Using multi-way admixture mapping to elucidate TB susceptibility in the South African Coloured population

BMC Genomics

Table 1 Percentage of miss-called ancestry

This table reports the interquartile range (IQR) of the percentage of SNPs that were miss-called by LAMP-LD and RFMix per each of the six possible miss-call categories. The known ancestry of a simulated data set of 1500 SAC chromosomes was compared to the ancestry called by the software program (chromosome 1). The median percentage of miss-called SNPs across all SNPs as well as the median percentage of miss-called SNPs across SNPs of that source ancestry are shown. San ancestry can for example be miss-called as either Bantu or non-African ancestry. The median percentage of all SNPs that were miss-called as such are shown in the second and third columns of the first two rows, and the median percentage of San SNPs that were miss-called as such are shown in the fourth and fifth columns of the first two rows. The mean proportion of San, Bantu and non-African ancestry in the simulated data set was 0.3342, 0.2772 and 0.3885 respectively. The difference in number of SNPs miss-called by RFMix, compared to the corresponding number of SNPs miss-called by LAMP-LD, were significant with p-values <2×10^-16 for each of the six possible miss-call categories.

ISSN: 1471-2164