Table 2. The Ti/Tv ratios of 28 different aligner-caller combinations for samples 02B, 12L and 20T.

Ti/Tv for Exonic SNPs		BWA	BFAST	BOWTIE	STAMPY	NovoMPI	SMALT	SSAHA
02B	Samtools	3.78	3.59	4.12	3.28	3.22	3.49	3.53
	GATK	2.73	2.73	2.86	2.77	2.77	2.79	2.75
	Freebayes	0.32	0.402	0.62	2.37	2.70	0.29	0.30
	Bambino	2.56	2.55	2.89	2.8	2.87	2.62	2.59
12L	Samtools	3.52	3.46	4.08	3.29	3.24	3.41	3.46
	GATK	2.69	2.72	2.90	2.76	2.75	2.78	2.74
	Freebayes	0.25	0.34	0.525	2.26	2.63	0.22	0.23
	Bambino	2.27	2.43	2.86	2.71	2.85	2.52	2.47
20T	Samtools	3.80	3.45	3.99	3.30	3.30	3.38	3.47
	GATK	2.74	2.73	2.85	2.75	2.77	2.78	2.75
	Freebayes	0.32	0.402	0.62	2.37	2.70	0.29	0.30
	Bambino	2.24	2.33	2.72	2.70	2.82	2.31	2.26