DGRPool

GWAS results were computed on dm3 genome.

If you want to make an independent analysis with DGRP2 or PLINK2, you can find here prepared input files for this phenotype: DGRP2 results PLINK2 results

Full results

Phenotype distribution and association to known covariates

Shapiro-Wilk test of normality (p-value=1.625e^-14)
Null Hypothesis is rejected (p<=0.05).
Interpretation: NOT NORMAL distribution of this phenotype

We tested for association of this phenotype with 6 known covariates Huang et al., 2014 using both ANOVA and Kruskal-Wallis association tests.

ANOVA test

Covariate	p-value	Significance
In_3R_P	0.029749

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1741 significant hits at p-value < 0.001. The 1000 top results are displayed in the table below.

We performed a gene enrichment calculation (Fisher's exact test) of all GWAS-associated genes at p < 0.001. Genesets were taken from two database: the Gene Ontology (GO) and the FlyBase phenotypes. GO enrichment FlyBase phenotype enrichment

Variant impact HIGH MODERATE LOW MODIFIER

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Chromosome	Position	ID	Reference	Variant	p-value	FDR_BH	Transcript annotation	Binding site annotation
2L	718007	2L_718007_INS [dm3] 2L_718007_INS [dm6]	T	TT	7.088e^-8	0.133	INTERGENIC
3R	10175600	3R_10175600_SNP [dm3] 3R_14349878_SNP [dm6]	G	A	1.297e^-6	0.994	INTRON NK7.1	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
X	2925636	X_2925636_SNP [dm3] X_3031603_SNP [dm6]	G	A	2.413e^-6	0.994	INTRON kirre
3R	11269036	3R_11269036_SNP [dm3] 3R_15443314_SNP [dm6]	T	A	2.588e^-6	0.994	SYNONYMOUS_CODING AdamTS-A	TF binding site mE1_TFBS_cad
3R	10187299	3R_10187299_SNP [dm3] 3R_14361577_SNP [dm6]	A	G	4.330e^-6	0.994	UTR_5_PRIME CG31320 INTRON NK7.1	TF binding site mE1_TFBS_cad mE1_TFBS_eve mE1_TFBS_HSA
3L	18259275	3L_18259275_SNP [dm3] 3L_18266175_SNP [dm6]	C	T	6.220e^-6	0.994	INTERGENIC
2L	20994435	2L_20994435_SNP [dm3] 2L_20994435_SNP [dm6]	T	A	7.685e^-6	0.994	INTRON CG42238	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cnc
2R	18682008	2R_18682008_SNP [dm3] 2R_22794503_SNP [dm6]	A	G	7.883e^-6	0.994	INTRON CG42260
2R	9638486	2R_9638486_SNP [dm3] 2R_13750981_SNP [dm6]	A	G	7.899e^-6	0.994	INTERGENIC
3R	18614460	3R_18614460_SNP [dm3] 3R_22788738_SNP [dm6]	C	T	7.963e^-6	0.994	NON_SYNONYMOUS_CODING CG7029	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3L	2502057	3L_2502057_SNP [dm3] 3L_2502057_SNP [dm6]	A	T	9.515e^-6	0.994	INTRON CG16758
X	2924664	X_2924664_SNP [dm3] X_3030631_SNP [dm6]	T	A	1.011e^-5	0.994	INTRON kirre
3R	10174595	3R_10174595_SNP [dm3] 3R_14348873_SNP [dm6]	T	A	1.051e^-5	0.994	INTRON NK7.1
2L	548546	2L_548546_SNP [dm3] 2L_548546_SNP [dm6]	G	A	1.232e^-5	0.994	INTRON Ets21C	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_chinmo
3R	14523040	3R_14523040_INS [dm3] 3R_18697318_INS [dm6]	A	AA	1.235e^-5	0.994	INTERGENIC
X	2924670	X_2924670_SNP [dm3] X_3030637_SNP [dm6]	A	C	1.240e^-5	0.994	INTRON kirre
3R	19032608	3R_19032608_SNP [dm3] 3R_23206886_SNP [dm6]	A	T	1.290e^-5	0.994	INTRON cnc	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cnc mE1_TFBS_HSA mE1_TFBS_sens
X	8716511	X_8716511_SNP [dm3] X_8822478_SNP [dm6]	C	A	1.369e^-5	0.994	INTERGENIC
2R	19600120	2R_19600120_SNP [dm3] 2R_23712597_SNP [dm6]	T	C	1.376e^-5	0.994	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2R	2931492	2R_2931492_SNP [dm3] 2R_7043987_SNP [dm6]	A	G	1.411e^-5	0.994	SYNONYMOUS_CODING Tsp42Ek
3R	13129051	3R_13129051_SNP [dm3] 3R_17303329_SNP [dm6]	C	G	1.418e^-5	0.994	INTERGENIC
3R	10174385	3R_10174385_SNP [dm3] 3R_14348663_SNP [dm6]	G	T	1.535e^-5	0.994	INTRON NK7.1
X	2924663	X_2924663_SNP [dm3] X_3030630_SNP [dm6]	G	C	1.568e^-5	0.994	INTRON kirre
3L	10147805	3L_10147805_SNP [dm3] 3L_10154705_SNP [dm6]	A	G	1.583e^-5	0.994	INTRON dpr10
3R	25440339	3R_25440339_SNP [dm3] 3R_29614617_SNP [dm6]	G	A	1.866e^-5	0.994	INTRON alph
3L	16759510	3L_16759510_SNP [dm3] 3L_16766410_SNP [dm6]	G	C	2.075e^-5	0.994	UTR_5_PRIME Nrt	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
X	8716503	X_8716503_SNP [dm3] X_8822470_SNP [dm6]	A	G	2.217e^-5	0.994	INTERGENIC
3R	25301272	3R_25301272_SNP [dm3] 3R_29475550_SNP [dm6]	C	T	2.304e^-5	0.994	INTRON Ptp99A
2L	8982738	2L_8982738_INS [dm3] 2L_8982738_INS [dm6]	T	TT	2.330e^-5	0.994	INTRON CG13101
2L	21725984	2L_21725984_SNP [dm3] 2L_21725984_SNP [dm6]	G	T	2.430e^-5	0.994	INTRON CG31619
3R	21991396	3R_21991396_SNP [dm3] 3R_26165674_SNP [dm6]	C	A	2.439e^-5	0.994	INTERGENIC
3R	25301087	3R_25301087_SNP [dm3] 3R_29475365_SNP [dm6]	T	A	2.459e^-5	0.994	INTRON Ptp99A
2L	5594925	2L_5594925_SNP [dm3] 2L_5594925_SNP [dm6]	C	T	2.551e^-5	0.994	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3L	16036130	3L_16036130_SNP [dm3] 3L_16043030_SNP [dm6]	C	T	2.793e^-5	0.994	UTR_5_PRIME th UPSTREAM th INTRON th	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_inv
2L	16598505	2L_16598505_SNP [dm3] 2L_16598505_SNP [dm6]	A	C	2.848e^-5	0.994	INTRON CG42389	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
3L	6487225	3L_6487225_SNP [dm3] 3L_6494125_SNP [dm6]	A	G	3.169e^-5	0.994	SYNONYMOUS_CODING CG10144	TF binding site mE1_TFBS_sens
3R	11237326	3R_11237326_SNP [dm3] 3R_15411604_SNP [dm6]	A	G	3.180e^-5	0.994	INTRON Atx2	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	21991397	3R_21991397_SNP [dm3] 3R_26165675_SNP [dm6]	G	C	3.185e^-5	0.994	INTERGENIC
3R	10180947	3R_10180947_DEL [dm3] 3R_14355225_DEL [dm6]	TCACAGGACCCCGTTCGTAC...	T	3.194e^-5	0.994	INTRON NK7.1
3L	16874599	3L_16874599_SNP [dm3] 3L_16881499_SNP [dm6]	A	T	3.293e^-5	0.994	INTRON Lmpt
X	4112735	X_4112735_SNP [dm3] X_4218702_SNP [dm6]	C	G	3.326e^-5	0.994	SYNONYMOUS_CODING CG15570	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3L	10147810	3L_10147810_SNP [dm3] 3L_10154710_SNP [dm6]	C	G	3.394e^-5	0.994	INTRON dpr10
3R	25440479	3R_25440479_SNP [dm3] 3R_29614757_SNP [dm6]	G	A	3.419e^-5	0.994	INTRON alph
2L	11175976	2L_11175976_SNP [dm3] 2L_11175976_SNP [dm6]	A	G	3.558e^-5	0.994	INTRON Ca-beta	TF binding site BDTNP1_TFBS_dl
3R	25439910	3R_25439910_SNP [dm3] 3R_29614188_SNP [dm6]	A	T	3.606e^-5	0.994	INTRON alph
3R	25439940	3R_25439940_SNP [dm3] 3R_29614218_SNP [dm6]	T	C	3.606e^-5	0.994	INTRON alph
3R	25439973	3R_25439973_SNP [dm3] 3R_29614251_SNP [dm6]	A	G	3.606e^-5	0.994	INTRON alph
2L	18159274	2L_18159274_SNP [dm3] 2L_18159274_SNP [dm6]	A	G	3.630e^-5	0.994	UPSTREAM CG7200 DOWNSTREAM CG42750 INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad transposable element FlyBase
2R	6853899	2R_6853899_DEL [dm3] 2R_10966394_DEL [dm6]	CCC	C	3.652e^-5	0.994	INTERGENIC
3L	10614333	3L_10614333_SNP [dm3] 3L_10621233_SNP [dm6]	G	T	3.656e^-5	0.994	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv
2L	5594926	2L_5594926_SNP [dm3] 2L_5594926_SNP [dm6]	C	G	3.699e^-5	0.994	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2L	20994440	2L_20994440_SNP [dm3] 2L_20994440_SNP [dm6]	A	G	3.756e^-5	0.994	INTRON CG42238	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cnc
2R	16462737	2R_16462737_SNP [dm3] 2R_20575232_SNP [dm6]	C	A	3.885e^-5	0.994	INTRON qsm
3R	25433107	3R_25433107_SNP [dm3] 3R_29607385_SNP [dm6]	A	T	3.927e^-5	0.994	INTRON alph
2R	6727888	2R_6727888_SNP [dm3] 2R_10840383_SNP [dm6]	A	G	3.959e^-5	0.994	SYNONYMOUS_CODING CG30015	TF binding site mE1_TFBS_cad
3R	10183714	3R_10183714_SNP [dm3] 3R_14357992_SNP [dm6]	C	T	3.994e^-5	0.994	DOWNSTREAM CG31320 INTRON NK7.1
3R	26986359	3R_26986359_SNP [dm3] 3R_31160637_SNP [dm6]	G	A	4.005e^-5	0.994	INTRON Gycbeta100B & 1 other
3R	25301258	3R_25301258_INS [dm3] 3R_29475536_INS [dm6]	A	AA	4.093e^-5	0.994	INTRON Ptp99A
2R	11241959	2R_11241959_SNP [dm3] 2R_15354454_SNP [dm6]	T	C	4.100e^-5	0.994	INTRON unc-5	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Ubx
3L	14560735	3L_14560735_SNP [dm3] 3L_14567635_SNP [dm6]	G	A	4.141e^-5	0.994	UTR_5_PRIME CG42758
2R	9431748	2R_9431748_SNP [dm3] 2R_13544243_SNP [dm6]	C	T	4.259e^-5	0.994	INTRON CG6145	TF binding site BDTNP1_TFBS_twi
2L	2636261	2L_2636261_SNP [dm3] 2L_2636261_SNP [dm6]	T	C	4.281e^-5	0.994	INTERGENIC
3L	1964504	3L_1964504_SNP [dm3] 3L_1964504_SNP [dm6]	T	C	4.378e^-5	0.994	UTR_5_PRIME SCOT UPSTREAM mv INTRON SCOT	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Ubx
2R	17497137	2R_17497137_SNP [dm3] 2R_21609632_SNP [dm6]	C	T	4.726e^-5	0.994	INTRON CG15673
2R	17095083	2R_17095083_SNP [dm3] 2R_21207578_SNP [dm6]	T	A	4.784e^-5	0.994	INTRON CG44245 & 1 other
3R	25946483	3R_25946483_SNP [dm3] 3R_30120761_SNP [dm6]	T	A	4.812e^-5	0.994	UTR_3_PRIME sima	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3L	10400978	3L_10400978_SNP [dm3] 3L_10407878_SNP [dm6]	A	G	4.915e^-5	0.994	INTERGENIC
3R	24977109	3R_24977109_SNP [dm3] 3R_29151387_SNP [dm6]	T	C	4.943e^-5	0.994	SYNONYMOUS_CODING ligatin DOWNSTREAM Slbp	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
X	12406122	X_12406122_SNP [dm3] X_12512089_SNP [dm6]	C	A	4.956e^-5	0.994	INTRON CG2556
3L	16740216	3L_16740216_SNP [dm3] 3L_16747116_SNP [dm6]	A	T	4.969e^-5	0.994	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3R	25436983	3R_25436983_INS [dm3] 3R_29611261_INS [dm6]	C	CCGACTCAGGCGCAGATACA...	5.018e^-5	0.994	INTRON alph	TF binding site mE1_TFBS_chinmo
2L	16598527	2L_16598527_SNP [dm3] 2L_16598527_SNP [dm6]	A	T	5.039e^-5	0.994	INTRON CG42389	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
3R	18098277	3R_18098277_SNP [dm3] 3R_22272555_SNP [dm6]	G	T	5.074e^-5	0.994	INTRON SKIP
2R	12604439	2R_12604439_SNP [dm3] 2R_16716934_SNP [dm6]	A	C	5.227e^-5	0.994	INTRON CG30463
2R	17379838	2R_17379838_SNP [dm3] 2R_21492333_SNP [dm6]	T	A	5.257e^-5	0.994	INTRON Fkbp14
3R	22773386	3R_22773386_DEL [dm3] 3R_26947664_DEL [dm6]	GG	G	5.262e^-5	0.994	UPSTREAM CG18472 & 2 others DOWNSTREAM CG14252 INTERGENIC	TF binding site BDTNP1_TFBS_dl
2R	16462751	2R_16462751_SNP [dm3] 2R_20575246_SNP [dm6]	C	T	5.301e^-5	0.994	INTRON qsm
2L	939874	2L_939874_SNP [dm3] 2L_939874_SNP [dm6]	G	A	5.371e^-5	0.994	INTRON CG4341
2L	954620	2L_954620_INS [dm3] 2L_954620_INS [dm6]	G	GGGGAAAAG	5.435e^-5	0.994	INTRON CG4341
2R	1370826	2R_1370826_SNP [dm3] 2R_5483321_SNP [dm6]	G	C	5.447e^-5	0.994	INTRON CG30440	transposable element FlyBase
2L	10167726	2L_10167726_SNP [dm3] 2L_10167726_SNP [dm6]	T	C	5.530e^-5	0.994	INTRON CG44153
3L	4970341	3L_4970341_SNP [dm3] 3L_4970341_SNP [dm6]	A	G	5.619e^-5	0.994	INTRON Con	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	20987276	2R_20987276_SNP [dm3] 2R_25099753_SNP [dm6]	G	C	5.713e^-5	0.994	UPSTREAM lov INTRON lov	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
3R	10578018	3R_10578018_SNP [dm3] 3R_14752296_SNP [dm6]	T	A	5.881e^-5	0.994	SYNONYMOUS_CODING CG7362 INTRON jvl
X	9071079	X_9071079_SNP [dm3] X_9177046_SNP [dm6]	A	G	6.101e^-5	0.994	UTR_3_PRIME mei-P26
3R	25301047	3R_25301047_SNP [dm3] 3R_29475325_SNP [dm6]	C	T	6.132e^-5	0.994	INTRON Ptp99A
2R	7667019	2R_7667019_SNP [dm3] 2R_11779514_SNP [dm6]	C	G	6.231e^-5	0.994	DOWNSTREAM CG42493 INTRON ths
3L	10151073	3L_10151073_SNP [dm3] 3L_10157973_SNP [dm6]	G	A	6.388e^-5	0.994	INTRON dpr10
2L	717968	2L_717968_SNP [dm3] 2L_717968_SNP [dm6]	C	T	6.567e^-5	0.994	INTERGENIC
2R	6568455	2R_6568455_SNP [dm3] 2R_10680950_SNP [dm6]	C	T	6.631e^-5	0.994	INTRON stan	TF binding site mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2L	16855827	2L_16855827_SNP [dm3] 2L_16855827_SNP [dm6]	A	T	6.693e^-5	0.994	INTRON CG31809	transposable element FlyBase
2R	6859464	2R_6859464_SNP [dm3] 2R_10971959_SNP [dm6]	A	T	6.701e^-5	0.994	INTERGENIC
3R	25947586	3R_25947586_SNP [dm3] 3R_30121864_SNP [dm6]	T	A	6.800e^-5	0.994	DOWNSTREAM CG45072 & 1 other INTERGENIC	TF binding site mE1_TFBS_bab1
3R	26081019	3R_26081019_SNP [dm3] 3R_30255297_SNP [dm6]	A	G	6.893e^-5	0.994	INTERGENIC
3R	10183658	3R_10183658_SNP [dm3] 3R_14357936_SNP [dm6]	A	T	6.951e^-5	0.994	DOWNSTREAM CG31320 INTRON NK7.1
2L	7039459	2L_7039459_SNP [dm3] 2L_7039459_SNP [dm6]	T	C	7.050e^-5	0.994	INTRON milt	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	19599999	2R_19599999_SNP [dm3] 2R_23712476_SNP [dm6]	T	C	7.067e^-5	0.994	INTERGENIC	TF binding site mE1_TFBS_sens mE1_TFBS_Trl
3R	11964081	3R_11964081_SNP [dm3] 3R_16138359_SNP [dm6]	A	G	7.166e^-5	0.994	INTRON Sb	TF binding site mE1_TFBS_inv
2R	8665783	2R_8665783_SNP [dm3] 2R_12778278_SNP [dm6]	C	T	7.323e^-5	0.994	EXON CR45266	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_twi
2L	7297381	2L_7297381_SNP [dm3] 2L_7297381_SNP [dm6]	C	G	7.435e^-5	0.994	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA

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By genomic position
Variant impact
Gene name

lsm_Week7_Fecundity phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results