Figure 3

Single and combined pipeline performances for SNP detection. FPR denotes false positive rate, bwa denotes BWA+SAMtools, clc denotes CLC Genomics Workbench, giga denotes Mosaik+GigaBayes, smalt denotes SMALT+SAMtools, bc denotes the combination of bwa and clc, bcs denotes the combination of bwa, clc and smalt, bcgs denotes the combination of bwa, clc, giga and smalt. False positive rate for the heterozygous SNPs was calculated based on the heterozygous SNPs observed in an identical by descent region (IBD); the false positive rate for homozygous SNPs was calculated based on the homozygous SNPs observed in an IBD region in which the sequences are identical to the reference sequences. Pipelines without the implementation of alignment mapping quality parameter resulted in a higher FPR for heterozygous SNP detection.