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=2.429e^-4)
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

1164 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
3L	2622009	3L_2622009_SNP [dm3] 3L_2622009_SNP [dm6]	A	T	2.321e^-6	0.82	INTRON Pxn
3L	2659050	3L_2659050_SNP [dm3] 3L_2659050_SNP [dm6]	T	C	2.638e^-6	0.82	SYNONYMOUS_CODING Fife UTR_3_PRIME Fife UPSTREAM CG33233	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_prd mE1_TFBS_chinmo
3L	8246620	3L_8246620_SNP [dm3] 3L_8253520_SNP [dm6]	A	T	3.348e^-6	0.82	INTRON Dscam4
X	3899950	X_3899950_SNP [dm3] X_4005917_SNP [dm6]	A	G	7.378e^-6	0.82	INTERGENIC
2R	8782901	2R_8782901_SNP [dm3] 2R_12895396_SNP [dm6]	A	G	8.956e^-6	0.82	INTRON vg	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi
2L	2350486	2L_2350486_SNP [dm3] 2L_2350486_SNP [dm6]	T	C	1.148e^-5	0.82	INTRON CG9967 & 1 other
3L	970831	3L_970831_SNP [dm3] 3L_970831_SNP [dm6]	A	G	1.195e^-5	0.82	INTRON Glut1
2R	11707989	2R_11707989_SNP [dm3] 2R_15820484_SNP [dm6]	T	A	1.263e^-5	0.82	INTRON tun & 1 other
3L	7984136	3L_7984136_SNP [dm3] 3L_7991036_SNP [dm6]	T	C	1.388e^-5	0.82	INTRON nmo	TF binding site mE1_TFBS_cnc
3R	24366641	3R_24366641_SNP [dm3] 3R_28540919_SNP [dm6]	G	A	1.476e^-5	0.82	UPSTREAM Ppn INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	17693124	3L_17693124_SNP [dm3] 3L_17700024_SNP [dm6]	G	T	2.078e^-5	0.82	INTRON Ccn
2L	6176837	2L_6176837_SNP [dm3] 2L_6176837_SNP [dm6]	C	T	2.378e^-5	0.82	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	6508615	2R_6508615_SNP [dm3] 2R_10621110_SNP [dm6]	A	G	2.482e^-5	0.82	INTRON CG11883
3R	11140143	3R_11140143_SNP [dm3] 3R_15314421_SNP [dm6]	T	C	2.482e^-5	0.82	INTRON Tm2	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
2R	6379235	2R_6379235_SNP [dm3] 2R_10491730_SNP [dm6]	C	T	2.489e^-5	0.82	UTR_3_PRIME lola INTRON lola
2R	6508001	2R_6508001_SNP [dm3] 2R_10620496_SNP [dm6]	A	C	2.489e^-5	0.82	INTRON CG11883
3L	1605240	3L_1605240_SNP [dm3] 3L_1605240_SNP [dm6]	A	C	2.983e^-5	0.82	SYNONYMOUS_CODING CG33791 UTR_3_PRIME CG18170
3L	14642038	3L_14642038_SNP [dm3] 3L_14648938_SNP [dm6]	T	A	3.020e^-5	0.82	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
2L	4427850	2L_4427850_SNP [dm3] 2L_4427850_SNP [dm6]	A	G	3.022e^-5	0.82	INTRON CG15431
3L	5956442	3L_5956442_SNP [dm3] 3L_5963342_SNP [dm6]	G	C	3.054e^-5	0.82	INTERGENIC
2R	11059590	2R_11059590_SNP [dm3] 2R_15172085_SNP [dm6]	T	C	3.068e^-5	0.82	INTRON igl
2R	6508603	2R_6508603_SNP [dm3] 2R_10621098_SNP [dm6]	T	G	3.068e^-5	0.82	INTRON CG11883
3L	14642070	3L_14642070_SNP [dm3] 3L_14648970_SNP [dm6]	C	T	3.185e^-5	0.82	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3L	14642095	3L_14642095_SNP [dm3] 3L_14648995_SNP [dm6]	T	A	3.185e^-5	0.82	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3L	14642098	3L_14642098_SNP [dm3] 3L_14648998_SNP [dm6]	A	T	3.185e^-5	0.82	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3L	14642110	3L_14642110_SNP [dm3] 3L_14649010_SNP [dm6]	T	C	3.185e^-5	0.82	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3L	3039454	3L_3039454_SNP [dm3] 3L_3039454_SNP [dm6]	T	C	3.375e^-5	0.82	SYNONYMOUS_CODING CG2162	TF binding site BDTNP1_TFBS_dl mE1_TFBS_sens
3R	16739498	3R_16739498_SNP [dm3] 3R_20913776_SNP [dm6]	T	C	3.375e^-5	0.82	UPSTREAM snoRNA:CG31191-a & 1 other DOWNSTREAM CR44106 INTRON CG31191	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	7909123	3L_7909123_SNP [dm3] 3L_7916023_SNP [dm6]	G	C	3.497e^-5	0.82	UPSTREAM CG8111 DOWNSTREAM syd & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
2L	7944635	2L_7944635_SNP [dm3] 2L_7944635_SNP [dm6]	C	T	3.526e^-5	0.82	INTRON Snoo
3L	9088728	3L_9088728_SNP [dm3] 3L_9095628_SNP [dm6]	C	T	3.624e^-5	0.82	DOWNSTREAM CG32032 INTERGENIC
2R	16309182	2R_16309182_SNP [dm3] 2R_20421677_SNP [dm6]	A	G	3.720e^-5	0.82	INTERGENIC
3R	26119375	3R_26119375_SNP [dm3] 3R_30293653_SNP [dm6]	T	A	3.864e^-5	0.82	INTRON hdc	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	14642039	3L_14642039_SNP [dm3] 3L_14648939_SNP [dm6]	T	G	4.029e^-5	0.82	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3L	14642051	3L_14642051_SNP [dm3] 3L_14648951_SNP [dm6]	T	C	4.029e^-5	0.82	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3L	14642089	3L_14642089_SNP [dm3] 3L_14648989_SNP [dm6]	A	T	4.142e^-5	0.82	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3L	14642055	3L_14642055_SNP [dm3] 3L_14648955_SNP [dm6]	A	T	4.145e^-5	0.82	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3L	14642058	3L_14642058_SNP [dm3] 3L_14648958_SNP [dm6]	G	A	4.145e^-5	0.82	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3L	14642078	3L_14642078_MNP [dm3] 3L_14648978_MNP [dm6]	GGG	AAA	4.145e^-5	0.82	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3L	14641921	3L_14641921_SNP [dm3] 3L_14648821_SNP [dm6]	A	G	4.283e^-5	0.82	INTRON dlp	TF binding site mE1_TFBS_HSA
2L	492383	2L_492383_SNP [dm3] 2L_492383_SNP [dm6]	C	T	4.296e^-5	0.82	INTRON ush	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl mE1_TFBS_zfh1
3L	7909156	3L_7909156_SNP [dm3] 3L_7916056_SNP [dm6]	C	T	4.341e^-5	0.82	UPSTREAM CG8111 DOWNSTREAM syd & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
2L	492331	2L_492331_SNP [dm3] 2L_492331_SNP [dm6]	A	T	4.568e^-5	0.82	INTRON ush	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl mE1_TFBS_zfh1
2L	493550	2L_493550_SNP [dm3] 2L_493550_SNP [dm6]	G	A	4.568e^-5	0.82	INTRON ush
2L	5954899	2L_5954899_SNP [dm3] 2L_5954899_SNP [dm6]	G	A	4.568e^-5	0.82	SYNONYMOUS_CODING CG9044 DOWNSTREAM CG13999	TF binding site mE1_TFBS_inv
X	17304679	X_17304679_DEL [dm3] X_17410646_DEL [dm6]	CC	C	4.568e^-5	0.82	INTERGENIC
3R	12384171	3R_12384171_SNP [dm3] 3R_16558449_SNP [dm6]	C	T	4.617e^-5	0.82	INTRON CG42342
3L	14642109	3L_14642109_SNP [dm3] 3L_14649009_SNP [dm6]	A	T	4.771e^-5	0.82	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3L	14642171	3L_14642171_SNP [dm3] 3L_14649071_SNP [dm6]	A	T	4.896e^-5	0.82	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3L	2622023	3L_2622023_INS [dm3] 3L_2622023_INS [dm6]	A	AGGTCTCA	4.923e^-5	0.82	INTRON Pxn
2L	9585406	2L_9585406_SNP [dm3] 2L_9585406_SNP [dm6]	C	G	4.972e^-5	0.82	INTRON CR43621	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_sens
2R	12456810	2R_12456810_SNP [dm3] 2R_16569305_SNP [dm6]	A	G	5.193e^-5	0.82	SYNONYMOUS_CODING CG4945 DOWNSTREAM RpS15	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3L	2627277	3L_2627277_SNP [dm3] 3L_2627277_SNP [dm6]	A	G	5.222e^-5	0.82	INTRON Pxn
X	16443395	X_16443395_SNP [dm3] X_16549362_SNP [dm6]	A	G	5.238e^-5	0.82	SYNONYMOUS_CODING Arp2
2R	6954898	2R_6954898_SNP [dm3] 2R_11067393_SNP [dm6]	T	C	5.444e^-5	0.82	INTRON luna	TF binding site mE1_TFBS_chinmo
2L	15343669	2L_15343669_SNP [dm3] 2L_15343669_SNP [dm6]	A	T	5.462e^-5	0.82	INTERGENIC
2L	15343684	2L_15343684_MNP [dm3] 2L_15343684_MNP [dm6]	GTT	ACA	5.462e^-5	0.82	INTERGENIC
2L	15343691	2L_15343691_DEL [dm3] 2L_15343691_DEL [dm6]	CAC	A	5.462e^-5	0.82	INTERGENIC
3R	26119383	3R_26119383_SNP [dm3] 3R_30293661_SNP [dm6]	G	C	5.876e^-5	0.82	INTRON hdc	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	25834938	3R_25834938_SNP [dm3] 3R_30009216_SNP [dm6]	G	A	6.021e^-5	0.82	UPSTREAM CG7912 INTRON Nlp
3L	14642063	3L_14642063_SNP [dm3] 3L_14648963_SNP [dm6]	T	G	6.302e^-5	0.82	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
2R	18741395	2R_18741395_SNP [dm3] 2R_22853872_SNP [dm6]	T	G	6.906e^-5	0.82	UPSTREAM RpL23 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA
2R	18741492	2R_18741492_SNP [dm3] 2R_22853969_SNP [dm6]	G	A	6.906e^-5	0.82	UPSTREAM RpL23 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_HSA
3L	7986614	3L_7986614_SNP [dm3] 3L_7993514_SNP [dm6]	C	G	6.926e^-5	0.82	INTRON nmo	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_hb mE1_TFBS_cad mE1_TFBS_HSA
2R	11039807	2R_11039807_SNP [dm3] 2R_15152302_SNP [dm6]	G	T	7.055e^-5	0.82	INTERGENIC
3R	9784390	3R_9784390_SNP [dm3] 3R_13958668_SNP [dm6]	T	A	7.493e^-5	0.82	UPSTREAM Ipp INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	9784391	3R_9784391_SNP [dm3] 3R_13958669_SNP [dm6]	T	A	7.493e^-5	0.82	UPSTREAM Ipp INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	18875209	2L_18875209_SNP [dm3] 2L_18875209_SNP [dm6]	T	C	7.551e^-5	0.82	INTRON tup	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	12778968	3L_12778968_SNP [dm3] 3L_12785868_SNP [dm6]	T	C	7.625e^-5	0.82	SPLICE_SITE_REGION Atg1 INTRON Atg1	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
X	19517597	X_19517597_SNP [dm3] X_19623564_SNP [dm6]	G	A	7.872e^-5	0.82	UPSTREAM NAA20 INTRON MKP-4	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2R	12456846	2R_12456846_SNP [dm3] 2R_16569341_SNP [dm6]	G	A	7.936e^-5	0.82	SYNONYMOUS_CODING CG4945 DOWNSTREAM RpS15	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3L	13724195	3L_13724195_SNP [dm3] 3L_13731095_SNP [dm6]	C	T	8.232e^-5	0.82	INTRON bru-3
X	12130287	X_12130287_SNP [dm3] X_12236254_SNP [dm6]	A	C	8.408e^-5	0.82	UPSTREAM CG32655 INTRON Ten-a
2L	1196368	2L_1196368_SNP [dm3] 2L_1196368_SNP [dm6]	C	T	8.564e^-5	0.82	SYNONYMOUS_CODING CG5001
2L	11361516	2L_11361516_SNP [dm3] 2L_11361516_SNP [dm6]	T	C	8.641e^-5	0.82	INTRON salr	regulatory region REDfly_CRMs
2L	15343672	2L_15343672_DEL [dm3] 2L_15343672_DEL [dm6]	AAAT	A	8.646e^-5	0.82	INTERGENIC
2L	15343677	2L_15343677_SNP [dm3] 2L_15343677_SNP [dm6]	A	T	8.646e^-5	0.82	INTERGENIC
2L	15343679	2L_15343679_SNP [dm3] 2L_15343679_SNP [dm6]	T	C	8.646e^-5	0.82	INTERGENIC
2L	15343680	2L_15343680_SNP [dm3] 2L_15343680_SNP [dm6]	T	A	8.646e^-5	0.82	INTERGENIC
2L	15343689	2L_15343689_SNP [dm3] 2L_15343689_SNP [dm6]	T	A	8.646e^-5	0.82	INTERGENIC
2R	18180962	2R_18180962_SNP [dm3] 2R_22293457_SNP [dm6]	T	G	8.805e^-5	0.82	UTR_5_PRIME CG5819 INTRON CG5819
3R	15995537	3R_15995537_SNP [dm3] 3R_20169815_SNP [dm6]	A	G	9.232e^-5	0.82	INTRON CG5023
3L	2659386	3L_2659386_SNP [dm3] 3L_2659386_SNP [dm6]	T	G	9.400e^-5	0.82	UPSTREAM CG33233 INTRON Fife	TF binding site mE1_TFBS_chinmo
3L	6600205	3L_6600205_SNP [dm3] 3L_6607105_SNP [dm6]	T	G	9.400e^-5	0.82	INTRON CG8368	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3L	964153	3L_964153_SNP [dm3] 3L_964153_SNP [dm6]	T	C	9.441e^-5	0.82	INTRON Glut1
3L	964192	3L_964192_SNP [dm3] 3L_964192_SNP [dm6]	T	C	9.441e^-5	0.82	INTRON Glut1
3L	964204	3L_964204_SNP [dm3] 3L_964204_SNP [dm6]	G	A	9.441e^-5	0.82	INTRON Glut1
2L	19079753	2L_19079753_SNP [dm3] 2L_19079753_SNP [dm6]	C	A	9.460e^-5	0.82	UTR_3_PRIME Lim3 UPSTREAM CG10700	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
X	6396781	X_6396781_SNP [dm3] X_6502748_SNP [dm6]	A	T	9.468e^-5	0.82	INTRON CG42340
3R	5297393	3R_5297393_SNP [dm3] 3R_9471671_SNP [dm6]	C	T	9.497e^-5	0.82	SYNONYMOUS_CODING CG16779	TF binding site mE1_TFBS_chinmo
3R	26119373	3R_26119373_SNP [dm3] 3R_30293651_SNP [dm6]	G	C	9.510e^-5	0.82	INTRON hdc	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	2463585	2R_2463585_SNP [dm3] 2R_6576080_SNP [dm6]	C	A	9.543e^-5	0.82	INTRON jing	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
X	12821561	X_12821561_SNP [dm3] X_12927528_SNP [dm6]	T	C	9.587e^-5	0.82	INTRON fne
3L	12779776	3L_12779776_SNP [dm3] 3L_12786676_SNP [dm6]	C	T	9.623e^-5	0.82	SYNONYMOUS_CODING Atg1	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
X	6060803	X_6060803_DEL [dm3] X_6166770_DEL [dm6]	TT	T	9.677e^-5	0.82	INTRON Ca-alpha1T
2L	9405070	2L_9405070_INS [dm3] 2L_9405070_INS [dm6]	A	ACATACA	9.682e^-5	0.82	INTRON Shawl
2R	11039792	2R_11039792_SNP [dm3] 2R_15152287_SNP [dm6]	T	A	9.847e^-5	0.82	INTERGENIC
2R	12408082	2R_12408082_SNP [dm3] 2R_16520577_SNP [dm6]	T	G	9.994e^-5	0.82	INTRON Sema-2a	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi
2L	14722937	2L_14722937_SNP [dm3] 2L_14722937_SNP [dm6]	G	C	1.022e^-4	0.82	INTERGENIC
3R	25526883	3R_25526883_SNP [dm3] 3R_29701161_SNP [dm6]	A	T	1.041e^-4	0.82	INTERGENIC	enhancer mE1_CBP_Enhancers

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Phenotype distribution and association to known covariates

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GWAS results