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=6.543e^-13)
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	0.01149

Kruskal-Wallis test

Covariate	χ²	p-value
In_2L_t	8.0478	0.0179
In_2R_NS	8.2366	0.0163
In_3R_P	7.517	0.0233

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

4622 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	10702960	2R_10702960_SNP [dm3] 2R_14815455_SNP [dm6]	A	C	1.620e^-10	1.450e^-4	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
2R	10749489	2R_10749489_SNP [dm3] 2R_14861984_SNP [dm6]	C	T	1.620e^-10	1.450e^-4	NON_SYNONYMOUS_CODING Inr-a	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2R	10715639	2R_10715639_SNP [dm3] 2R_14828134_SNP [dm6]	A	T	3.467e^-10	1.450e^-4	INTERGENIC
2R	10705677	2R_10705677_SNP [dm3] 2R_14818172_SNP [dm6]	G	T	4.108e^-10	1.450e^-4	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	4.108e^-10	1.450e^-4	UPSTREAM CG10205 INTERGENIC
2R	10713301	2R_10713301_SNP [dm3] 2R_14825796_SNP [dm6]	T	G	4.640e^-10	1.450e^-4	INTERGENIC
2R	10700525	2R_10700525_SNP [dm3] 2R_14813020_SNP [dm6]	G	A	5.737e^-10	1.498e^-4	INTERGENIC	regulatory region REDfly_CRMs
2R	10721948	2R_10721948_SNP [dm3] 2R_14834443_SNP [dm6]	C	A	6.391e^-10	1.498e^-4	DOWNSTREAM CG10205 INTERGENIC
2R	10701426	2R_10701426_SNP [dm3] 2R_14813921_SNP [dm6]	G	A	8.395e^-10	1.750e^-4	INTERGENIC	TF binding site mE1_TFBS_Trl
2R	10721104	2R_10721104_SNP [dm3] 2R_14833599_SNP [dm6]	G	A	3.707e^-9	6.953e^-4	NON_SYNONYMOUS_CODING CG10205 UTR_3_PRIME CG10205
X	7331771	X_7331771_SNP [dm3] X_7437738_SNP [dm6]	C	G	4.742e^-9	8.086e^-4	INTERGENIC
X	7331220	X_7331220_SNP [dm3] X_7437187_SNP [dm6]	C	A	5.433e^-9	8.492e^-4	INTERGENIC
X	7329536	X_7329536_SNP [dm3] X_7435503_SNP [dm6]	T	C	9.356e^-9	0.001	INTERGENIC
X	7329519	X_7329519_SNP [dm3] X_7435486_SNP [dm6]	A	G	1.570e^-8	0.002	INTERGENIC
2R	12066229	2R_12066229_SNP [dm3] 2R_16178724_SNP [dm6]	G	A	2.481e^-8	0.003	UPSTREAM Lis-1 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl mE1_TFBS_Ubx
2R	12066234	2R_12066234_SNP [dm3] 2R_16178729_SNP [dm6]	T	A	2.766e^-8	0.003	UPSTREAM Lis-1 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl mE1_TFBS_Ubx
2R	12245315	2R_12245315_SNP [dm3] 2R_16357810_SNP [dm6]	G	A	3.052e^-8	0.003	DOWNSTREAM CR45322 EXON CR43416
2R	10674472	2R_10674472_SNP [dm3] 2R_14786967_SNP [dm6]	A	G	3.406e^-8	0.003	INTRON kn	TF binding site BDTNP1_TFBS_dl
2R	10675354	2R_10675354_SNP [dm3] 2R_14787849_SNP [dm6]	C	A	3.406e^-8	0.003	INTRON kn	TF binding site BDTNP1_TFBS_da
2R	10616116	2R_10616116_SNP [dm3] 2R_14728611_SNP [dm6]	G	A	3.496e^-8	0.003	INTERGENIC
2L	9261424	2L_9261424_SNP [dm3] 2L_9261424_SNP [dm6]	G	A	4.072e^-8	0.004	DOWNSTREAM CR45262 INTRON Ggamma30A
2R	15436212	2R_15436212_SNP [dm3] 2R_19548707_SNP [dm6]	C	T	7.897e^-8	0.007	INTRON sm
2L	9259902	2L_9259902_DEL [dm3] 2L_9259902_DEL [dm6]	CTCTTC	C	1.036e^-7	0.008	INTRON Ggamma30A
2L	4376521	2L_4376521_SNP [dm3] 2L_4376521_SNP [dm6]	A	T	1.451e^-7	0.01	INTRON Traf4	TF binding site mE1_TFBS_cad
2L	9346349	2L_9346349_SNP [dm3] 2L_9346349_SNP [dm6]	A	G	1.455e^-7	0.01	INTERGENIC
2R	15203387	2R_15203387_SNP [dm3] 2R_19315882_SNP [dm6]	T	C	1.476e^-7	0.01	INTRON Rgk1
2R	10700594	2R_10700594_SNP [dm3] 2R_14813089_SNP [dm6]	A	G	1.497e^-7	0.01	INTERGENIC
2L	9258652	2L_9258652_SNP [dm3] 2L_9258652_SNP [dm6]	A	T	1.728e^-7	0.011	INTRON Ggamma30A
X	11164117	X_11164117_SNP [dm3] X_11270084_SNP [dm6]	T	C	1.749e^-7	0.011	INTRON CG44422
2R	9632088	2R_9632088_INS [dm3] 2R_13744583_INS [dm6]	T	TT	2.210e^-7	0.014	INTRON fas
2R	10711040	2R_10711040_SNP [dm3] 2R_14823535_SNP [dm6]	G	A	2.503e^-7	0.015	DOWNSTREAM CR45329 INTERGENIC
2R	10676596	2R_10676596_SNP [dm3] 2R_14789091_SNP [dm6]	G	T	2.682e^-7	0.015	INTRON kn	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
2R	9637298	2R_9637298_SNP [dm3] 2R_13749793_SNP [dm6]	A	C	2.713e^-7	0.015	DOWNSTREAM fas INTERGENIC
2R	11328080	2R_11328080_SNP [dm3] 2R_15440575_SNP [dm6]	C	T	3.045e^-7	0.016	INTRON CG43729
2L	8363433	2L_8363433_DEL [dm3] 2L_8363433_DEL [dm6]	CC	C	3.099e^-7	0.016	UPSTREAM CG7627 DOWNSTREAM RpS13 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z
X	10941853	X_10941853_SNP [dm3] X_11047820_SNP [dm6]	G	T	3.144e^-7	0.016	SYNONYMOUS_CODING CG11160	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Mad BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2R	10688036	2R_10688036_SNP [dm3] 2R_14800531_SNP [dm6]	A	G	3.171e^-7	0.016	INTRON kn	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_eve mE1_TFBS_HSA
2L	9253428	2L_9253428_INS [dm3] 2L_9253428_INS [dm6]	G	CACGACATAAAAACAAAAA...	3.409e^-7	0.017	UPSTREAM borr DOWNSTREAM lectin-30A INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl
2L	9253430	2L_9253430_SNP [dm3] 2L_9253430_SNP [dm6]	T	A	3.519e^-7	0.017	UPSTREAM borr DOWNSTREAM lectin-30A INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl
2L	10637038	2L_10637038_SNP [dm3] 2L_10637038_SNP [dm6]	T	C	3.996e^-7	0.019	INTRON CG7329
3L	12138468	3L_12138468_SNP [dm3] 3L_12145368_SNP [dm6]	T	C	4.351e^-7	0.02	INTRON CG5642	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_GATAe mE1_TFBS_h mE1_TFBS_sens
2L	17054282	2L_17054282_SNP [dm3] 2L_17054282_SNP [dm6]	A	T	4.620e^-7	0.02	INTERGENIC
2L	9252708	2L_9252708_SNP [dm3] 2L_9252708_SNP [dm6]	G	A	4.787e^-7	0.02	SYNONYMOUS_CODING borr	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	11661653	2R_11661653_SNP [dm3] 2R_15774148_SNP [dm6]	G	C	4.834e^-7	0.02	INTRON Zasp52	TF binding site mE1_TFBS_chinmo
2L	9253421	2L_9253421_MNP [dm3] 2L_9253421_MNP [dm6]	CCC	GAA	4.856e^-7	0.02	UPSTREAM borr DOWNSTREAM lectin-30A INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl
2L	9255723	2L_9255723_SNP [dm3] 2L_9255723_SNP [dm6]	T	C	5.022e^-7	0.02	UPSTREAM lectin-30A & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_z
2L	9254412	2L_9254412_SNP [dm3] 2L_9254412_SNP [dm6]	G	A	5.185e^-7	0.021	SYNONYMOUS_CODING lectin-30A
2R	9632106	2R_9632106_SNP [dm3] 2R_13744601_SNP [dm6]	A	T	5.370e^-7	0.021	INTRON fas
2R	15044694	2R_15044694_SNP [dm3] 2R_19157189_SNP [dm6]	A	C	5.567e^-7	0.021	INTRON ena
2R	7166346	2R_7166346_SNP [dm3] 2R_11278841_SNP [dm6]	G	A	5.863e^-7	0.022	UPSTREAM Cpr47Eg & 1 other DOWNSTREAM CG9067 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med
2R	11613733	2R_11613733_SNP [dm3] 2R_15726228_SNP [dm6]	G	C	5.973e^-7	0.022	INTERGENIC
2L	9252592	2L_9252592_SNP [dm3] 2L_9252592_SNP [dm6]	C	G	6.026e^-7	0.022	INTRON borr	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	12198042	2R_12198042_SNP [dm3] 2R_16310537_SNP [dm6]	C	T	6.522e^-7	0.023	INTRON Nox	TF binding site mE1_TFBS_chinmo
2L	9262205	2L_9262205_SNP [dm3] 2L_9262205_SNP [dm6]	G	C	6.621e^-7	0.023	INTRON Ggamma30A EXON CR45262
2L	9253529	2L_9253529_SNP [dm3] 2L_9253529_SNP [dm6]	C	A	7.052e^-7	0.024	UPSTREAM borr DOWNSTREAM lectin-30A INTERGENIC	TF binding site BDTNP1_TFBS_dl
X	7333551	X_7333551_SNP [dm3] X_7439518_SNP [dm6]	A	C	7.060e^-7	0.024	INTERGENIC
2L	10630550	2L_10630550_SNP [dm3] 2L_10630550_SNP [dm6]	C	T	7.217e^-7	0.024	SYNONYMOUS_CODING CG7329	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	10608610	2R_10608610_SNP [dm3] 2R_14721105_SNP [dm6]	C	G	7.511e^-7	0.024	INTERGENIC
2R	13191066	2R_13191066_SNP [dm3] 2R_17303561_SNP [dm6]	A	T	7.633e^-7	0.024	INTRON mbl
2R	10368189	2R_10368189_SNP [dm3] 2R_14480684_SNP [dm6]	G	C	7.781e^-7	0.024	UPSTREAM L INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_bab1
2R	15044697	2R_15044697_INS [dm3] 2R_19157192_INS [dm6]	A	AT	7.944e^-7	0.024	INTRON ena
2R	15044705	2R_15044705_SNP [dm3] 2R_19157200_SNP [dm6]	T	C	8.384e^-7	0.025	INTRON ena
2L	9253255	2L_9253255_SNP [dm3] 2L_9253255_SNP [dm6]	A	G	8.415e^-7	0.025	UPSTREAM borr DOWNSTREAM lectin-30A INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
3L	9801356	3L_9801356_SNP [dm3] 3L_9808256_SNP [dm6]	A	G	8.909e^-7	0.026	UTR_3_PRIME CG32052	TF binding site BDTNP1_TFBS_twi
2L	19336830	2L_19336830_SNP [dm3] 2L_19336830_SNP [dm6]	G	T	9.348e^-7	0.026	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad
2L	9259041	2L_9259041_SNP [dm3] 2L_9259041_SNP [dm6]	T	A	9.469e^-7	0.026	INTRON Ggamma30A
2R	10700592	2R_10700592_SNP [dm3] 2R_14813087_SNP [dm6]	G	A	9.592e^-7	0.026	INTERGENIC
2L	19320516	2L_19320516_SNP [dm3] 2L_19320516_SNP [dm6]	T	C	9.601e^-7	0.026	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_Kr
2R	15044703	2R_15044703_SNP [dm3] 2R_19157198_SNP [dm6]	T	G	9.827e^-7	0.027	INTRON ena
2L	19313601	2L_19313601_SNP [dm3] 2L_19313601_SNP [dm6]	C	T	1.005e^-6	0.027	INTERGENIC	TF binding site mE1_TFBS_cad
2R	9632130	2R_9632130_SNP [dm3] 2R_13744625_SNP [dm6]	A	G	1.011e^-6	0.027	INTRON fas
2L	9263647	2L_9263647_SNP [dm3] 2L_9263647_SNP [dm6]	G	A	1.068e^-6	0.028	UPSTREAM CR45262 INTRON Ggamma30A	TF binding site mE1_TFBS_inv
2R	11957750	2R_11957750_SNP [dm3] 2R_16070245_SNP [dm6]	G	A	1.073e^-6	0.028	INTERGENIC	TF binding site mE1_TFBS_cad
2L	9259372	2L_9259372_SNP [dm3] 2L_9259372_SNP [dm6]	C	A	1.137e^-6	0.028	UTR_5_PRIME Ggamma30A INTRON Ggamma30A
2R	10700192	2R_10700192_SNP [dm3] 2R_14812687_SNP [dm6]	G	C	1.158e^-6	0.028	INTERGENIC	regulatory region REDfly_CRMs
2L	9253367	2L_9253367_SNP [dm3] 2L_9253367_SNP [dm6]	A	T	1.176e^-6	0.028	UPSTREAM borr DOWNSTREAM lectin-30A INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl
2L	9260169	2L_9260169_SNP [dm3] 2L_9260169_SNP [dm6]	T	C	1.187e^-6	0.028	INTRON Ggamma30A
2L	5483007	2L_5483007_SNP [dm3] 2L_5483007_SNP [dm6]	A	G	1.210e^-6	0.028	INTERGENIC
2L	9261094	2L_9261094_SNP [dm3] 2L_9261094_SNP [dm6]	C	T	1.210e^-6	0.028	DOWNSTREAM CR45262 INTRON Ggamma30A
2L	9261095	2L_9261095_SNP [dm3] 2L_9261095_SNP [dm6]	C	T	1.210e^-6	0.028	DOWNSTREAM CR45262 INTRON Ggamma30A
2L	9257288	2L_9257288_SNP [dm3] 2L_9257288_SNP [dm6]	C	T	1.215e^-6	0.028	INTRON Ggamma30A	TF binding site BDTNP1_TFBS_z mE1_TFBS_Trl
2L	9261448	2L_9261448_SNP [dm3] 2L_9261448_SNP [dm6]	T	A	1.227e^-6	0.028	DOWNSTREAM CR45262 INTRON Ggamma30A
3L	481733	3L_481733_SNP [dm3] 3L_481733_SNP [dm6]	T	C	1.248e^-6	0.028	INTRON klar
2R	10608749	2R_10608749_SNP [dm3] 2R_14721244_SNP [dm6]	C	G	1.283e^-6	0.029	INTERGENIC	TF binding site mE1_TFBS_inv
2L	11969832	2L_11969832_SNP [dm3] 2L_11969832_SNP [dm6]	T	A	1.296e^-6	0.029	INTRON CR43314	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad
3L	9376172	3L_9376172_SNP [dm3] 3L_9383072_SNP [dm6]	G	A	1.330e^-6	0.029	UPSTREAM Hsp27 DOWNSTREAM Hsp23 INTERGENIC	TF binding site BDTNP1_TFBS_dl
2L	9262563	2L_9262563_SNP [dm3] 2L_9262563_SNP [dm6]	A	G	1.344e^-6	0.029	INTRON Ggamma30A EXON CR45262
2R	13671439	2R_13671439_SNP [dm3] 2R_17783934_SNP [dm6]	T	A	1.376e^-6	0.029	UPSTREAM mir-31a INTERGENIC	TF binding site BDTNP1_TFBS_dl
2L	17060671	2L_17060671_SNP [dm3] 2L_17060671_SNP [dm6]	G	A	1.424e^-6	0.03	INTERGENIC
X	11031712	X_11031712_SNP [dm3] X_11137679_SNP [dm6]	T	C	1.452e^-6	0.03	UPSTREAM Klp10A & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_h mE1_TFBS_hkb mE1_TFBS_HSA mE1_TFBS_Ubx
2L	9259433	2L_9259433_SNP [dm3] 2L_9259433_SNP [dm6]	C	T	1.479e^-6	0.03	UTR_5_PRIME Ggamma30A INTRON Ggamma30A
2L	6677459	2L_6677459_SNP [dm3] 2L_6677459_SNP [dm6]	T	C	1.515e^-6	0.031	SYNONYMOUS_CODING CG11329 UPSTREAM cort DOWNSTREAM Nhe3	TF binding site mE1_TFBS_HSA mE1_TFBS_ttk
2R	15272659	2R_15272659_SNP [dm3] 2R_19385154_SNP [dm6]	A	C	1.517e^-6	0.031	UPSTREAM CG10081 DOWNSTREAM CG10073 INTERGENIC
2R	18587506	2R_18587506_SNP [dm3] 2R_22700001_SNP [dm6]	G	A	1.646e^-6	0.033	UTR_5_PRIME robo	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_sens
2L	9259419	2L_9259419_SNP [dm3] 2L_9259419_SNP [dm6]	C	G	1.655e^-6	0.033	UTR_5_PRIME Ggamma30A INTRON Ggamma30A
2R	14706594	2R_14706594_DEL [dm3] 2R_18819089_DEL [dm6]	TTG	T	1.772e^-6	0.034	UPSTREAM Phb2 INTERGENIC	TF binding site BDTNP1_TFBS_dl
2L	9253293	2L_9253293_SNP [dm3] 2L_9253293_SNP [dm6]	C	G	1.775e^-6	0.034	UPSTREAM borr DOWNSTREAM lectin-30A INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med
2R	15272650	2R_15272650_DEL [dm3] 2R_19385145_DEL [dm6]	CCA	C	1.893e^-6	0.036	UPSTREAM CG10081 DOWNSTREAM CG10073 INTERGENIC
2L	19332081	2L_19332081_SNP [dm3] 2L_19332081_SNP [dm6]	C	A	1.893e^-6	0.036	INTERGENIC
2R	14959850	2R_14959850_SNP [dm3] 2R_19072345_SNP [dm6]	T	A	1.909e^-6	0.036	INTRON 5-HT1A

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By genomic position
Variant impact
Gene name

Delta_Alive.at.48h Experience 1 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results