Table 2. Counts of SNP that converted to successful assays predicted by different pipelines.

Validation result	BWA pileup	BWA GATK	Bowtie pileup	Bowtie mpileup
Monomorphic	20 (12)	31 (23)	71 (11)	46 (21)
Polymorphic	45 (6)	68 (12)	75 (4)	73 (13)
Not amplified. Number, (%)	12, 16% (1)	20, 17% (1)	27, 16% (0)	23, 13% (0)
Validated %	58%	57%	43%	51%
Percent of assays correctly identified as polymorphic	58% (67%)	57% (67%)	43% (45%)	54% (74%)

Figures in brackets are the number of loci that were predicted monomorphic (fixed for alternate allele) by the corresponding pipeline. The percentage correctly identified as polymorphic shows the percentage of all assays that were polymorphic and in brackets the percentage of assays predicted polymorphic that were confirmed.