Why does the SOPHiA Platform present a systematic variant different than the reference sequence (e.g. T instead of C)?

Variants displayed within the SOPHiA Platform are relative to the reference genome (hg19).

There are some cases where the reference genome contains a minor allele. In these cases RefSeq sequences overlapping this region may differ from the reference genome and show the major allele instead. Comparing the sequencing data with the RefSeq sequence, no variant will be identified. However since the SOPHiA Platform uses the reference genome, it will systematically detect a difference and report it.

TIP : The population frequency of the variant is provided within the SOPHiA Platform, making it easy to spot that the variant has a population frequency of almost 100% (and therefore is the major allele) and not clinically relevant.