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=1.828e^-21)
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
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2307 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
X	2474864	X_2474864_SNP [dm3] X_2580831_SNP [dm6]	T	C	4.154e^-8	0.041	UPSTREAM CG13759 & 1 other INTERGENIC
X	2474861	X_2474861_INS [dm3] X_2580828_INS [dm6]	A	ACGTG	4.340e^-8	0.041	UPSTREAM CG13759 & 1 other INTERGENIC
X	2706208	X_2706208_DEL [dm3] X_2812175_DEL [dm6]	CAAT	C	1.576e^-7	0.074	INTRON kirre
X	2706213	X_2706213_SNP [dm3] X_2812180_SNP [dm6]	C	T	1.576e^-7	0.074	INTRON kirre
X	2474802	X_2474802_INS [dm3] X_2580769_INS [dm6]	A	ATGTA	2.095e^-7	0.076	UPSTREAM CG13759 & 1 other INTERGENIC
2L	10137758	2L_10137758_SNP [dm3] 2L_10137758_SNP [dm6]	T	A	2.517e^-7	0.076	INTRON CG44153
X	2477618	X_2477618_SNP [dm3] X_2583585_SNP [dm6]	C	G	2.842e^-7	0.076	SYNONYMOUS_CODING CG13759 DOWNSTREAM CG13760	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2R	9269114	2R_9269114_SNP [dm3] 2R_13381609_SNP [dm6]	T	G	4.559e^-7	0.107	INTERGENIC
3R	17365836	3R_17365836_SNP [dm3] 3R_21540114_SNP [dm6]	A	T	7.117e^-7	0.148	INTERGENIC
2R	15870314	2R_15870314_SNP [dm3] 2R_19982809_SNP [dm6]	A	T	9.147e^-7	0.172	INTRON CG8654	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad mE1_TFBS_HSA
2R	9269124	2R_9269124_DEL [dm3] 2R_13381619_DEL [dm6]	TG	T	1.232e^-6	0.203	INTERGENIC
2R	9269137	2R_9269137_SNP [dm3] 2R_13381632_SNP [dm6]	T	A	1.342e^-6	0.203	INTERGENIC
3R	16051186	3R_16051186_SNP [dm3] 3R_20225464_SNP [dm6]	C	A	1.404e^-6	0.203	INTRON Nlg4
2L	10137806	2L_10137806_SNP [dm3] 2L_10137806_SNP [dm6]	G	T	1.689e^-6	0.215	INTRON CG44153
2L	17366277	2L_17366277_SNP [dm3] 2L_17366277_SNP [dm6]	G	A	1.824e^-6	0.215	INTERGENIC
3R	14656152	3R_14656152_SNP [dm3] 3R_18830430_SNP [dm6]	G	T	1.940e^-6	0.215	INTRON CG18208
2L	10137798	2L_10137798_SNP [dm3] 2L_10137798_SNP [dm6]	C	A	1.949e^-6	0.215	INTRON CG44153
3R	24205174	3R_24205174_SNP [dm3] 3R_28379452_SNP [dm6]	A	G	2.170e^-6	0.226	INTERGENIC
3L	11443063	3L_11443063_DEL [dm3] 3L_11449963_DEL [dm6]	TTACCCTCAACC...	T	2.509e^-6	0.248	INTERGENIC
2L	5160237	2L_5160237_SNP [dm3] 2L_5160237_SNP [dm6]	C	G	2.884e^-6	0.25	NON_SYNONYMOUS_CODING Msp300 INTRON Msp300	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
X	5449728	X_5449728_SNP [dm3] X_5555695_SNP [dm6]	C	A	3.127e^-6	0.25	INTRON Vsx2	TF binding site mE1_TFBS_cnc mE1_TFBS_Kr
X	6408199	X_6408199_SNP [dm3] X_6514166_SNP [dm6]	C	T	3.409e^-6	0.25	INTRON CG42340
3R	26027516	3R_26027516_SNP [dm3] 3R_30201794_SNP [dm6]	A	T	3.460e^-6	0.25	INTRON CG9743	TF binding site mE1_TFBS_inv
2R	15852928	2R_15852928_SNP [dm3] 2R_19965423_SNP [dm6]	G	T	3.671e^-6	0.25	INTERGENIC	TF binding site BDTNP1_TFBS_dl
3R	9734838	3R_9734838_SNP [dm3] 3R_13909116_SNP [dm6]	T	C	3.671e^-6	0.25	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 mE1_TFBS_HSA
X	2470586	X_2470586_SNP [dm3] X_2576553_SNP [dm6]	C	G	3.744e^-6	0.25	UTR_3_PRIME Pdfr INTRON Pdfr
X	2470664	X_2470664_SNP [dm3] X_2576631_SNP [dm6]	C	A	3.744e^-6	0.25	UTR_3_PRIME Pdfr INTRON Pdfr
3L	7533576	3L_7533576_SNP [dm3] 3L_7540476_SNP [dm6]	C	T	3.834e^-6	0.25	SYNONYMOUS_CODING CG32374 UPSTREAM CG16998 DOWNSTREAM lqf
2R	9269117	2R_9269117_DEL [dm3] 2R_13381612_DEL [dm6]	AAAGA	TCT	3.920e^-6	0.25	INTERGENIC
2R	9269138	2R_9269138_SNP [dm3] 2R_13381633_SNP [dm6]	T	C	4.004e^-6	0.25	INTERGENIC
3R	14196902	3R_14196902_SNP [dm3] 3R_18371180_SNP [dm6]	A	G	4.462e^-6	0.27	INTRON gl	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
2R	9269128	2R_9269128_SNP [dm3] 2R_13381623_SNP [dm6]	A	T	4.612e^-6	0.27	INTERGENIC
2L	5160239	2L_5160239_SNP [dm3] 2L_5160239_SNP [dm6]	A	G	5.134e^-6	0.283	SYNONYMOUS_CODING Msp300 INTRON Msp300	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	19601009	2L_19601009_SNP [dm3] 2L_19601009_SNP [dm6]	C	A	5.323e^-6	0.283	INTRON CR44978 & 1 other
2R	6960668	2R_6960668_SNP [dm3] 2R_11073163_SNP [dm6]	C	T	5.550e^-6	0.283	INTRON luna	TF binding site mE1_TFBS_HSA
3R	26027492	3R_26027492_SNP [dm3] 3R_30201770_SNP [dm6]	T	A	5.577e^-6	0.283	INTRON CG9743	TF binding site mE1_TFBS_inv
3R	16761488	3R_16761488_SNP [dm3] 3R_20935766_SNP [dm6]	T	A	5.973e^-6	0.283	INTRON CG31191
3R	24206117	3R_24206117_SNP [dm3] 3R_28380395_SNP [dm6]	T	G	5.976e^-6	0.283	INTERGENIC
2L	6515306	2L_6515306_SNP [dm3] 2L_6515306_SNP [dm6]	T	A	6.020e^-6	0.283	INTRON CG31637
3R	19446955	3R_19446955_INS [dm3] 3R_23621233_INS [dm6]	C	CCACC	6.204e^-6	0.283	INTRON CG31145
3L	2393411	3L_2393411_SNP [dm3] 3L_2393411_SNP [dm6]	G	A	6.345e^-6	0.283	INTRON CG45186	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	16677292	3R_16677292_SNP [dm3] 3R_20851570_SNP [dm6]	T	A	6.485e^-6	0.283	DOWNSTREAM Ir93a & 1 other INTERGENIC
2R	9269202	2R_9269202_SNP [dm3] 2R_13381697_SNP [dm6]	G	A	6.487e^-6	0.283	INTERGENIC
2L	2836985	2L_2836985_SNP [dm3] 2L_2836985_SNP [dm6]	G	A	6.815e^-6	0.29	INTRON CG3119
X	3421142	X_3421142_SNP [dm3] X_3527109_SNP [dm6]	T	A	7.020e^-6	0.29	INTRON CG32791
X	2698884	X_2698884_SNP [dm3] X_2804851_SNP [dm6]	A	C	7.110e^-6	0.29	INTRON kirre	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3R	7529701	3R_7529701_SNP [dm3] 3R_11703979_SNP [dm6]	T	G	8.751e^-6	0.346	UPSTREAM I-t INTERGENIC
2R	15038134	2R_15038134_SNP [dm3] 2R_19150629_SNP [dm6]	T	A	8.846e^-6	0.346	INTRON ena	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
X	13370179	X_13370179_SNP [dm3] X_13476146_SNP [dm6]	T	G	9.312e^-6	0.356	INTRON Neto
2L	9853018	2L_9853018_SNP [dm3] 2L_9853018_SNP [dm6]	T	C	9.669e^-6	0.363	INTRON nAChRalpha6
2R	9269155	2R_9269155_SNP [dm3] 2R_13381650_SNP [dm6]	T	C	1.037e^-5	0.382	INTERGENIC
3R	9738831	3R_9738831_SNP [dm3] 3R_13913109_SNP [dm6]	C	T	1.154e^-5	0.41	INTERGENIC	TF binding site mE1_TFBS_inv
3L	11924188	3L_11924188_SNP [dm3] 3L_11931088_SNP [dm6]	T	C	1.187e^-5	0.41	INTRON CG44837 & 1 other	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	9269197	2R_9269197_SNP [dm3] 2R_13381692_SNP [dm6]	A	G	1.232e^-5	0.41	INTERGENIC
3L	2158707	3L_2158707_SNP [dm3] 3L_2158707_SNP [dm6]	A	C	1.237e^-5	0.41	NON_SYNONYMOUS_CODING CG15822	TF binding site mE1_TFBS_chinmo mE1_TFBS_inv
3R	16761878	3R_16761878_SNP [dm3] 3R_20936156_SNP [dm6]	T	C	1.244e^-5	0.41	INTRON CG31191	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2R	16299765	2R_16299765_SNP [dm3] 2R_20412260_SNP [dm6]	T	C	1.262e^-5	0.41	INTERGENIC
3R	9738642	3R_9738642_SNP [dm3] 3R_13912920_SNP [dm6]	T	G	1.360e^-5	0.41	INTERGENIC	TF binding site mE1_TFBS_inv
X	8957546	X_8957546_SNP [dm3] X_9063513_SNP [dm6]	A	T	1.377e^-5	0.41	INTRON CG15365
2L	8150892	2L_8150892_SNP [dm3] 2L_8150892_SNP [dm6]	C	A	1.435e^-5	0.41	INTRON CG8552 & 1 other
2L	10487587	2L_10487587_SNP [dm3] 2L_10487587_SNP [dm6]	A	G	1.437e^-5	0.41	INTRON CG7456	TF binding site mE1_TFBS_inv
X	4161266	X_4161266_SNP [dm3] X_4267233_SNP [dm6]	T	A	1.463e^-5	0.41	DOWNSTREAM CG12691 INTERGENIC
3R	24401316	3R_24401316_SNP [dm3] 3R_28575594_SNP [dm6]	T	G	1.485e^-5	0.41	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_sens
3L	14372394	3L_14372394_SNP [dm3] 3L_14379294_SNP [dm6]	C	T	1.503e^-5	0.41	INTERGENIC
2R	17810174	2R_17810174_SNP [dm3] 2R_21922669_SNP [dm6]	C	T	1.508e^-5	0.41	INTRON Fili
2R	9866032	2R_9866032_INS [dm3] 2R_13978527_INS [dm6]	C	CA	1.509e^-5	0.41	INTRON CG6701	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	4709865	3L_4709865_SNP [dm3] 3L_4709865_SNP [dm6]	T	C	1.512e^-5	0.41	UTR_5_PRIME CG13712 INTRON RhoGEF64C	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	4709870	3L_4709870_SNP [dm3] 3L_4709870_SNP [dm6]	A	C	1.512e^-5	0.41	UTR_5_PRIME CG13712 INTRON RhoGEF64C	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	16761336	3R_16761336_SNP [dm3] 3R_20935614_SNP [dm6]	T	C	1.525e^-5	0.41	INTRON CG31191
2L	10145612	2L_10145612_SNP [dm3] 2L_10145612_SNP [dm6]	A	G	1.537e^-5	0.41	UTR_5_PRIME CG4839 INTRON CG44153 & 1 other
3L	11440886	3L_11440886_SNP [dm3] 3L_11447786_SNP [dm6]	T	C	1.567e^-5	0.41	INTERGENIC	TF binding site BDTNP1_TFBS_twi
3L	3263234	3L_3263234_SNP [dm3] 3L_3263234_SNP [dm6]	T	C	1.612e^-5	0.41	INTRON ckd
3R	25931725	3R_25931725_SNP [dm3] 3R_30106003_SNP [dm6]	T	C	1.644e^-5	0.41	INTRON sima
2R	12474784	2R_12474784_SNP [dm3] 2R_16587279_SNP [dm6]	A	C	1.668e^-5	0.41	UTR_3_PRIME CG8311 DOWNSTREAM RpLP2	TF binding site mE1_TFBS_cad
3L	18364980	3L_18364980_SNP [dm3] 3L_18371880_SNP [dm6]	C	T	1.676e^-5	0.41	INTERGENIC
3L	12056934	3L_12056934_SNP [dm3] 3L_12063834_SNP [dm6]	T	G	1.683e^-5	0.41	INTRON rols
3L	15881100	3L_15881100_SNP [dm3] 3L_15888000_SNP [dm6]	A	G	1.713e^-5	0.41	INTRON pHCl
3L	19274845	3L_19274845_SNP [dm3] 3L_19281745_SNP [dm6]	G	A	1.717e^-5	0.41	UTR_3_PRIME Gbs-76A UPSTREAM CG14089 DOWNSTREAM Gbs-76A
3L	9866385	3L_9866385_INS [dm3] 3L_9873285_INS [dm6]	T	TGTTCCAAGATT...	1.736e^-5	0.41	INTERGENIC
3L	12853276	3L_12853276_SNP [dm3] 3L_12860176_SNP [dm6]	G	A	1.758e^-5	0.41	SYNONYMOUS_CODING CG32107	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	14569437	3L_14569437_SNP [dm3] 3L_14576337_SNP [dm6]	A	G	1.771e^-5	0.41	INTERGENIC	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
3L	16448530	3L_16448530_INS [dm3] 3L_16455430_INS [dm6]	A	AGTTT	1.804e^-5	0.412	INTRON CG33158	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	2630464	2L_2630464_SNP [dm3] 2L_2630464_SNP [dm6]	T	C	1.848e^-5	0.412	INTERGENIC
X	7670790	X_7670790_SNP [dm3] X_7776757_SNP [dm6]	G	C	1.871e^-5	0.412	INTERGENIC
3L	13009371	3L_13009371_SNP [dm3] 3L_13016271_SNP [dm6]	T	G	1.889e^-5	0.412	UPSTREAM MICAL-like DOWNSTREAM mRpL20 INTRON CG11267	TF binding site mE1_TFBS_sens
3L	9106134	3L_9106134_INS [dm3] 3L_9113034_INS [dm6]	A	AGCTGAAGGA	1.891e^-5	0.412	INTRON bol	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi
3R	1024171	3R_1024171_SNP [dm3] 3R_5198449_SNP [dm6]	T	G	1.920e^-5	0.414	UPSTREAM cno INTRON cno	TF binding site mE1_TFBS_HSA
3R	14196891	3R_14196891_SNP [dm3] 3R_18371169_SNP [dm6]	T	G	1.942e^-5	0.414	INTRON gl	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
3L	22650620	3L_22650620_SNP [dm3] 3L_22657520_SNP [dm6]	G	C	1.992e^-5	0.419	INTERGENIC
3L	14372390	3L_14372390_SNP [dm3] 3L_14379290_SNP [dm6]	T	A	2.021e^-5	0.419	INTERGENIC
2L	12368143	2L_12368143_SNP [dm3] 2L_12368143_SNP [dm6]	C	T	2.049e^-5	0.419	INTRON bru-2
2R	9803780	2R_9803780_SNP [dm3] 2R_13916275_SNP [dm6]	G	A	2.069e^-5	0.419	INTRON shot
3R	16763347	3R_16763347_SNP [dm3] 3R_20937625_SNP [dm6]	T	C	2.086e^-5	0.419	INTRON CG31191
2L	5160017	2L_5160017_SNP [dm3] 2L_5160017_SNP [dm6]	G	T	2.103e^-5	0.419	SYNONYMOUS_CODING Msp300 INTRON Msp300
X	2540756	X_2540756_SNP [dm3] X_2646723_SNP [dm6]	C	G	2.143e^-5	0.419	UTR_5_PRIME sgg INTRON sgg	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
3L	9824838	3L_9824838_SNP [dm3] 3L_9831738_SNP [dm6]	A	T	2.162e^-5	0.419	INTRON CG43897
X	12910742	X_12910742_SNP [dm3] X_13016709_SNP [dm6]	T	A	2.194e^-5	0.419	INTRON rad
2L	6083755	2L_6083755_SNP [dm3] 2L_6083755_SNP [dm6]	T	A	2.199e^-5	0.419	INTRON Kr-h1	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_inv
2L	9446064	2L_9446064_SNP [dm3] 2L_9446064_SNP [dm6]	T	C	2.282e^-5	0.419	INTRON numb	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb mE1_TFBS_cad mE1_TFBS_HSA
3L	18844569	3L_18844569_SNP [dm3] 3L_18851469_SNP [dm6]	G	T	2.294e^-5	0.419	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA

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By genomic position
Variant impact
Gene name

idx_Surv_15MeHg phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results