Table 4. Differential allelic expression between low and high KPY samples in two populations.

Gene ID	SNPPosition	SNPType	Meunna						Florentine						TAIR gene annotation
			High KPY			Low KPY			High KPY			Low KPY
			Allele-A	Allele-B	Freq	Allele-A	Allele-B	Freq	Allele-A	Allele-B	Freq	Allele-A	Allele-B	Freq
Eucgr.E01218*	13097458	5′UTR	830	917	0.52	941	290	0.24	1090	934	0.46	1821	275	0.13	acyl-CoA-binding protein 6
Eucgr.K02930*	37329597	3′UTR	2373	1057	0.31	1962	337	0.15	2469	916	0.27	3386	166	0.05	ATP binding cassette subfamily B1
Eucgr.D01413*	25222772	3′UTR	299	3254	0.92	2014	1680	0.45	893	2983	0.77	1898	1798	0.49	clone eighty-four
Eucgr.K02283*	29962223	Non-Syn	522	3116	0.86	915	1870	0.67	674	3163	0.82	1670	2176	0.57	glutamine synthase clone R1
Eucgr.I00879	18049108	Syn	2323	1410	0.38	1744	1723	0.50	3091	765	0.20	1797	1504	0.46	Granulin repeat cysteine protease family protein
Eucgr.F00715	9407802	Syn	3398	444	0.12	3067	718	0.19	2346	0	0.00	2863	788	0.22	mannose-1-phosphate guanylyltransferase (GDP)s
Eucgr.J01079*	11780983	Syn	2701	1037	0.28	1691	1317	0.44	2796	895	0.24	1394	1811	0.57	phenylalanine ammonia-lyase 2
Eucgr.J01079*	11781814	Syn	3883	55	0.01	1574	292	0.16	3108	91	0.03	1351	498	0.27	phenylalanine ammonia-lyase 2
Eucgr.H01079*	13113728	Syn	160	3701	0.96	192	1273	0.87	1	3765	1.00	460	2565	0.85	P-loop nucleoside triphosphate hydrolases superfamily protein
Eucgr.B02229*	43555157	Syn	488	2946	0.86	398	991	0.71	690	2874	0.81	1698	1692	0.50	Protein kinase superfamily protein
Eucgr.C04168	76452675	Syn	1477	2453	0.62	2424	1449	0.37	873	2234	0.72	1874	1405	0.43	RAN GTPase 3
Eucgr.F02028*	27195221	3′UTR	2739	998	0.27	1280	937	0.42	3769	181	0.05	2815	1112	0.28	RING/U-box superfamily protein
Eucgr.G01417*	24500040	Syn	2543	1367	0.35	2059	591	0.22	2950	759	0.20	3727	99	0.03	S-adenosyl-L-methionine-dependent methyltransferases superfamily protein
Eucgr.D00982*	17649968	Syn	3765	88	0.02	839	168	0.17	3372	210	0.06	1488	584	0.28	Single hybrid motif superfamily protein
Eucgr.J02983	37072540	Syn	2296	1426	0.38	2901	855	0.23	1579	2126	0.57	2673	1044	0.28	Translation machinery associated TMA7
Eucgr.D01612*	29807599	3′UTR	2151	1757	0.45	758	1267	0.63	2204	1754	0.44	681	2295	0.77	tubulin beta 8
Eucgr.F00470*	5900107	Syn	2716	1173	0.30	3483	299	0.08	2547	1399	0.35	3363	469	0.12	Tubulin/FtsZ family protein
Eucgr.F00470*	5900855	Syn	1864	1932	0.51	2246	1572	0.41	1864	1983	0.52	2871	1033	0.26	Tubulin/FtsZ family protein
Eucgr.F00119	2072476	3′UTR	662	2869	0.81	401	2974	0.88	763	2861	0.79	17	3593	1.00	Uncharacterised protein family SERF
Eucgr.F00119	2072453	3′UTR	699	2973	0.81	436	3257	0.88	647	2102	0.76	72	2613	0.97	Uncharacterised protein family SERF
	37773406	Intergenic	515	643	0.56	2300	374	0.14	136	251	0.65	2413	249	0.09	No-Hit
	21970009	Intergenic	0	1755	1.00	297	1129	0.79	3	2240	1.00	294	702	0.70	No-Hit
	22010089	Intergenic	288	3622	0.93	464	3452	0.88	11	2001	0.99	955	2890	0.75	No-Hit
Eucgr.K00671*	7466804	Intron	3329	142	0.04	2302	246	0.10	2349	409	0.15	651	1846	0.74	No-Hit
Eucgr.A01856*	28919720	3′UTR	3877	7	0.00	2384	57	0.02	3781	142	0.04	2506	690	0.22	unknown protein

Freq – Frequency of Allele-B; DGE - Differential Gene Expression; *Genes also showing DGE.