@genebe/qatar

Qatari Genome allele frequencies

Alternate allele frequency, allele count, and total allele number for single-nucleotide variants observed in a Qatari population cohort, originally reported on GRCh37 and lifted over to GRCh38 with Picard LiftoverVcf.

Only biallelic SNVs are included. The total allele number (an) is not uniform across the genome: not every sample in the underlying cohort was genotyped at every position, so an should be read per-variant rather than assumed constant. No homozygote-count field is available from the source, so this database does not have a hom column. A small number of variants (about 1 in 20,000) map to the same GRCh38 position as another variant after liftover; where that happens, the record with the highest allele frequency (then allele count, then allele number) is kept.

Source

Allele frequencies computed from Qatari genome sequencing data and originally published on GRCh37.

Citation

Fakhro KA, Staudt MR, Ramstetter MD, Robay A, Malek JA, Badii R, Al-Marri AA, Abi Khalil C, Al-Shakaki A, Chidiac O, Stadler D, Zirie M, Jayyousi A, Salit J, Mezey JG, Crystal RG, Rodriguez-Flores JL. The Qatar genome: a population-specific tool for precision medicine in the Middle East. Human Genome Variation. 2016;3:16016. doi:10.1038/hgv.2016.16.