VarSome correctly maps mitochondrial codons to amino acids, annotates mitochondrial variants and genes with all databases where data is available and includes the Mitomap database.
The standard mitochondrial genome is the revised Cambridge Reference Sequence (rCRS), GenBank number: NC_012920.1. This is the mitochondrial sequence included in the hg38 human genome. However, the older hg19 genome contains NC_001807.4 instead. Since the rCRS is the standard in the field, VarSome uses a version of hg19 which has been modified to include the rCRS (NC_012920.1) instead of NC_001807.4.
- VarSome Clinical
When users run an analysis from fastq files on VarSome Clinical, using either hg19 or hg38, any mitochondrial sequences will be aligned to the rCRS.
Additionally, for VCF-based analyses run against hg19, if the VCF file contains variants reported on "chrM" (the name of the mitochondrial sequence in the hg19 genome), then those will be annotated with respect to the NC_001807.4 sequence, the original mitochondrial sequence of hg19. If the variant is instead reported on "MT" (the name of the mitochondrial sequence in the hg38 genome) then they will be annotated with respect to the rCRS.
- VarSome.com / VarSome Premium
When querying a variant on VarSome, we follow this convention:
-
- hg19: "chrM" = NC_001807.4, "MT" = NC_012920.1 (rCRS)
- hg38: "chrM" = "MT" = NC_012920.1 (rCRS)
- hg19: "chrM" = NC_001807.4, "MT" = NC_012920.1 (rCRS)
VarSome lifts over variants from source databases to cover both versions of the mitochondrial genome on hg19. Please note, however, that as for any lift-over on variants, the results may be inaccurate or missing from the target genome.