Table 1.

SNPs significantly associated with virgin egg retention (P < 10 ^− 5). MAF is minor allele frequency, Del,  deletion, for non-synonymous SNPs, A55G is interpreted as a mutation that causes a change from alanine to glycine in the 55th position of the protein, SNPs downstream of the gene are denoted as “Down (position)”.

Chr	Pos	MAF	Effect	P-value	Gene	Class
X	22394286	0.384	−0.120	5.86E−07	StnA/B	Del (78bp—intron)
X	22385304	0.333	−0.130	5.93E−07	StnA/B	Intron
3L	9356607	0.180	−0.158	7.53E−07	Klp67A	Nonsyn (S691N)
X	22386644	0.356	−0.121	1.08E−06	StnA/B	Intron
2R	16443531	0.227	−0.143	1.32E−06	lms	Up(833)
3L	1696552	0.218	−0.148	1.38E−06	CG7991	Intron
3L	9356604	0.191	−0.151	1.44E−06	Klp67A	Nonsyn (T692S)
3L	9356609	0.171	−0.156	1.60E−06	Klp67A	Syn
3R	25293837	0.165	−0.157	2.24E−06	Ptp99A	Intron
3R	22722373	0.446	−0.105	2.56E−06	T48	Intron
3R	23759237	0.302	−0.124	3.95E−06	Mes-4	Intron
3R	16293867	0.140	−0.166	4.11E−06	mun	Intron
X	11867221	0.253	−0.132	4.13E−06	cac	Intron
X	3655147	0.144	−0.153	4.36E−06	tlk	Intron
3L	12152503	0.130	−0.164	4.57E−06	CG9760	Syn.
X	22385502	0.366	−0.117	5.89E−06	StnA/B	Intron
3R	24327835	0.193	−0.141	6.18E−06	Dhc98D	Intron
X	22397621	0.364	−0.112	6.42E−06	StnA/B	5’ UTR
3R	16259969	0.056	−0.236	6.45E−06	mun	Intron
3L	9356600	0.227	−0.123	6.70E−06	Klp67A	Syn.
3L	16448208	0.216	−0.130	6.75E−06	CG33158	Intron
3R	9294054	0.057	−0.229	6.83E−06	NA	NA
3R	25816726	0.112	−0.178	7.05E−06	Acph-1	Down (140)
X	3655346	0.148	−0.151	7.27E−06	tlk	Intron
3R	23719399	0.250	−0.135	8.61E−06	CG34353	Intron
3R	6329823	0.229	0.137	8.66E−06	NA	NA
3R	25816740	0.122	−0.167	9.23E−06	Acph-1	Down (126)
X	22382756	0.345	−0.112	9.34E−06	StnA/B	3’ UTR
3R	27115805	0.333	0.109	9.86E−06	NA	NA