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. 2018 Apr 5;14(4):e1007308. doi: 10.1371/journal.pgen.1007308

Fig 6. Phasing accuracy of SHAPEIT approaches and the choice of reference panels used.

Fig 6

(a) Effect of population supergroups on phasing accuracy. Five supergroups of the same size (n = 347) were collected from the 1000GP and used as the reference panel for SHAPEIT (no read) phasing, or together with Illumina or PacBio reads for the NA12878 individual. The best SER was achieved by EUR, to which the NA12878 individual belongs. (b) Effect of population subgroups on phasing accuracy. Population subgroups of the same size (n = 85) were collected from the 1000GP, EUR, and each of five subpopulations in EUR and used as the reference panel for SHAPEIT phasing of the NA12878 individual. No major improvement on SER was observed among EUR and its 5 subgroups including EUR/CEU to which the individual NA12878 belongs. (c) Effect on phasing accuracy as SER as a function of reference panel size, compared with the inclusion of WGS reads or familial information from parental genotype. Reference panels containing up to 502 individuals from the 1000GP EUR group or 23k individuals from HRC were used as the population background for SHAPEIT phasing of the NA12878 individual.