Why doesn the reference nucleotide listed in the substitution match the nucleotide in the Browser?
First check the strand that is displayed and make sure it is the same strand as the variant’s reference sequence (usually the same as a nearby gene). Also, for polymorphisms, the allele that is considered to be “wild type” is somewhat arbitrary. The nucleotide changes listed for a variant are based on the stated reference sequence used by the source LSDB, which may differ from the whole-genome assembly you are currently viewing in the Browser. The LSDB’s reference sequence is often specified as part of the HGVS-style name.
Related Questions
- Why does a mutation that deletes one or two DNA nucleotides changes gene function more drastically than a substitution of one nucleotide for another type?
- I can’t see a reference sequence in the IGV (Illumina Genome Viewer) or ICB (Illumina Chromosome Browser). How can I display a reference sequence?
- Why doesn the reference nucleotide listed in the substitution match the nucleotide in the Browser?
