Fig. 4

Example of a false negative variant call. a SNP on gene NUP210 at position chr3:13361391 cannot be detected while using hg19 as the allele reported at this position is the major allele. Using hg19KIndel the minor allele at this position can be detected. b UCSC snapshot of the position chr3:13361391 shows that Leucine is there at that position in humans whereas it is Serine which is conserved across other species. If we replace the allele with its major allele it will be Leucine in humans as well. We have corrected for such positions as well in hg19KIndel