highly significantp = 2.6×10−55
When we compared these data to the breakpoint homology from 16,783 CNV breakpoints assembled for the 1,000 Genomes Pilot 1 study using identical methods, we find a highly significant difference from either the BWA-SW analysis (χ 2 = 244.6, 1 d.f., p = 2.6×10−55) or the EMBOSS method (χ 2 = 201.6, 1 d.f., p = 1.26×10−45) ( Fig. 3 ).