Table 2. Number of RNA-seq based SNPs called by the various tools in comparison with the genomic framework of barley.

Species	Accession	No. of SNPs
		freebayes	glfMultiples	samtools	fgs*
H. spontaneum	H602	67,462	147,417	91,442	55,403
H. vulgare	B669	64,472	210,241	108,105	49,094
	C319	100,387	257,743	150,167	79,903
	C346	99,545	262,354	149,535	78,364
	C656	100,366	257,088	148,563	77,253
	E245	90,395	241,736	137,109	69,761
	E612	62,054	155,797	88,866	49,325
	I304	50,712	119,733	71,578	41,676
	I335	85,453	229,912	131,492	66,382
	I622	102,344	262,084	152,592	79,949
	I626	92,970	243,682	141,367	72,405
	J064	75,308	161,268	101,226	59,153
	J247	51,806	130,889	73,312	38,729
	J647	63,195	148,909	89,326	51,591
	K692	93,428	242,556	139,799	75,444
	K735	54,103	134,995	78,892	41,098
	N009	95,951	244,587	144,688	75,198
	T567	72,187	211,850	114,637	55,206
	U051	83,207	230,728	128,448	64,319
	U353	78,417	213,824	119,391	59,136

^*Intersection of the identified SNPs using the three SNP callers: freebayes, glfMultiples, and samtools.