Table 2 Candidate regions identified at LOD peaks

LOD Peak No.	Chromosome	Peak Position	Credible Interval Start	Credible Interval End	Span (kb)	Genes	Selection Type
1	X	1252000	1237000	1339000	102	CG11417, CG11418, CG11448, CG12773, CG14770, CG14773, CG3056, CG32813, CG3719, SNF1A, futsch, png	3
2	X	13237000	13211000	13250000	39	CG15747, IP3K2, Jafrac1, RpS15Aa	2
3	2L	1515000	1476000	1559000	83	CG14351, CG18131, CG18132, CG31661, CG31926, CG31928, CG33128, CG7420, Or22a, Or22b, halo	2
4	2L	13159000	13316000	13438000	122	CG10859, CG16826, CG16848, CG16956, CG16957, CG16970, CG31855, CG6523, CG6565, CG7099, CG7110, CG9293, CG9302, CG9305, CG9306, CG9377, CG9395, Nnp-1, RpL24, Tap42, Tehao, Vm34Ca, beta’Cop, loqs	1
7	3R	9109000	9061000	9192000	131	Ace, CG11686, CG15887, CG15888, CG32473, CG8449, CG8630, CG8773, CG8774, CG8784, CG8790, CG8795, CheA87a, Lip3, Osi22, Ravus, Su(var)3-7, mthl12, poly, wntD	2
8	3R	9608000	9601000	9638000	37	CG42375, CG9286, CG9288, CG9297, Cht5, Dip-B, tRNA:CR31331, tRNA:CR31588, tal-1A, tal-2A, tal-3A, tal-AA	2
9	3R	25260000	25245000	25271000	26	Ptp99A	2

Seven candidate regions showing significant difference in SNP frequency between LD and DD conditions and high score of LOD. Chromosome, positions, start and end of 90% credible interval, span, genes, and selection types (Figure 5) are given for each region.