Table 1. Comparison of SNPs identified after mapping with BWA and Bowtie.

Number of SNPs	BWA pileup	BWA GATK	Bowtie pileup	Bowtie mpileup
Relative to reference sequence	445,546	3,739,203	6,881,214	4,234,692
Within buffalo population	109,361	276,847	2,222,665	933,948
Within gene regions	28,807	76,615	493,578	224,087

Gene regions are from the gene start to the gene end and include introns.