions are interchanges between purine and pyrimidine bases (for example, A to T). |
|
Mean Variant Frequency |
Number of reads in which the variant was detected divided by the number of reads. |
In the following table, genes include exons, introns, and UTR regions. Exons include coding and UTR regions. UTR regions include 5′ and 3′ UTR regions. Splice site regions include regions annotated as splice acceptor, splice donor, splice site, or splice region.
|
Statistic |
Description |
|---|---|
|
In Genes |
The number of variants that occur in a gene. |
|
In Exons |
The number of variants that occur in an exon. |
|
In Coding Regions |
The number of variants that occur in a coding region. |
|
In UTR Region |
The number of variants that occur in an untranslated region (UTR). |
|
In Splice Site Regions |
The number of variants that occur in a splice site region. |
|
In Mature microRNA |
The number of variants that occur in a mature microRNA. |
For the Variants by Consequence table, we calculate variation consequences using the guideline at uswest.ensembl.org/info/genome/variation/predicted_data.html#consequences.
|
Statistic |
Description |
|---|---|
|
Frameshifts |
The number of variants that cause a frameshift. |
|
Nonsynonymous |
The number of variants that cause an amino acid change in a coding region. |
|
Synonymous |
The number of variants that are within a coding region but do not cause an amino acid change. |
|
Stop Gained |
The number of variants that cause an additional stop codon. |
|
Stop Lost |
The number of variants that cause the loss of a stop codon. |