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=1.110e^-16)
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
No significant result.

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2R_NS	5.0649	0.0795
In_3R_P	9.4516	0.0089

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2391 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
2R	10608749	2R_10608749_SNP [dm3] 2R_14721244_SNP [dm6]	C	G	8.049e^-12	1.510e^-5	INTERGENIC	TF binding site mE1_TFBS_inv
2R	10608747	2R_10608747_SNP [dm3] 2R_14721242_SNP [dm6]	C	T	1.766e^-11	1.656e^-5	INTERGENIC	TF binding site mE1_TFBS_inv
2R	10621372	2R_10621372_SNP [dm3] 2R_14733867_SNP [dm6]	C	A	1.609e^-9	0.001	INTERGENIC
3L	12710777	3L_12710777_SNP [dm3] 3L_12717677_SNP [dm6]	G	T	3.193e^-9	0.001	INTERGENIC
3L	12710782	3L_12710782_SNP [dm3] 3L_12717682_SNP [dm6]	G	A	3.412e^-9	0.001	INTERGENIC
2R	10608696	2R_10608696_SNP [dm3] 2R_14721191_SNP [dm6]	G	A	1.713e^-8	0.005	INTERGENIC
2R	15159096	2R_15159096_SNP [dm3] 2R_19271591_SNP [dm6]	G	C	2.107e^-8	0.005	INTRON rib	enhancer mE1_CBP_Enhancers TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad
2R	10787392	2R_10787392_SNP [dm3] 2R_14899887_SNP [dm6]	A	T	2.242e^-8	0.005	SYNONYMOUS_CODING Cyp317a1	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2R	10787362	2R_10787362_SNP [dm3] 2R_14899857_SNP [dm6]	T	C	4.668e^-8	0.008	SYNONYMOUS_CODING Cyp317a1	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2R	10715639	2R_10715639_SNP [dm3] 2R_14828134_SNP [dm6]	A	T	4.932e^-8	0.008	INTERGENIC
2R	10368189	2R_10368189_SNP [dm3] 2R_14480684_SNP [dm6]	G	C	5.092e^-8	0.008	UPSTREAM L INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_bab1
2R	10701426	2R_10701426_SNP [dm3] 2R_14813921_SNP [dm6]	G	A	5.407e^-8	0.008	INTERGENIC	TF binding site mE1_TFBS_Trl
2R	10705677	2R_10705677_SNP [dm3] 2R_14818172_SNP [dm6]	G	T	6.256e^-8	0.008	NON_SYNONYMOUS_CODING CG10202	TF binding site BDTNP1_TFBS_twi mE1_TFBS_sens
2R	10719564	2R_10719564_SNP [dm3] 2R_14832059_SNP [dm6]	G	A	6.256e^-8	0.008	UPSTREAM CG10205 INTERGENIC
2R	10713301	2R_10713301_SNP [dm3] 2R_14825796_SNP [dm6]	T	G	6.902e^-8	0.009	INTERGENIC
2L	17088640	2L_17088640_SNP [dm3] 2L_17088640_SNP [dm6]	G	A	7.563e^-8	0.009	UTR_3_PRIME CG12620
2R	10721948	2R_10721948_SNP [dm3] 2R_14834443_SNP [dm6]	C	A	8.333e^-8	0.009	DOWNSTREAM CG10205 INTERGENIC
2R	10700525	2R_10700525_SNP [dm3] 2R_14813020_SNP [dm6]	G	A	8.427e^-8	0.009	INTERGENIC	regulatory region REDfly_CRMs
2R	10608631	2R_10608631_SNP [dm3] 2R_14721126_SNP [dm6]	G	A	8.855e^-8	0.009	INTERGENIC
2R	9632088	2R_9632088_INS [dm3] 2R_13744583_INS [dm6]	T	TT	1.172e^-7	0.011	INTRON fas
2R	7475070	2R_7475070_SNP [dm3] 2R_11587565_SNP [dm6]	A	T	1.237e^-7	0.011	SYNONYMOUS_CODING tou DOWNSTREAM snoRNA:Psi28S-1936 INTRON tou
2R	15159019	2R_15159019_SNP [dm3] 2R_19271514_SNP [dm6]	A	T	1.444e^-7	0.012	INTRON rib	enhancer mE1_CBP_Enhancers TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad
2R	15159014	2R_15159014_SNP [dm3] 2R_19271509_SNP [dm6]	G	T	1.506e^-7	0.012	INTRON rib	enhancer mE1_CBP_Enhancers TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad
2R	10749489	2R_10749489_SNP [dm3] 2R_14861984_SNP [dm6]	C	T	1.628e^-7	0.013	NON_SYNONYMOUS_CODING Inr-a	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2R	10787579	2R_10787579_SNP [dm3] 2R_14900074_SNP [dm6]	T	C	1.962e^-7	0.015	SYNONYMOUS_CODING Cyp317a1	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	17923262	2L_17923262_SNP [dm3] 2L_17923262_SNP [dm6]	G	C	2.414e^-7	0.017	INTERGENIC
X	16159941	X_16159941_MNP [dm3] X_16265908_MNP [dm6]	CAT	TTG	2.663e^-7	0.019	INTRON CG12507
2R	15158993	2R_15158993_DEL [dm3] 2R_19271488_DEL [dm6]	CA	T	2.857e^-7	0.019	INTRON rib	enhancer mE1_CBP_Enhancers TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad
X	16159938	X_16159938_SNP [dm3] X_16265905_SNP [dm6]	T	C	2.959e^-7	0.019	INTRON CG12507
2L	2425224	2L_2425224_SNP [dm3] 2L_2425224_SNP [dm6]	C	T	3.288e^-7	0.021	DOWNSTREAM CG9886 & 1 other INTERGENIC
2R	10608610	2R_10608610_SNP [dm3] 2R_14721105_SNP [dm6]	C	G	3.438e^-7	0.021	INTERGENIC
2R	10666546	2R_10666546_SNP [dm3] 2R_14779041_SNP [dm6]	T	C	3.564e^-7	0.021	INTRON kn
3L	1267484	3L_1267484_SNP [dm3] 3L_1267484_SNP [dm6]	A	G	4.005e^-7	0.023	INTRON CG9134
2R	10366370	2R_10366370_SNP [dm3] 2R_14478865_SNP [dm6]	T	C	4.747e^-7	0.025	DOWNSTREAM CR44462 INTERGENIC	TF binding site mE1_TFBS_cad
2R	3495195	2R_3495195_INS [dm3] 2R_7607690_INS [dm6]	C	CTTCATTGTCCGAAGGCCTT...	4.779e^-7	0.025	INTRON CG1358
2R	10460322	2R_10460322_SNP [dm3] 2R_14572817_SNP [dm6]	C	A	4.817e^-7	0.025	SYNONYMOUS_CODING LamC INTRON ttv
2R	10666534	2R_10666534_SNP [dm3] 2R_14779029_SNP [dm6]	G	A	5.098e^-7	0.026	INTRON kn
2R	15595811	2R_15595811_SNP [dm3] 2R_19708306_SNP [dm6]	C	A	5.233e^-7	0.026	INTERGENIC
2R	17775940	2R_17775940_SNP [dm3] 2R_21888435_SNP [dm6]	G	A	5.303e^-7	0.026	INTRON Fili
2R	15159007	2R_15159007_SNP [dm3] 2R_19271502_SNP [dm6]	G	A	6.204e^-7	0.029	INTRON rib	enhancer mE1_CBP_Enhancers TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad
2R	7475262	2R_7475262_SNP [dm3] 2R_11587757_SNP [dm6]	C	A	6.300e^-7	0.029	DOWNSTREAM snoRNA:Psi28S-1936 INTRON tou
X	16159947	X_16159947_SNP [dm3] X_16265914_SNP [dm6]	C	T	6.520e^-7	0.029	INTRON CG12507
2R	9632130	2R_9632130_SNP [dm3] 2R_13744625_SNP [dm6]	A	G	6.775e^-7	0.03	INTRON fas
2R	10721104	2R_10721104_SNP [dm3] 2R_14833599_SNP [dm6]	G	A	7.434e^-7	0.032	NON_SYNONYMOUS_CODING CG10205 UTR_3_PRIME CG10205
2L	8363433	2L_8363433_DEL [dm3] 2L_8363433_DEL [dm6]	CC	C	8.121e^-7	0.034	UPSTREAM CG7627 DOWNSTREAM RpS13 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z
2R	9632106	2R_9632106_SNP [dm3] 2R_13744601_SNP [dm6]	A	T	9.573e^-7	0.038	INTRON fas
2R	17775943	2R_17775943_SNP [dm3] 2R_21888438_SNP [dm6]	A	T	9.753e^-7	0.038	INTRON Fili
2R	10585509	2R_10585509_SNP [dm3] 2R_14698004_SNP [dm6]	G	T	9.842e^-7	0.038	INTRON mspo
2R	10294461	2R_10294461_SNP [dm3] 2R_14406956_SNP [dm6]	T	A	9.921e^-7	0.038	INTERGENIC
X	9584882	X_9584882_SNP [dm3] X_9690849_SNP [dm6]	C	G	1.033e^-6	0.038	DOWNSTREAM CR44016 INTERGENIC	regulatory region FlyBase REDfly_CRMs TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	17081741	2L_17081741_SNP [dm3] 2L_17081741_SNP [dm6]	G	A	1.037e^-6	0.038	INTERGENIC
2R	10585346	2R_10585346_SNP [dm3] 2R_14697841_SNP [dm6]	C	T	1.132e^-6	0.041	INTRON mspo
2R	15595812	2R_15595812_SNP [dm3] 2R_19708307_SNP [dm6]	G	A	1.145e^-6	0.041	INTERGENIC
2R	7475118	2R_7475118_SNP [dm3] 2R_11587613_SNP [dm6]	G	T	1.176e^-6	0.041	DOWNSTREAM snoRNA:Psi28S-1936 INTRON tou
2R	15595908	2R_15595908_SNP [dm3] 2R_19708403_SNP [dm6]	A	C	1.205e^-6	0.041	INTERGENIC
2R	10666533	2R_10666533_SNP [dm3] 2R_14779028_SNP [dm6]	G	A	1.368e^-6	0.046	INTRON kn
2R	10549497	2R_10549497_SNP [dm3] 2R_14661992_SNP [dm6]	T	G	1.549e^-6	0.051	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	10927438	2R_10927438_SNP [dm3] 2R_15039933_SNP [dm6]	T	A	1.735e^-6	0.056	SYNONYMOUS_CODING hbs	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2R	17775947	2R_17775947_SNP [dm3] 2R_21888442_SNP [dm6]	C	A	1.770e^-6	0.056	INTRON Fili
2R	17775930	2R_17775930_SNP [dm3] 2R_21888425_SNP [dm6]	G	C	1.799e^-6	0.056	INTRON Fili
2R	12370631	2R_12370631_SNP [dm3] 2R_16483126_SNP [dm6]	G	A	1.878e^-6	0.058	INTERGENIC
2R	10676596	2R_10676596_SNP [dm3] 2R_14789091_SNP [dm6]	G	T	1.946e^-6	0.059	INTRON kn	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
2R	10674472	2R_10674472_SNP [dm3] 2R_14786967_SNP [dm6]	A	G	2.022e^-6	0.059	INTRON kn	TF binding site BDTNP1_TFBS_dl
2R	10675354	2R_10675354_SNP [dm3] 2R_14787849_SNP [dm6]	C	A	2.022e^-6	0.059	INTRON kn	TF binding site BDTNP1_TFBS_da
2R	10616116	2R_10616116_SNP [dm3] 2R_14728611_SNP [dm6]	G	A	2.119e^-6	0.061	INTERGENIC
2R	10549501	2R_10549501_SNP [dm3] 2R_14661996_SNP [dm6]	T	G	2.194e^-6	0.062	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	9334599	2R_9334599_SNP [dm3] 2R_13447094_SNP [dm6]	A	G	2.394e^-6	0.067	UPSTREAM CG30062 INTRON cnn	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi
2R	7474501	2R_7474501_SNP [dm3] 2R_11586996_SNP [dm6]	G	A	2.495e^-6	0.069	SYNONYMOUS_CODING tou
2L	17999630	2L_17999630_SNP [dm3] 2L_17999630_SNP [dm6]	C	T	2.616e^-6	0.07	INTERGENIC
2L	17999633	2L_17999633_SNP [dm3] 2L_17999633_SNP [dm6]	C	T	2.616e^-6	0.07	INTERGENIC
2R	15060790	2R_15060790_DEL [dm3] 2R_19173285_DEL [dm6]	TCCT	T	2.728e^-6	0.07	INTRON CG10737
2L	17923288	2L_17923288_SNP [dm3] 2L_17923288_SNP [dm6]	T	A	2.762e^-6	0.07	INTERGENIC
2R	15595891	2R_15595891_SNP [dm3] 2R_19708386_SNP [dm6]	G	A	2.784e^-6	0.07	INTERGENIC
2R	15595892	2R_15595892_SNP [dm3] 2R_19708387_SNP [dm6]	A	G	2.784e^-6	0.07	INTERGENIC
2R	15595906	2R_15595906_SNP [dm3] 2R_19708401_SNP [dm6]	C	G	2.784e^-6	0.07	INTERGENIC
X	16159933	X_16159933_SNP [dm3] X_16265900_SNP [dm6]	A	C	2.867e^-6	0.07	INTRON CG12507
2R	15595905	2R_15595905_SNP [dm3] 2R_19708400_SNP [dm6]	T	A	2.893e^-6	0.07	INTERGENIC
2R	10585511	2R_10585511_SNP [dm3] 2R_14698006_SNP [dm6]	T	A	2.964e^-6	0.071	INTRON mspo
2R	10787494	2R_10787494_SNP [dm3] 2R_14899989_SNP [dm6]	C	T	3.039e^-6	0.072	SYNONYMOUS_CODING Cyp317a1	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
2L	17066954	2L_17066954_SNP [dm3] 2L_17066954_SNP [dm6]	T	A	3.286e^-6	0.077	INTERGENIC
2R	10709770	2R_10709770_SNP [dm3] 2R_14822265_SNP [dm6]	C	T	3.467e^-6	0.08	INTERGENIC
2R	15863357	2R_15863357_SNP [dm3] 2R_19975852_SNP [dm6]	G	A	4.292e^-6	0.098	INTERGENIC
X	9585103	X_9585103_SNP [dm3] X_9691070_SNP [dm6]	A	G	4.492e^-6	0.102	DOWNSTREAM CR44016 INTERGENIC	regulatory region FlyBase REDfly_CRMs TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	15195124	2R_15195124_SNP [dm3] 2R_19307619_SNP [dm6]	T	A	4.804e^-6	0.107	UTR_3_PRIME EndoB DOWNSTREAM CG7461
2R	10151602	2R_10151602_SNP [dm3] 2R_14264097_SNP [dm6]	C	T	5.029e^-6	0.111	INTRON CG8547	TF binding site mE1_TFBS_cad
2R	8702260	2R_8702260_DEL [dm3] 2R_12814755_DEL [dm6]	TTAGCT	T	5.347e^-6	0.116	INTERGENIC
2L	4367595	2L_4367595_SNP [dm3] 2L_4367595_SNP [dm6]	G	A	5.373e^-6	0.116	INTRON Traf4	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	14010795	2R_14010795_SNP [dm3] 2R_18123290_SNP [dm6]	G	A	5.669e^-6	0.121	INTRON stau	TF binding site BDTNP1_TFBS_Med mE1_TFBS_cad
2R	6064333	2R_6064333_SNP [dm3] 2R_10176828_SNP [dm6]	G	A	5.867e^-6	0.124	INTRON KCNQ
2R	10788315	2R_10788315_SNP [dm3] 2R_14900810_SNP [dm6]	G	A	6.087e^-6	0.127	NON_SYNONYMOUS_CODING Cyp317a1 DOWNSTREAM CG10249	TF binding site mE1_TFBS_sens
2R	10234617	2R_10234617_SNP [dm3] 2R_14347112_SNP [dm6]	A	G	6.318e^-6	0.13	INTRON Shroom
X	9584618	X_9584618_SNP [dm3] X_9690585_SNP [dm6]	C	T	6.802e^-6	0.139	DOWNSTREAM CR44016 INTERGENIC	regulatory region FlyBase REDfly_CRMs TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_Kr
X	9471620	X_9471620_SNP [dm3] X_9577587_SNP [dm6]	G	T	6.888e^-6	0.139	INTRON CG32699
2R	7476111	2R_7476111_SNP [dm3] 2R_11588606_SNP [dm6]	C	G	7.384e^-6	0.147	SYNONYMOUS_CODING tou UPSTREAM snoRNA:Psi28S-1936	TF binding site mE1_TFBS_cad
2R	10702960	2R_10702960_SNP [dm3] 2R_14815455_SNP [dm6]	A	C	7.679e^-6	0.15	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv
X	9585081	X_9585081_SNP [dm3] X_9691048_SNP [dm6]	T	A	7.687e^-6	0.15	DOWNSTREAM CR44016 INTERGENIC	regulatory region FlyBase REDfly_CRMs TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	10791745	2R_10791745_SNP [dm3] 2R_14904240_SNP [dm6]	C	A	7.768e^-6	0.15	SYNONYMOUS_CODING CG10249 UPSTREAM CG10249	TF binding site mE1_TFBS_chinmo
2R	10453850	2R_10453850_SNP [dm3] 2R_14566345_SNP [dm6]	T	C	8.320e^-6	0.156	INTRON ttv
2R	4969919	2R_4969919_SNP [dm3] 2R_9082414_SNP [dm6]	A	C	8.325e^-6	0.156	UTR_5_PRIME CNT1 DOWNSTREAM CG8083
2R	8631536	2R_8631536_DEL [dm3] 2R_12744031_DEL [dm6]	TGCGTAAGTTTAGTTTCGT...	T	8.481e^-6	0.156	INTRON CG42663	TF binding site mE1_TFBS_Trl

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By genomic position
Variant impact
Gene name

Delta_Alive.at.48h Experience 5 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results