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=5.416e^-22)
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

2279 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	5.445e^-8	0.056	UPSTREAM CG13759 & 1 other INTERGENIC
X	2474861	X_2474861_INS [dm3] X_2580828_INS [dm6]	A	ACGTG	5.996e^-8	0.056	UPSTREAM CG13759 & 1 other INTERGENIC
X	2706208	X_2706208_DEL [dm3] X_2812175_DEL [dm6]	CAAT	C	1.819e^-7	0.085	INTRON kirre
X	2706213	X_2706213_SNP [dm3] X_2812180_SNP [dm6]	C	T	1.819e^-7	0.085	INTRON kirre
2L	10137758	2L_10137758_SNP [dm3] 2L_10137758_SNP [dm6]	T	A	2.781e^-7	0.096	INTRON CG44153
X	2474802	X_2474802_INS [dm3] X_2580769_INS [dm6]	A	ATGTA	3.181e^-7	0.096	UPSTREAM CG13759 & 1 other INTERGENIC
X	2477618	X_2477618_SNP [dm3] X_2583585_SNP [dm6]	C	G	4.213e^-7	0.096	SYNONYMOUS_CODING CG13759 DOWNSTREAM CG13760	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	17365836	3R_17365836_SNP [dm3] 3R_21540114_SNP [dm6]	A	T	4.333e^-7	0.096	INTERGENIC
2R	9269114	2R_9269114_SNP [dm3] 2R_13381609_SNP [dm6]	T	G	4.592e^-7	0.096	INTERGENIC
2L	10137806	2L_10137806_SNP [dm3] 2L_10137806_SNP [dm6]	G	T	1.393e^-6	0.248	INTRON CG44153
2R	9269124	2R_9269124_DEL [dm3] 2R_13381619_DEL [dm6]	TG	T	1.452e^-6	0.248	INTERGENIC
2L	10137798	2L_10137798_SNP [dm3] 2L_10137798_SNP [dm6]	C	A	1.710e^-6	0.251	INTRON CG44153
3R	16051186	3R_16051186_SNP [dm3] 3R_20225464_SNP [dm6]	C	A	1.740e^-6	0.251	INTRON Nlg4
3R	26027516	3R_26027516_SNP [dm3] 3R_30201794_SNP [dm6]	A	T	1.907e^-6	0.256	INTRON CG9743	TF binding site mE1_TFBS_inv
3R	14656152	3R_14656152_SNP [dm3] 3R_18830430_SNP [dm6]	G	T	2.145e^-6	0.256	INTRON CG18208
2R	9269137	2R_9269137_SNP [dm3] 2R_13381632_SNP [dm6]	T	A	2.183e^-6	0.256	INTERGENIC
3L	11443063	3L_11443063_DEL [dm3] 3L_11449963_DEL [dm6]	TTACCCTCAACC...	T	2.527e^-6	0.263	INTERGENIC
2R	15870314	2R_15870314_SNP [dm3] 2R_19982809_SNP [dm6]	A	T	2.633e^-6	0.263	INTRON CG8654	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad mE1_TFBS_HSA
X	6408199	X_6408199_SNP [dm3] X_6514166_SNP [dm6]	C	T	2.672e^-6	0.263	INTRON CG42340
X	5449728	X_5449728_SNP [dm3] X_5555695_SNP [dm6]	C	A	2.804e^-6	0.263	INTRON Vsx2	TF binding site mE1_TFBS_cnc mE1_TFBS_Kr
3R	26027492	3R_26027492_SNP [dm3] 3R_30201770_SNP [dm6]	T	A	3.116e^-6	0.266	INTRON CG9743	TF binding site mE1_TFBS_inv
3L	2393411	3L_2393411_SNP [dm3] 3L_2393411_SNP [dm6]	G	A	3.349e^-6	0.266	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
2L	2836985	2L_2836985_SNP [dm3] 2L_2836985_SNP [dm6]	G	A	3.437e^-6	0.266	INTRON CG3119
2L	17366277	2L_17366277_SNP [dm3] 2L_17366277_SNP [dm6]	G	A	3.634e^-6	0.266	INTERGENIC
3R	9734838	3R_9734838_SNP [dm3] 3R_13909116_SNP [dm6]	T	C	3.924e^-6	0.266	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 mE1_TFBS_HSA
3R	24205174	3R_24205174_SNP [dm3] 3R_28379452_SNP [dm6]	A	G	3.954e^-6	0.266	INTERGENIC
2R	9269117	2R_9269117_DEL [dm3] 2R_13381612_DEL [dm6]	AAAGA	TCT	4.003e^-6	0.266	INTERGENIC
2L	5160237	2L_5160237_SNP [dm3] 2L_5160237_SNP [dm6]	C	G	4.270e^-6	0.266	NON_SYNONYMOUS_CODING Msp300 INTRON Msp300	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	6960668	2R_6960668_SNP [dm3] 2R_11073163_SNP [dm6]	C	T	4.470e^-6	0.266	INTRON luna	TF binding site mE1_TFBS_HSA
3R	16761488	3R_16761488_SNP [dm3] 3R_20935766_SNP [dm6]	T	A	4.549e^-6	0.266	INTRON CG31191
2L	6515306	2L_6515306_SNP [dm3] 2L_6515306_SNP [dm6]	T	A	4.645e^-6	0.266	INTRON CG31637
2R	9269138	2R_9269138_SNP [dm3] 2R_13381633_SNP [dm6]	T	C	4.670e^-6	0.266	INTERGENIC
3R	7529701	3R_7529701_SNP [dm3] 3R_11703979_SNP [dm6]	T	G	4.684e^-6	0.266	UPSTREAM I-t INTERGENIC
3R	24206117	3R_24206117_SNP [dm3] 3R_28380395_SNP [dm6]	T	G	4.882e^-6	0.266	INTERGENIC
X	2470586	X_2470586_SNP [dm3] X_2576553_SNP [dm6]	C	G	5.114e^-6	0.266	UTR_3_PRIME Pdfr INTRON Pdfr
X	2470664	X_2470664_SNP [dm3] X_2576631_SNP [dm6]	C	A	5.114e^-6	0.266	UTR_3_PRIME Pdfr INTRON Pdfr
3R	19446955	3R_19446955_INS [dm3] 3R_23621233_INS [dm6]	C	CCACC	5.334e^-6	0.27	INTRON CG31145
3R	14196902	3R_14196902_SNP [dm3] 3R_18371180_SNP [dm6]	A	G	5.621e^-6	0.274	INTRON gl	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
X	3421142	X_3421142_SNP [dm3] X_3527109_SNP [dm6]	T	A	5.700e^-6	0.274	INTRON CG32791
2R	9269128	2R_9269128_SNP [dm3] 2R_13381623_SNP [dm6]	A	T	6.002e^-6	0.277	INTERGENIC
3R	16677292	3R_16677292_SNP [dm3] 3R_20851570_SNP [dm6]	T	A	6.106e^-6	0.277	DOWNSTREAM Ir93a & 1 other INTERGENIC
3L	7533576	3L_7533576_SNP [dm3] 3L_7540476_SNP [dm6]	C	T	6.333e^-6	0.277	SYNONYMOUS_CODING CG32374 UPSTREAM CG16998 DOWNSTREAM lqf
X	2698884	X_2698884_SNP [dm3] X_2804851_SNP [dm6]	A	C	6.343e^-6	0.277	INTRON kirre	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2R	15852928	2R_15852928_SNP [dm3] 2R_19965423_SNP [dm6]	G	T	6.797e^-6	0.283	INTERGENIC	TF binding site BDTNP1_TFBS_dl
2L	19601009	2L_19601009_SNP [dm3] 2L_19601009_SNP [dm6]	C	A	6.986e^-6	0.283	INTRON CR44978 & 1 other
2L	10487587	2L_10487587_SNP [dm3] 2L_10487587_SNP [dm6]	A	G	7.016e^-6	0.283	INTRON CG7456	TF binding site mE1_TFBS_inv
2L	5160239	2L_5160239_SNP [dm3] 2L_5160239_SNP [dm6]	A	G	7.098e^-6	0.283	SYNONYMOUS_CODING Msp300 INTRON Msp300	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	11924188	3L_11924188_SNP [dm3] 3L_11931088_SNP [dm6]	T	C	8.100e^-6	0.316	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	16299765	2R_16299765_SNP [dm3] 2R_20412260_SNP [dm6]	T	C	8.676e^-6	0.328	INTERGENIC
3L	2158707	3L_2158707_SNP [dm3] 3L_2158707_SNP [dm6]	A	C	8.902e^-6	0.328	NON_SYNONYMOUS_CODING CG15822	TF binding site mE1_TFBS_chinmo mE1_TFBS_inv
2R	9269202	2R_9269202_SNP [dm3] 2R_13381697_SNP [dm6]	G	A	8.906e^-6	0.328	INTERGENIC
2R	9269155	2R_9269155_SNP [dm3] 2R_13381650_SNP [dm6]	T	C	1.013e^-5	0.359	INTERGENIC
X	7670790	X_7670790_SNP [dm3] X_7776757_SNP [dm6]	G	C	1.051e^-5	0.359	INTERGENIC
X	13370179	X_13370179_SNP [dm3] X_13476146_SNP [dm6]	T	G	1.074e^-5	0.359	INTRON Neto
2L	9853018	2L_9853018_SNP [dm3] 2L_9853018_SNP [dm6]	T	C	1.079e^-5	0.359	INTRON nAChRalpha6
3L	13009371	3L_13009371_SNP [dm3] 3L_13016271_SNP [dm6]	T	G	1.091e^-5	0.359	UPSTREAM MICAL-like DOWNSTREAM mRpL20 INTRON CG11267	TF binding site mE1_TFBS_sens
3L	12056934	3L_12056934_SNP [dm3] 3L_12063834_SNP [dm6]	T	G	1.092e^-5	0.359	INTRON rols
2R	9803780	2R_9803780_SNP [dm3] 2R_13916275_SNP [dm6]	G	A	1.136e^-5	0.361	INTRON shot
2L	12368143	2L_12368143_SNP [dm3] 2L_12368143_SNP [dm6]	C	T	1.138e^-5	0.361	INTRON bru-2
2L	12368223	2L_12368223_SNP [dm3] 2L_12368223_SNP [dm6]	T	A	1.155e^-5	0.361	INTRON bru-2
2L	8150892	2L_8150892_SNP [dm3] 2L_8150892_SNP [dm6]	C	A	1.207e^-5	0.364	INTRON CG8552 & 1 other
3L	18364980	3L_18364980_SNP [dm3] 3L_18371880_SNP [dm6]	C	T	1.224e^-5	0.364	INTERGENIC
3R	16761878	3R_16761878_SNP [dm3] 3R_20936156_SNP [dm6]	T	C	1.238e^-5	0.364	INTRON CG31191	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3L	14372394	3L_14372394_SNP [dm3] 3L_14379294_SNP [dm6]	C	T	1.243e^-5	0.364	INTERGENIC
3L	9824838	3L_9824838_SNP [dm3] 3L_9831738_SNP [dm6]	A	T	1.337e^-5	0.383	INTRON CG43897
3L	15881100	3L_15881100_SNP [dm3] 3L_15888000_SNP [dm6]	A	G	1.356e^-5	0.383	INTRON pHCl
2R	17810174	2R_17810174_SNP [dm3] 2R_21922669_SNP [dm6]	C	T	1.384e^-5	0.383	INTRON Fili
3R	16761336	3R_16761336_SNP [dm3] 3R_20935614_SNP [dm6]	T	C	1.388e^-5	0.383	INTRON CG31191
3R	16763347	3R_16763347_SNP [dm3] 3R_20937625_SNP [dm6]	T	C	1.506e^-5	0.392	INTRON CG31191
3L	3263234	3L_3263234_SNP [dm3] 3L_3263234_SNP [dm6]	T	C	1.524e^-5	0.392	INTRON ckd
2L	6083755	2L_6083755_SNP [dm3] 2L_6083755_SNP [dm6]	T	A	1.527e^-5	0.392	INTRON Kr-h1	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_inv
2R	14762500	2R_14762500_SNP [dm3] 2R_18874995_SNP [dm6]	A	C	1.548e^-5	0.392	INTERGENIC
3R	9738831	3R_9738831_SNP [dm3] 3R_13913109_SNP [dm6]	C	T	1.551e^-5	0.392	INTERGENIC	TF binding site mE1_TFBS_inv
2R	9269197	2R_9269197_SNP [dm3] 2R_13381692_SNP [dm6]	A	G	1.553e^-5	0.392	INTERGENIC
3L	14372390	3L_14372390_SNP [dm3] 3L_14379290_SNP [dm6]	T	A	1.567e^-5	0.392	INTERGENIC
2L	10145612	2L_10145612_SNP [dm3] 2L_10145612_SNP [dm6]	A	G	1.606e^-5	0.395	UTR_5_PRIME CG4839 INTRON CG44153 & 1 other
3L	12853276	3L_12853276_SNP [dm3] 3L_12860176_SNP [dm6]	G	A	1.652e^-5	0.395	SYNONYMOUS_CODING CG32107	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
X	8957546	X_8957546_SNP [dm3] X_9063513_SNP [dm6]	A	T	1.662e^-5	0.395	INTRON CG15365
3L	13009752	3L_13009752_SNP [dm3] 3L_13016652_SNP [dm6]	T	C	1.664e^-5	0.395	SYNONYMOUS_CODING CG11267 DOWNSTREAM mRpL20	TF binding site mE1_TFBS_sens
3L	9106134	3L_9106134_INS [dm3] 3L_9113034_INS [dm6]	A	AGCTGAAGGA	1.715e^-5	0.401	INTRON bol	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi
2R	9866032	2R_9866032_INS [dm3] 2R_13978527_INS [dm6]	C	CA	1.735e^-5	0.401	INTRON CG6701	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	9738642	3R_9738642_SNP [dm3] 3R_13912920_SNP [dm6]	T	G	1.753e^-5	0.401	INTERGENIC	TF binding site mE1_TFBS_inv
3L	3538043	3L_3538043_SNP [dm3] 3L_3538043_SNP [dm6]	C	T	1.778e^-5	0.402	INTRON Eip63E
3L	22650620	3L_22650620_SNP [dm3] 3L_22657520_SNP [dm6]	G	C	1.816e^-5	0.405	INTERGENIC
3L	11440886	3L_11440886_SNP [dm3] 3L_11447786_SNP [dm6]	T	C	1.871e^-5	0.408	INTERGENIC	TF binding site BDTNP1_TFBS_twi
3L	18844569	3L_18844569_SNP [dm3] 3L_18851469_SNP [dm6]	G	T	1.877e^-5	0.408	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	12853279	3L_12853279_SNP [dm3] 3L_12860179_SNP [dm6]	A	G	1.891e^-5	0.408	SYNONYMOUS_CODING CG32107	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	25931725	3R_25931725_SNP [dm3] 3R_30106003_SNP [dm6]	T	C	1.954e^-5	0.414	INTRON sima
3R	1024171	3R_1024171_SNP [dm3] 3R_5198449_SNP [dm6]	T	G	1.966e^-5	0.414	UPSTREAM cno INTRON cno	TF binding site mE1_TFBS_HSA
3L	11268973	3L_11268973_SNP [dm3] 3L_11275873_SNP [dm6]	T	A	2.008e^-5	0.418	INTERGENIC
X	4161266	X_4161266_SNP [dm3] X_4267233_SNP [dm6]	T	A	2.031e^-5	0.419	DOWNSTREAM CG12691 INTERGENIC
2R	15038134	2R_15038134_SNP [dm3] 2R_19150629_SNP [dm6]	T	A	2.082e^-5	0.422	INTRON ena	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
3L	16448530	3L_16448530_INS [dm3] 3L_16455430_INS [dm6]	A	AGTTT	2.103e^-5	0.422	INTRON CG33158	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	14569437	3L_14569437_SNP [dm3] 3L_14576337_SNP [dm6]	A	G	2.117e^-5	0.422	INTERGENIC	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
3L	19274845	3L_19274845_SNP [dm3] 3L_19281745_SNP [dm6]	G	A	2.184e^-5	0.429	UTR_3_PRIME Gbs-76A UPSTREAM CG14089 DOWNSTREAM Gbs-76A
2L	9446064	2L_9446064_SNP [dm3] 2L_9446064_SNP [dm6]	T	C	2.197e^-5	0.429	INTRON numb	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb mE1_TFBS_cad mE1_TFBS_HSA
3L	9866385	3L_9866385_INS [dm3] 3L_9873285_INS [dm6]	T	TGTTCCAAGATT...	2.274e^-5	0.433	INTERGENIC
3L	4709865	3L_4709865_SNP [dm3] 3L_4709865_SNP [dm6]	T	C	2.297e^-5	0.433	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	2.297e^-5	0.433	UTR_5_PRIME CG13712 INTRON RhoGEF64C	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	12813263	2L_12813263_SNP [dm3] 2L_12813263_SNP [dm6]	C	A	2.326e^-5	0.433	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA

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By genomic position
Variant impact
Gene name

pc_Surv_MeHg_15 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results