Small Variants
When available, the Illumina Annotation Engine provides the following fields for each small variant.
|
Metric |
Description |
|---|---|
|
Gene (HGVS) |
Human Genome Variation Society (HGVS) gene notation. |
|
Chromosome |
The chromosome where the SNV, insertion, or deletion is detected. |
|
Genomic Position |
The chromosome coordinate where the SNV, insertion, or deletion is detected. |
|
Reference Call |
The hg19 reference call for the respective chromosome:position. |
|
Alternative Call |
The observed variant call for the respective chromosome:position. |
|
P-Dot Notation |
HGVS protein change notation. |
|
C-Dot Notation |
HGVS nucleotide change notation. |
|
Consequence |
Consequence on protein function. |
|
Allele Frequency |
Fraction of reads in which the variant is detected. |
|
COSMIC ID |
Catalogue of Somatic Mutations in Cancer (COSMIC) ID for this variant. |
|
Affected Exon |
The exons affected by the variant. For example, 4-6/7 indicates that exons 4, 5, and 6 are affected, and that the respective transcript contains a total of seven exons. |
|
Depth |
Unique read count for the detected variant. |
|
GQX Value |
Genotype quality. |