Table 3. Selective sweep regions and number of corresponding genes for (A) BRE and (B) GH2 strains.

A	Start	End	Length	Number of genes	CI
Chr1	1,194,541	2,357,392	1,162,852	56	Inf
	61,387,283	62,009,343	622,061	23	11.15
	62,218,658	62,721,763	503,106	19	6.67
	62,877,538	63,098,318	220,781	9	2.71
Chr2	24,145,118	24,315,462	170,345	6	2.83
Chr3	22,823,405	23,467,278	643,874	35	Inf
	24,930,649	25,380,787	450,139	14	Inf
Chr4	20,500,484	21,005,970	505,487	24	8.63
	31,100,629	31,804,241	703,613	36	Inf
Chr5	2,117,276	2,386,209	268,934	17	7.53
	8,814,688	9,017,158	202,471	12	9.05
Chr6	17,508,128	17,649,604	141,477	6	3.94
Chr7	-	-	-	-	-

Confidence Index (CI) was calculated as the maximum of −log(1-q) over the window, where q is the posterior probability of hidden state “Selection”. (Inf. = infiny).