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=5.101e^-1)
Null hypothesis is not rejected (p>0.05).
Interpretation: 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
wolba	0.09746

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2074 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
3R	15137983	3R_15137983_SNP [dm3] 3R_19312261_SNP [dm6]	G	A	5.814e^-7	0.864	INTRON Dl	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
2L	8492891	2L_8492891_SNP [dm3] 2L_8492891_SNP [dm6]	G	A	1.979e^-6	0.864	INTRON Dh31
2R	12148290	2R_12148290_SNP [dm3] 2R_16260785_SNP [dm6]	A	T	2.961e^-6	0.864	UPSTREAM CngA INTERGENIC
X	5078311	X_5078311_INS [dm3] X_5184278_INS [dm6]	C	CC	3.818e^-6	0.864	INTRON rg & 1 other
3R	6930710	3R_6930710_SNP [dm3] 3R_11104988_SNP [dm6]	C	T	4.156e^-6	0.864	INTERGENIC
3L	10146873	3L_10146873_SNP [dm3] 3L_10153773_SNP [dm6]	A	G	4.180e^-6	0.864	DOWNSTREAM CG8072 INTRON dpr10
2R	16659349	2R_16659349_SNP [dm3] 2R_20771844_SNP [dm6]	C	T	5.720e^-6	0.864	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
2L	10956638	2L_10956638_SNP [dm3] 2L_10956638_SNP [dm6]	A	G	6.807e^-6	0.864	INTRON dpr2
X	2662858	X_2662858_SNP [dm3] X_2768825_SNP [dm6]	G	A	7.739e^-6	0.864	INTRON kirre
2L	8129633	2L_8129633_SNP [dm3] 2L_8129633_SNP [dm6]	C	A	8.011e^-6	0.864	INTRON CG8668
2R	9526622	2R_9526622_SNP [dm3] 2R_13639117_SNP [dm6]	A	C	9.145e^-6	0.864	INTRON fas	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
X	10446569	X_10446569_SNP [dm3] X_10552536_SNP [dm6]	G	C	9.826e^-6	0.864	INTRON spri
2R	19535680	2R_19535680_SNP [dm3] 2R_23648157_SNP [dm6]	G	A	9.960e^-6	0.864	INTRON retn	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	14266904	X_14266904_SNP [dm3] X_14372871_SNP [dm6]	T	G	9.975e^-6	0.864	INTRON dpr8
3R	24476268	3R_24476268_SNP [dm3] 3R_28650546_SNP [dm6]	G	A	1.033e^-5	0.864	UPSTREAM CG31050 INTERGENIC
2R	9526621	2R_9526621_SNP [dm3] 2R_13639116_SNP [dm6]	C	A	1.043e^-5	0.864	INTRON fas	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3L	12867573	3L_12867573_SNP [dm3] 3L_12874473_SNP [dm6]	C	A	1.124e^-5	0.864	INTERGENIC
3R	15172277	3R_15172277_SNP [dm3] 3R_19346555_SNP [dm6]	C	A	1.164e^-5	0.864	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	2757738	2L_2757738_DEL [dm3] 2L_2757738_DEL [dm6]	AT	A	1.247e^-5	0.864	UTR_3_PRIME Bacc DOWNSTREAM CR44772 & 2 others	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_disco mE1_TFBS_GATAe mE1_TFBS_h mE1_TFBS_hkb mE1_TFBS_HSA mE1_TFBS_sens
X	19181465	X_19181465_SNP [dm3] X_19287432_SNP [dm6]	C	T	1.262e^-5	0.864	INTRON CG8034	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	13929147	3L_13929147_SNP [dm3] 3L_13936047_SNP [dm6]	T	C	1.487e^-5	0.864	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
X	16993142	X_16993142_DEL [dm3] X_17099109_DEL [dm6]	GATATGCATGG...	G	1.734e^-5	0.864	DOWNSTREAM CG16700 INTRON CG4991
3R	3460573	3R_3460573_SNP [dm3] 3R_7634851_SNP [dm6]	T	A	1.856e^-5	0.864	INTRON CG34127
3L	7157764	3L_7157764_INS [dm3] 3L_7164664_INS [dm6]	A	AAAATGATCAGA...	1.992e^-5	0.864	INTRON Dscam2
2R	16659539	2R_16659539_SNP [dm3] 2R_20772034_SNP [dm6]	C	A	2.007e^-5	0.864	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
3L	1083500	3L_1083500_DEL [dm3] 3L_1083500_DEL [dm6]	AA	A	2.132e^-5	0.864	INTRON bab1	TF binding site BDTNP1_TFBS_dl
2R	9526623	2R_9526623_INS [dm3] 2R_13639118_INS [dm6]	C	CCCCTGTTTTCC...	2.251e^-5	0.864	INTRON fas	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	10955682	3R_10955682_SNP [dm3] 3R_15129960_SNP [dm6]	G	T	2.403e^-5	0.864	DOWNSTREAM mir-2493 INTRON CG42788
3L	1352732	3L_1352732_SNP [dm3] 3L_1352732_SNP [dm6]	T	C	2.414e^-5	0.864	UTR_3_PRIME 312 DOWNSTREAM 312 INTRON Ptp61F	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_hkb mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_zfh1
2R	11815557	2R_11815557_SNP [dm3] 2R_15928052_SNP [dm6]	T	G	2.437e^-5	0.864	UTR_5_PRIME bdg INTRON bdg
3R	8241764	3R_8241764_SNP [dm3] 3R_12416042_SNP [dm6]	T	C	2.478e^-5	0.864	SYNONYMOUS_CODING pps	TF binding site mE1_TFBS_sens
2L	2718851	2L_2718851_SNP [dm3] 2L_2718851_SNP [dm6]	G	A	2.513e^-5	0.864	SYNONYMOUS_CODING CG31690	TF binding site mE1_TFBS_chinmo
2L	11198371	2L_11198371_SNP [dm3] 2L_11198371_SNP [dm6]	T	A	2.520e^-5	0.864	INTRON Ca-beta
X	21093150	X_21093150_DEL [dm3] X_21222123_DEL [dm6]	AATTCATATGATTTTTGGGC...	A	2.646e^-5	0.864	INTRON CG32521
2R	16659519	2R_16659519_SNP [dm3] 2R_20772014_SNP [dm6]	C	T	2.711e^-5	0.864	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
2R	10009183	2R_10009183_SNP [dm3] 2R_14121678_SNP [dm6]	C	G	2.736e^-5	0.864	INTRON Prosap	TF binding site mE1_TFBS_chinmo
2R	4398671	2R_4398671_SNP [dm3] 2R_8511166_SNP [dm6]	T	C	2.765e^-5	0.864	INTRON mtt
2L	2424463	2L_2424463_INS [dm3] 2L_2424463_INS [dm6]	A	AA	2.786e^-5	0.864	UTR_3_PRIME CG9886 UPSTREAM CG44139
3R	13562706	3R_13562706_SNP [dm3] 3R_17736984_SNP [dm6]	T	A	2.808e^-5	0.864	UTR_5_PRIME TyrRII
3L	12867574	3L_12867574_SNP [dm3] 3L_12874474_SNP [dm6]	C	T	2.848e^-5	0.864	INTERGENIC
X	16993155	X_16993155_SNP [dm3] X_17099122_SNP [dm6]	G	A	2.943e^-5	0.864	DOWNSTREAM CG16700 INTRON CG4991
2L	1274643	2L_1274643_SNP [dm3] 2L_1274643_SNP [dm6]	A	T	3.007e^-5	0.864	INTRON robo3
3L	3966356	3L_3966356_SNP [dm3] 3L_3966356_SNP [dm6]	T	C	3.037e^-5	0.864	INTERGENIC
X	10812553	X_10812553_SNP [dm3] X_10918520_SNP [dm6]	G	A	3.054e^-5	0.864	SPLICE_SITE_REGION CG43901 INTRON CG43901	TF binding site BDTNP1_TFBS_sna mE1_TFBS_cad
3R	10955290	3R_10955290_SNP [dm3] 3R_15129568_SNP [dm6]	C	T	3.059e^-5	0.864	INTRON CG42788
3R	14442770	3R_14442770_SNP [dm3] 3R_18617048_SNP [dm6]	T	C	3.076e^-5	0.864	INTRON qin & 2 others	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_cad
2L	2424473	2L_2424473_SNP [dm3] 2L_2424473_SNP [dm6]	C	T	3.267e^-5	0.864	UTR_3_PRIME CG9886 UPSTREAM CG44139
3L	13646673	3L_13646673_SNP [dm3] 3L_13653573_SNP [dm6]	G	A	3.321e^-5	0.864	INTRON bru-3	TF binding site mE1_TFBS_HSA
X	9589889	X_9589889_SNP [dm3] X_9695856_SNP [dm6]	T	C	3.372e^-5	0.864	SYNONYMOUS_CODING btd	TF binding site BDTNP1_TFBS_sna mE1_TFBS_cad
3R	23207459	3R_23207459_SNP [dm3] 3R_27381737_SNP [dm6]	T	C	3.411e^-5	0.864	UTR_3_PRIME side INTRON side
3R	6930647	3R_6930647_SNP [dm3] 3R_11104925_SNP [dm6]	C	G	3.421e^-5	0.864	INTERGENIC
3R	14523268	3R_14523268_SNP [dm3] 3R_18697546_SNP [dm6]	A	C	3.494e^-5	0.864	INTERGENIC
3R	4810084	3R_4810084_SNP [dm3] 3R_8984362_SNP [dm6]	G	A	3.630e^-5	0.864	UPSTREAM CG11970 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Ubx
3L	1083512	3L_1083512_SNP [dm3] 3L_1083512_SNP [dm6]	T	C	3.641e^-5	0.864	INTRON bab1	TF binding site BDTNP1_TFBS_dl
2L	10958177	2L_10958177_SNP [dm3] 2L_10958177_SNP [dm6]	A	G	3.740e^-5	0.864	INTRON dpr2	TF binding site BDTNP1_TFBS_twi
3L	2825393	3L_2825393_SNP [dm3] 3L_2825393_SNP [dm6]	C	T	3.808e^-5	0.864	INTRON CG43444	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
2L	11881357	2L_11881357_SNP [dm3] 2L_11881357_SNP [dm6]	C	T	3.842e^-5	0.864	INTRON Pde1c	TF binding site mE1_TFBS_inv
2L	8891499	2L_8891499_SNP [dm3] 2L_8891499_SNP [dm6]	G	C	3.915e^-5	0.864	UTR_5_PRIME CG42713
3L	3837822	3L_3837822_SNP [dm3] 3L_3837822_SNP [dm6]	T	G	4.067e^-5	0.864	SYNONYMOUS_CODING enc	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	290190	3L_290190_SNP [dm3] 3L_290190_SNP [dm6]	T	C	4.121e^-5	0.864	SYNONYMOUS_CODING RhoGEF3
2L	14735067	2L_14735067_SNP [dm3] 2L_14735067_SNP [dm6]	T	A	4.204e^-5	0.864	UPSTREAM CG31835 INTERGENIC
2R	9691708	2R_9691708_SNP [dm3] 2R_13804203_SNP [dm6]	A	C	4.216e^-5	0.864	INTRON Cpr50Cb	TF binding site mE1_TFBS_cad
3L	2641281	3L_2641281_SNP [dm3] 3L_2641281_SNP [dm6]	T	G	4.236e^-5	0.864	UTR_3_PRIME CG42245 & 1 other DOWNSTREAM CG14949
3L	18914456	3L_18914456_SNP [dm3] 3L_18921356_SNP [dm6]	G	C	4.275e^-5	0.864	SYNONYMOUS_CODING CG3819	TF binding site mE1_TFBS_cad
2R	11815752	2R_11815752_SNP [dm3] 2R_15928247_SNP [dm6]	G	A	4.288e^-5	0.864	UTR_5_PRIME bdg INTRON bdg
X	2662864	X_2662864_SNP [dm3] X_2768831_SNP [dm6]	A	G	4.292e^-5	0.864	INTRON kirre
2R	18279183	2R_18279183_SNP [dm3] 2R_22391678_SNP [dm6]	T	C	4.313e^-5	0.864	SPLICE_SITE_REGION CG13506 INTRON CG13506	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	13929599	3L_13929599_SNP [dm3] 3L_13936499_SNP [dm6]	C	A	4.345e^-5	0.864	INTERGENIC	TF binding site mE1_TFBS_cad
3R	14523254	3R_14523254_SNP [dm3] 3R_18697532_SNP [dm6]	A	T	4.354e^-5	0.864	INTERGENIC
3L	16553942	3L_16553942_SNP [dm3] 3L_16560842_SNP [dm6]	C	A	4.381e^-5	0.864	INTERGENIC
X	21094842	X_21094842_SNP [dm3] X_21223815_SNP [dm6]	G	C	4.387e^-5	0.864	INTRON CG32521	TF binding site mE1_TFBS_inv
2L	13258775	2L_13258775_DEL [dm3] 2L_13258775_DEL [dm6]	GTATATG	G	4.394e^-5	0.864	DOWNSTREAM CG31730 & 1 other INTERGENIC
2L	8891492	2L_8891492_SNP [dm3] 2L_8891492_SNP [dm6]	G	A	4.397e^-5	0.864	UTR_5_PRIME CG42713
2L	8492926	2L_8492926_SNP [dm3] 2L_8492926_SNP [dm6]	C	G	4.405e^-5	0.864	INTRON Dh31
2L	13082829	2L_13082829_SNP [dm3] 2L_13082829_SNP [dm6]	G	A	4.419e^-5	0.864	INTERGENIC
3L	16452175	3L_16452175_SNP [dm3] 3L_16459075_SNP [dm6]	C	A	4.516e^-5	0.864	INTRON CG33158
3L	1083495	3L_1083495_SNP [dm3] 3L_1083495_SNP [dm6]	T	A	4.532e^-5	0.864	INTRON bab1	TF binding site BDTNP1_TFBS_dl
2R	9689492	2R_9689492_SNP [dm3] 2R_13801987_SNP [dm6]	T	C	4.565e^-5	0.864	INTRON Cpr50Cb
2L	1309777	2L_1309777_SNP [dm3] 2L_1309777_SNP [dm6]	G	A	4.648e^-5	0.864	INTERGENIC
2L	6445478	2L_6445478_SNP [dm3] 2L_6445478_SNP [dm6]	A	G	4.662e^-5	0.864	SYNONYMOUS_CODING CG9527
3R	4823841	3R_4823841_SNP [dm3] 3R_8998119_SNP [dm6]	C	T	4.741e^-5	0.864	SYNONYMOUS_CODING CG11977 INTRON CG31100
3L	3838818	3L_3838818_SNP [dm3] 3L_3838818_SNP [dm6]	C	T	4.756e^-5	0.864	SYNONYMOUS_CODING enc	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	5376183	3R_5376183_SNP [dm3] 3R_9550461_SNP [dm6]	G	T	4.768e^-5	0.864	INTRON mura & 1 other	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
3R	3409309	3R_3409309_SNP [dm3] 3R_7583587_SNP [dm6]	G	A	4.888e^-5	0.864	INTRON CG34127
3R	14534645	3R_14534645_INS [dm3] 3R_18708923_INS [dm6]	A	AT	4.981e^-5	0.864	INTRON VAChT & 1 other
3L	13929983	3L_13929983_SNP [dm3] 3L_13936883_SNP [dm6]	A	T	5.077e^-5	0.864	INTERGENIC
2L	8620018	2L_8620018_SNP [dm3] 2L_8620018_SNP [dm6]	G	A	5.101e^-5	0.864	UPSTREAM tRNA:CR31602 INTRON Sema-1a
2L	1274641	2L_1274641_SNP [dm3] 2L_1274641_SNP [dm6]	T	A	5.117e^-5	0.864	INTRON robo3
3L	12773772	3L_12773772_SNP [dm3] 3L_12780672_SNP [dm6]	C	A	5.119e^-5	0.864	NON_SYNONYMOUS_CODING CG10969 UPSTREAM CG17666
3L	7024371	3L_7024371_SNP [dm3] 3L_7031271_SNP [dm6]	C	T	5.277e^-5	0.864	INTRON Mp
3L	7157739	3L_7157739_SNP [dm3] 3L_7164639_SNP [dm6]	T	C	5.312e^-5	0.864	INTRON Dscam2
X	7693651	X_7693651_SNP [dm3] X_7799618_SNP [dm6]	G	A	5.319e^-5	0.864	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2L	11967196	2L_11967196_SNP [dm3] 2L_11967196_SNP [dm6]	A	G	5.324e^-5	0.864	INTRON CR43314	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_slp1
X	2662880	X_2662880_SNP [dm3] X_2768847_SNP [dm6]	T	A	5.383e^-5	0.864	INTRON kirre
X	2662877	X_2662877_SNP [dm3] X_2768844_SNP [dm6]	A	T	5.400e^-5	0.864	INTRON kirre
2R	17056329	2R_17056329_SNP [dm3] 2R_21168824_SNP [dm6]	A	C	5.499e^-5	0.864	UPSTREAM hng1 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd mE1_TFBS_HSA
3L	7161069	3L_7161069_SNP [dm3] 3L_7167969_SNP [dm6]	T	G	5.545e^-5	0.864	SYNONYMOUS_CODING Dscam2	TF binding site mE1_TFBS_chinmo
2L	13708932	2L_13708932_SNP [dm3] 2L_13708932_SNP [dm6]	G	T	5.547e^-5	0.864	INTRON CG31814 & 1 other	TF binding site mE1_TFBS_inv
3L	7157744	3L_7157744_INS [dm3] 3L_7164644_INS [dm6]	A	AATTACTGAATGAGA...	5.550e^-5	0.864	INTRON Dscam2
3L	7157748	3L_7157748_SNP [dm3] 3L_7164648_SNP [dm6]	T	A	5.550e^-5	0.864	INTRON Dscam2

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By genomic position
Variant impact
Gene name

MC phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results