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=1.502e^-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
No significant result.

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

10622 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	15999607	X_15999607_DEL [dm3] X_16105574_DEL [dm6]	ATACTGAAAACACGTCAATT...	A	1.409e^-59	2.621e^-53	UPSTREAM CG42354 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_cnc mE1_TFBS_D mE1_TFBS_GATAe mE1_TFBS_HSA mE1_TFBS_jumu mE1_TFBS_kn mE1_TFBS_ttk mE1_TFBS_zfh1
3L	4529063	3L_4529063_SNP [dm3] 3L_4529063_SNP [dm6]	A	G	1.311e^-58	1.219e^-52	INTRON Tie
X	15999596	X_15999596_DEL [dm3] X_16105563_DEL [dm6]	TTTAA	T	4.343e^-58	2.020e^-52	UPSTREAM CG42354 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_cnc mE1_TFBS_D mE1_TFBS_GATAe mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_ttk mE1_TFBS_zfh1
X	15999603	X_15999603_SNP [dm3] X_16105570_SNP [dm6]	A	C	4.343e^-58	2.020e^-52	UPSTREAM CG42354 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_cnc mE1_TFBS_D mE1_TFBS_GATAe mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_ttk mE1_TFBS_zfh1
2R	14751162	2R_14751162_SNP [dm3] 2R_18863657_SNP [dm6]	C	G	7.516e^-42	2.797e^-36	UPSTREAM CG43070 DOWNSTREAM CG43069 & 1 other INTERGENIC
3L	11299568	3L_11299568_SNP [dm3] 3L_11306468_SNP [dm6]	G	A	1.477e^-20	4.581e^-15	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	11299517	3L_11299517_SNP [dm3] 3L_11306417_SNP [dm6]	A	T	4.040e^-20	1.074e^-14	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2R	9310023	2R_9310023_SNP [dm3] 2R_13422518_SNP [dm6]	G	A	1.050e^-19	2.443e^-14	DOWNSTREAM CG30060 INTRON CG42321	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	22445385	3L_22445385_SNP [dm3] 3L_22452285_SNP [dm6]	G	A	1.325e^-19	2.738e^-14	INTERGENIC
2L	1139590	2L_1139590_SNP [dm3] 2L_1139590_SNP [dm6]	C	T	6.308e^-18	6.903e^-13	NON_SYNONYMOUS_CODING CG4577	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	10339932	3L_10339932_SNP [dm3] 3L_10346832_SNP [dm6]	T	C	6.308e^-18	6.903e^-13	INTERGENIC
3L	17541363	3L_17541363_SNP [dm3] 3L_17548263_SNP [dm6]	G	T	6.308e^-18	6.903e^-13	SYNONYMOUS_CODING Jon74E
3L	17541378	3L_17541378_SNP [dm3] 3L_17548278_SNP [dm6]	C	T	6.308e^-18	6.903e^-13	SYNONYMOUS_CODING Jon74E
3L	2805769	3L_2805769_SNP [dm3] 3L_2805769_SNP [dm6]	G	T	6.308e^-18	6.903e^-13	INTRON CG43444
3L	2805775	3L_2805775_DEL [dm3] 3L_2805775_DEL [dm6]	TGCATTTTTT	T	6.308e^-18	6.903e^-13	INTRON CG43444
3L	2813433	3L_2813433_SNP [dm3] 3L_2813433_SNP [dm6]	C	T	6.308e^-18	6.903e^-13	INTRON CG43444
X	3273509	X_3273509_SNP [dm3] X_3379476_SNP [dm6]	T	C	6.308e^-18	6.903e^-13	INTRON dm & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
2L	1606380	2L_1606380_INS [dm3] 2L_1606380_INS [dm6]	T	TT	1.177e^-17	1.053e^-12	INTRON CG31935 & 1 other
3L	1339101	3L_1339101_SNP [dm3] 3L_1339101_SNP [dm6]	C	T	1.177e^-17	1.053e^-12	SYNONYMOUS_CODING l_3_02640 DOWNSTREAM CG2199
2R	10862187	2R_10862187_SNP [dm3] 2R_14974682_SNP [dm6]	G	A	1.188e^-17	1.053e^-12	INTRON ckn	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_prd BDTNP1_TFBS_sna
2R	11862920	2R_11862920_SNP [dm3] 2R_15975415_SNP [dm6]	C	T	1.188e^-17	1.053e^-12	NON_SYNONYMOUS_CODING Strn-Mlck
3L	11307999	3L_11307999_SNP [dm3] 3L_11314899_SNP [dm6]	G	C	1.263e^-17	1.068e^-12	UPSTREAM CR44361 INTERGENIC
3L	18606241	3L_18606241_SNP [dm3] 3L_18613141_SNP [dm6]	A	T	2.088e^-17	1.562e^-12	SYNONYMOUS_CODING CG32199 INTRON CG4174 & 1 other	TF binding site mE1_TFBS_HSA
3R	20930743	3R_20930743_SNP [dm3] 3R_25105021_SNP [dm6]	A	T	2.088e^-17	1.562e^-12	SYNONYMOUS_CODING CG34027
3L	18686014	3L_18686014_SNP [dm3] 3L_18692914_SNP [dm6]	A	C	2.099e^-17	1.562e^-12	DOWNSTREAM CR43987 INTERGENIC
3R	12997579	3R_12997579_SNP [dm3] 3R_17171857_SNP [dm6]	C	A	2.617e^-17	1.872e^-12	INTRON Mur89F
3L	11300491	3L_11300491_SNP [dm3] 3L_11307391_SNP [dm6]	G	A	6.627e^-17	4.567e^-12	INTERGENIC
2R	4584918	2R_4584918_SNP [dm3] 2R_8697413_SNP [dm6]	T	A	7.113e^-17	4.657e^-12	INTRON CG8738	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2L	14395467	2L_14395467_SNP [dm3] 2L_14395467_SNP [dm6]	C	G	7.260e^-17	4.657e^-12	INTRON elB
2R	4584917	2R_4584917_SNP [dm3] 2R_8697412_SNP [dm6]	A	T	1.286e^-16	7.891e^-12	INTRON CG8738	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2R	11862665	2R_11862665_SNP [dm3] 2R_15975160_SNP [dm6]	A	G	1.315e^-16	7.891e^-12	SYNONYMOUS_CODING Strn-Mlck
2R	17749611	2R_17749611_SNP [dm3] 2R_21862106_SNP [dm6]	T	G	1.391e^-16	8.087e^-12	DOWNSTREAM CG9294 INTERGENIC
2R	9309216	2R_9309216_SNP [dm3] 2R_13421711_SNP [dm6]	C	T	2.433e^-16	1.371e^-11	SPLICE_SITE_REGION CG42321 INTRON CG42321
2L	13691200	2L_13691200_SNP [dm3] 2L_13691200_SNP [dm6]	T	G	3.149e^-16	1.723e^-11	INTRON CG31814
3L	11299527	3L_11299527_SNP [dm3] 3L_11306427_SNP [dm6]	G	A	3.495e^-16	1.858e^-11	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2R	11845302	2R_11845302_SNP [dm3] 2R_15957797_SNP [dm6]	C	T	8.446e^-16	4.365e^-11	UPSTREAM Strn-Mlck INTRON Strn-Mlck	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2R	14705610	2R_14705610_MNP [dm3] 2R_18818105_MNP [dm6]	TAG	ATT	8.825e^-16	4.437e^-11	INTERGENIC
2R	18206201	2R_18206201_SNP [dm3] 2R_22318696_SNP [dm6]	C	A	1.147e^-15	5.613e^-11	DOWNSTREAM CR44756 INTRON Gp150	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_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_disco mE1_TFBS_inv mE1_TFBS_sens mE1_TFBS_Trl mE1_TFBS_zfh1
2R	17144452	2R_17144452_SNP [dm3] 2R_21256947_SNP [dm6]	T	C	1.202e^-15	5.732e^-11	INTRON Rgk3
2R	14705596	2R_14705596_SNP [dm3] 2R_18818091_SNP [dm6]	A	C	1.592e^-15	7.051e^-11	INTERGENIC
2R	14705598	2R_14705598_DEL [dm3] 2R_18818093_DEL [dm6]	TA	T	1.592e^-15	7.051e^-11	INTERGENIC
2R	14705604	2R_14705604_DEL [dm3] 2R_18818099_DEL [dm6]	GTG	A	1.592e^-15	7.051e^-11	INTERGENIC
2L	13118560	2L_13118560_SNP [dm3] 2L_13118560_SNP [dm6]	T	C	3.860e^-15	1.670e^-10	UPSTREAM CG43050 DOWNSTREAM CR44198 INTERGENIC
3L	5330553	3L_5330553_SNP [dm3] 3L_5337453_SNP [dm6]	G	A	6.629e^-15	2.803e^-10	INTERGENIC
3L	14568299	3L_14568299_SNP [dm3] 3L_14575199_SNP [dm6]	T	A	7.247e^-15	2.996e^-10	INTERGENIC	regulatory region REDfly_CRMs
3L	22434233	3L_22434233_SNP [dm3] 3L_22441133_SNP [dm6]	C	T	1.772e^-14	7.168e^-10	INTERGENIC
2R	8176319	2R_8176319_INS [dm3] 2R_12288814_INS [dm6]	A	ATA	2.794e^-14	1.106e^-9	INTRON CG42700
2R	7070703	2R_7070703_SNP [dm3] 2R_11183198_SNP [dm6]	A	T	3.277e^-14	1.270e^-9	UPSTREAM shn INTRON shn	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_shn BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3R	10285026	3R_10285026_SNP [dm3] 3R_14459304_SNP [dm6]	C	T	4.276e^-14	1.623e^-9	INTRON cv-c
3L	672999	3L_672999_SNP [dm3] 3L_672999_SNP [dm6]	G	T	8.968e^-14	3.337e^-9	INTERGENIC	TF binding site mE1_TFBS_cad
2R	15484565	2R_15484565_SNP [dm3] 2R_19597060_SNP [dm6]	G	T	1.708e^-13	6.231e^-9	DOWNSTREAM CG16716 INTRON sm
2L	16341791	2L_16341791_SNP [dm3] 2L_16341791_SNP [dm6]	C	A	1.781e^-13	6.329e^-9	SYNONYMOUS_CODING CG44405 DOWNSTREAM chif & 1 other
2L	9540281	2L_9540281_SNP [dm3] 2L_9540281_SNP [dm6]	C	T	1.803e^-13	6.329e^-9	UPSTREAM CG17855 DOWNSTREAM Oatp30B INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA
2L	11018907	2L_11018907_SNP [dm3] 2L_11018907_SNP [dm6]	A	T	1.848e^-13	6.365e^-9	DOWNSTREAM CG14913 INTRON Samuel
3L	20147197	3L_20147197_SNP [dm3] 3L_20154097_SNP [dm6]	T	C	2.958e^-13	9.956e^-9	SYNONYMOUS_CODING CG42674	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2R	16153386	2R_16153386_SNP [dm3] 2R_20265881_SNP [dm6]	C	T	2.997e^-13	9.956e^-9	SYNONYMOUS_CODING CG8908 UPSTREAM CR43812	TF binding site mE1_TFBS_cad
3L	22430883	3L_22430883_SNP [dm3] 3L_22437783_SNP [dm6]	T	C	3.606e^-13	1.171e^-8	INTERGENIC
2L	1171061	2L_1171061_SNP [dm3] 2L_1171061_SNP [dm6]	T	C	3.651e^-13	1.171e^-8	SYNONYMOUS_CODING CG5118 UPSTREAM Plap DOWNSTREAM CG31922	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2L	10356404	2L_10356404_SNP [dm3] 2L_10356404_SNP [dm6]	G	T	3.829e^-13	1.207e^-8	UTR_5_PRIME CG5367 UPSTREAM CG5045	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Ubx
2R	7070714	2R_7070714_SNP [dm3] 2R_11183209_SNP [dm6]	A	G	4.224e^-13	1.310e^-8	UPSTREAM shn INTRON shn	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Mad BDTNP1_TFBS_Med BDTNP1_TFBS_shn BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3L	14563879	3L_14563879_SNP [dm3] 3L_14570779_SNP [dm6]	T	A	6.162e^-13	1.849e^-8	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3L	14563913	3L_14563913_SNP [dm3] 3L_14570813_SNP [dm6]	A	G	6.162e^-13	1.849e^-8	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2L	1151448	2L_1151448_DEL [dm3] 2L_1151448_DEL [dm6]	CCAACC	C	6.807e^-13	2.010e^-8	UTR_3_PRIME Vps29 UPSTREAM Tfb4 DOWNSTREAM capt	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2R	16599721	2R_16599721_SNP [dm3] 2R_20712216_SNP [dm6]	C	T	8.773e^-13	2.511e^-8	INTRON dpr
2R	16599834	2R_16599834_SNP [dm3] 2R_20712329_SNP [dm6]	C	T	8.773e^-13	2.511e^-8	INTRON dpr
2L	14402210	2L_14402210_SNP [dm3] 2L_14402210_SNP [dm6]	G	A	9.212e^-13	2.520e^-8	INTRON elB
2L	14405011	2L_14405011_SNP [dm3] 2L_14405011_SNP [dm6]	T	G	9.212e^-13	2.520e^-8	INTRON elB	TF binding site mE1_TFBS_cad
2L	14405090	2L_14405090_SNP [dm3] 2L_14405090_SNP [dm6]	T	C	9.212e^-13	2.520e^-8	INTRON elB	TF binding site mE1_TFBS_cad
X	10856368	X_10856368_SNP [dm3] X_10962335_SNP [dm6]	C	T	1.031e^-12	2.779e^-8	SYNONYMOUS_CODING Myo10A	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
X	10860418	X_10860418_DEL [dm3] X_10966385_DEL [dm6]	AAA	A	1.133e^-12	2.957e^-8	INTRON C901
X	10858856	X_10858856_SNP [dm3] X_10964823_SNP [dm6]	C	T	1.323e^-12	2.957e^-8	NON_SYNONYMOUS_CODING C901 DOWNSTREAM Myo10A	TF binding site mE1_TFBS_chinmo
2R	6442702	2R_6442702_SNP [dm3] 2R_10555197_SNP [dm6]	T	A	1.323e^-12	2.957e^-8	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
3L	1531542	3L_1531542_SNP [dm3] 3L_1531542_SNP [dm6]	C	G	1.323e^-12	2.957e^-8	UPSTREAM Ir62a INTRON CG12090	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3R	13822317	3R_13822317_SNP [dm3] 3R_17996595_SNP [dm6]	C	T	1.324e^-12	2.957e^-8	INTRON cpo
3L	16329130	3L_16329130_SNP [dm3] 3L_16336030_SNP [dm6]	C	G	1.342e^-12	2.957e^-8	INTERGENIC
3R	17997267	3R_17997267_SNP [dm3] 3R_22171545_SNP [dm6]	C	G	1.342e^-12	2.957e^-8	INTRON SKIP	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	2999103	3R_2999103_SNP [dm3] 3R_7173381_SNP [dm6]	G	A	1.342e^-12	2.957e^-8	INTRON sas	TF binding site BDTNP1_TFBS_Med
3R	3042293	3R_3042293_SNP [dm3] 3R_7216571_SNP [dm6]	G	T	1.342e^-12	2.957e^-8	INTRON CG14606
2R	12483928	2R_12483928_SNP [dm3] 2R_16596423_SNP [dm6]	A	T	1.358e^-12	2.957e^-8	INTRON CG8303
3L	14563847	3L_14563847_SNP [dm3] 3L_14570747_SNP [dm6]	G	A	1.364e^-12	2.957e^-8	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3L	14563862	3L_14563862_SNP [dm3] 3L_14570762_SNP [dm6]	A	T	1.364e^-12	2.957e^-8	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3L	14563875	3L_14563875_SNP [dm3] 3L_14570775_SNP [dm6]	T	A	1.364e^-12	2.957e^-8	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3L	14563876	3L_14563876_INS [dm3] 3L_14570776_INS [dm6]	A	ACGCTT	1.364e^-12	2.957e^-8	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2L	14399917	2L_14399917_SNP [dm3] 2L_14399917_SNP [dm6]	A	C	1.382e^-12	2.957e^-8	INTRON elB
2L	14395980	2L_14395980_SNP [dm3] 2L_14395980_SNP [dm6]	A	T	1.397e^-12	2.957e^-8	INTRON elB
2L	14396746	2L_14396746_SNP [dm3] 2L_14396746_SNP [dm6]	T	C	1.397e^-12	2.957e^-8	INTRON elB
2L	14405626	2L_14405626_SNP [dm3] 2L_14405626_SNP [dm6]	T	A	1.414e^-12	2.957e^-8	INTRON elB	TF binding site mE1_TFBS_cad
X	10859326	X_10859326_SNP [dm3] X_10965293_SNP [dm6]	G	T	1.414e^-12	2.957e^-8	INTRON C901	TF binding site mE1_TFBS_chinmo
X	10859337	X_10859337_DEL [dm3] X_10965304_DEL [dm6]	GTTTTGCTGTTA...	G	1.414e^-12	2.957e^-8	INTRON C901	TF binding site mE1_TFBS_chinmo
2L	15264038	2L_15264038_SNP [dm3] 2L_15264038_SNP [dm6]	G	A	1.480e^-12	3.044e^-8	NON_SYNONYMOUS_CODING yuri	TF binding site BDTNP1_TFBS_dl mE1_TFBS_sens mE1_TFBS_Trl
2L	11185403	2L_11185403_SNP [dm3] 2L_11185403_SNP [dm6]	G	A	1.489e^-12	3.044e^-8	INTRON Ca-beta	TF binding site BDTNP1_TFBS_prd
2L	22904698	2L_22904698_DEL [dm3] 2L_23011966_DEL [dm6]	TT	T	1.516e^-12	3.066e^-8	INTRON Cht3
2L	14402212	2L_14402212_SNP [dm3] 2L_14402212_SNP [dm6]	G	T	1.533e^-12	3.067e^-8	INTRON elB
3R	2991303	3R_2991303_SNP [dm3] 3R_7165581_SNP [dm6]	T	A	1.737e^-12	3.437e^-8	INTRON sas
X	10860593	X_10860593_SNP [dm3] X_10966560_SNP [dm6]	T	C	1.938e^-12	3.796e^-8	SPLICE_SITE_REGION C901 INTRON C901
2R	6442641	2R_6442641_SNP [dm3] 2R_10555136_SNP [dm6]	T	G	1.980e^-12	3.836e^-8	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_D mE1_TFBS_Trl
3R	11629877	3R_11629877_SNP [dm3] 3R_15804155_SNP [dm6]	T	C	2.019e^-12	3.872e^-8	UPSTREAM alpha-Man-IIb DOWNSTREAM CG9593 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Ubx
2L	14399451	2L_14399451_SNP [dm3] 2L_14399451_SNP [dm6]	C	T	2.252e^-12	4.257e^-8	INTRON elB
3L	14563976	3L_14563976_SNP [dm3] 3L_14570876_SNP [dm6]	G	A	2.265e^-12	4.257e^-8	INTERGENIC	TF binding site mE1_TFBS_HSA
2R	7351601	2R_7351601_SNP [dm3] 2R_11464096_SNP [dm6]	G	T	2.397e^-12	4.460e^-8	UTR_3_PRIME E_Pc_ DOWNSTREAM E_Pc_	TF binding site mE1_TFBS_kn

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By genomic position
Variant impact
Gene name

Microbiota_OTU031 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results