Table 2.

Total number of single nucleotide variants (SNVs), insertions and deletions (InDels), and Transition/Transversion Ratios found using single and multi sample calling methods with HaplotypeCaller (HC), Platypus (PL), Platypus results after multi-nucleotide variants were split into allelic primitives (PL_PRIM), Samtools (SAM), and the UnifiedGenotyper (UG) for 65 animals

Calling method	Total number of SNVs		Total number of InDels		Transition/Transversion ratio
	Single sample calling, combined	Multi sample calling	Single sample calling, combined	Multi sample calling	Single sample calling, combined	Multi sample calling
HC	-	19,901,885	-	2,685,032	-	2.138
PL	17,709,672	16,894,054	2,973,025	2,890,066	2.178	2.165
PL_PRIM	20,869,015	19,759,134	2,864,147	2,890,412	2.105	2.058
SAM	20,647,891	18,767,273	2,682,094	1,997,791	2.176	2.240
UG	21,984,283	22,048,382	2,485,677	2,741,468	2.024	1.974

The combined results of all 65 single samples represent single sample calling results.