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=1.485e^-2)
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

Covariate	p-value	Significance
In_3R_K	0.0747644

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1201 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	3179264	3L_3179264_SNP [dm3] 3L_3179264_SNP [dm6]	A	G	1.009e^-5	0.959	UTR_5_PRIME Girdin UPSTREAM CG14964	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2L	4812700	2L_4812700_SNP [dm3] 2L_4812700_SNP [dm6]	A	C	1.024e^-5	0.959	UPSTREAM CR45297 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_h
X	14324269	X_14324269_SNP [dm3] X_14430236_SNP [dm6]	T	A	1.090e^-5	0.959	INTRON dpr8
3L	3178812	3L_3178812_INS [dm3] 3L_3178812_INS [dm6]	G	AAAAAA	1.234e^-5	0.959	UPSTREAM Girdin & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_run mE1_TFBS_sens mE1_TFBS_Trl mE1_TFBS_Ubx
3L	3178846	3L_3178846_SNP [dm3] 3L_3178846_SNP [dm6]	T	A	1.234e^-5	0.959	UPSTREAM Girdin & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_run mE1_TFBS_sens mE1_TFBS_Trl mE1_TFBS_Ubx
2R	10088262	2R_10088262_SNP [dm3] 2R_14200757_SNP [dm6]	G	A	1.911e^-5	0.959	UTR_5_PRIME VGAT DOWNSTREAM Sox15	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	3179317	3L_3179317_SNP [dm3] 3L_3179317_SNP [dm6]	C	T	2.266e^-5	0.959	UTR_5_PRIME Girdin UPSTREAM CG14964	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
X	5252796	X_5252796_SNP [dm3] X_5358763_SNP [dm6]	A	T	2.663e^-5	0.959	INTRON SK
X	5252912	X_5252912_SNP [dm3] X_5358879_SNP [dm6]	C	T	2.972e^-5	0.959	INTRON SK
X	5252914	X_5252914_SNP [dm3] X_5358881_SNP [dm6]	G	A	2.972e^-5	0.959	INTRON SK
X	7951688	X_7951688_SNP [dm3] X_8057655_SNP [dm6]	C	T	3.036e^-5	0.959	UPSTREAM fs_1_h INTRON fs_1_h	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl mE1_TFBS_zfh1
3L	1870616	3L_1870616_SNP [dm3] 3L_1870616_SNP [dm6]	G	C	3.302e^-5	0.959	SYNONYMOUS_CODING CG13924 DOWNSTREAM dre4	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
X	17727386	X_17727386_SNP [dm3] X_17833353_SNP [dm6]	C	A	3.423e^-5	0.959	INTRON CG6398	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_z mE1_TFBS_sens
2L	8484977	2L_8484977_SNP [dm3] 2L_8484977_SNP [dm6]	C	G	3.576e^-5	0.959	SYNONYMOUS_CODING d UPSTREAM unsRNA:d-a	TF binding site mE1_TFBS_chinmo
2L	8485232	2L_8485232_SNP [dm3] 2L_8485232_SNP [dm6]	T	G	3.576e^-5	0.959	SYNONYMOUS_CODING d UPSTREAM unsRNA:d-a	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2L	8485304	2L_8485304_SNP [dm3] 2L_8485304_SNP [dm6]	G	T	3.576e^-5	0.959	SYNONYMOUS_CODING d UPSTREAM unsRNA:d-a	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2L	8485412	2L_8485412_SNP [dm3] 2L_8485412_SNP [dm6]	A	C	3.576e^-5	0.959	SYNONYMOUS_CODING d UPSTREAM unsRNA:d-a	TF binding site mE1_TFBS_chinmo
2L	8485526	2L_8485526_SNP [dm3] 2L_8485526_SNP [dm6]	C	T	3.576e^-5	0.959	UPSTREAM unsRNA:d-a INTRON d
2L	8485535	2L_8485535_SNP [dm3] 2L_8485535_SNP [dm6]	A	T	3.576e^-5	0.959	UPSTREAM unsRNA:d-a INTRON d
2L	8485546	2L_8485546_SNP [dm3] 2L_8485546_SNP [dm6]	G	T	3.576e^-5	0.959	UPSTREAM unsRNA:d-a INTRON d
2L	8485549	2L_8485549_SNP [dm3] 2L_8485549_SNP [dm6]	G	A	3.576e^-5	0.959	UPSTREAM unsRNA:d-a INTRON d
2L	8485561	2L_8485561_SNP [dm3] 2L_8485561_SNP [dm6]	C	A	3.576e^-5	0.959	UPSTREAM unsRNA:d-a INTRON d
2L	8485573	2L_8485573_SNP [dm3] 2L_8485573_SNP [dm6]	T	A	3.576e^-5	0.959	UPSTREAM unsRNA:d-a INTRON d
2L	8485592	2L_8485592_SNP [dm3] 2L_8485592_SNP [dm6]	T	C	3.576e^-5	0.959	UPSTREAM unsRNA:d-a INTRON d
2L	8485610	2L_8485610_SNP [dm3] 2L_8485610_SNP [dm6]	A	T	3.576e^-5	0.959	UPSTREAM unsRNA:d-a INTRON d
2L	8485629	2L_8485629_SNP [dm3] 2L_8485629_SNP [dm6]	C	T	3.576e^-5	0.959	UPSTREAM unsRNA:d-a INTRON d
2L	8485644	2L_8485644_SNP [dm3] 2L_8485644_SNP [dm6]	A	T	3.576e^-5	0.959	UPSTREAM unsRNA:d-a INTRON d
2L	8485649	2L_8485649_SNP [dm3] 2L_8485649_SNP [dm6]	C	A	3.576e^-5	0.959	UPSTREAM unsRNA:d-a INTRON d
2L	8485724	2L_8485724_SNP [dm3] 2L_8485724_SNP [dm6]	T	C	3.576e^-5	0.959	UPSTREAM unsRNA:d-a INTRON d
2L	8485991	2L_8485991_SNP [dm3] 2L_8485991_SNP [dm6]	T	A	3.576e^-5	0.959	DOWNSTREAM unsRNA:d-a INTRON d	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	8486002	2L_8486002_DEL [dm3] 2L_8486002_DEL [dm6]	TC	T	3.576e^-5	0.959	DOWNSTREAM unsRNA:d-a INTRON d	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	8486009	2L_8486009_SNP [dm3] 2L_8486009_SNP [dm6]	T	A	3.576e^-5	0.959	DOWNSTREAM unsRNA:d-a INTRON d	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	8486126	2L_8486126_SNP [dm3] 2L_8486126_SNP [dm6]	C	T	3.576e^-5	0.959	SYNONYMOUS_CODING d DOWNSTREAM unsRNA:d-a	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	8486177	2L_8486177_SNP [dm3] 2L_8486177_SNP [dm6]	T	C	3.576e^-5	0.959	SYNONYMOUS_CODING d DOWNSTREAM unsRNA:d-a	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	3178662	3L_3178662_SNP [dm3] 3L_3178662_SNP [dm6]	C	A	3.754e^-5	0.959	UPSTREAM Girdin & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna mE1_TFBS_GATAe mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_run mE1_TFBS_sens mE1_TFBS_Trl mE1_TFBS_Ubx
3L	18594882	3L_18594882_SNP [dm3] 3L_18601782_SNP [dm6]	T	G	4.002e^-5	0.959	NON_SYNONYMOUS_CODING CG4174 UTR_3_PRIME CG13380
2L	19112145	2L_19112145_SNP [dm3] 2L_19112145_SNP [dm6]	G	A	4.101e^-5	0.959	NON_SYNONYMOUS_CODING amd INTRON amd	TF binding site BDTNP1_TFBS_prd mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	9336699	3R_9336699_SNP [dm3] 3R_13510977_SNP [dm6]	G	C	4.637e^-5	0.959	INTERGENIC
3R	9336701	3R_9336701_SNP [dm3] 3R_13510979_SNP [dm6]	A	G	4.637e^-5	0.959	INTERGENIC
X	15888696	X_15888696_SNP [dm3] X_15994663_SNP [dm6]	A	G	4.901e^-5	0.959	INTRON exd	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
4	222361	4_222361_SNP [dm3] 4_201735_SNP [dm6]	A	T	5.111e^-5	0.959	INTRON CG31998
3L	4111883	3L_4111883_SNP [dm3] 3L_4111883_SNP [dm6]	C	T	5.353e^-5	0.959	SYNONYMOUS_CODING Ack	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
X	6249661	X_6249661_SNP [dm3] X_6355628_SNP [dm6]	C	T	5.378e^-5	0.959	INTRON kdn
2L	4223212	2L_4223212_SNP [dm3] 2L_4223212_SNP [dm6]	A	C	5.408e^-5	0.959	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med
2L	4239899	2L_4239899_SNP [dm3] 2L_4239899_SNP [dm6]	C	T	5.422e^-5	0.959	DOWNSTREAM CR45720 INTERGENIC
3R	17882203	3R_17882203_INS [dm3] 3R_22056481_INS [dm6]	T	TAT	5.981e^-5	0.959	INTRON how
2R	3174379	2R_3174379_SNP [dm3] 2R_7286874_SNP [dm6]	C	A	5.997e^-5	0.959	INTRON pwn
3R	18684565	3R_18684565_SNP [dm3] 3R_22858843_SNP [dm6]	T	G	6.441e^-5	0.959	INTERGENIC
3R	18988897	3R_18988897_SNP [dm3] 3R_23163175_SNP [dm6]	T	A	6.568e^-5	0.959	INTERGENIC
2R	9961920	2R_9961920_SNP [dm3] 2R_14074415_SNP [dm6]	C	T	6.593e^-5	0.959	INTRON Prosap	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad
2L	16450248	2L_16450248_SNP [dm3] 2L_16450248_SNP [dm6]	A	G	6.996e^-5	0.959	SYNONYMOUS_CODING Idgf2 UPSTREAM Idgf3
2R	14318431	2R_14318431_INS [dm3] 2R_18430926_INS [dm6]	A	AATTTGAGAA	7.354e^-5	0.959	UTR_3_PRIME CG30118 DOWNSTREAM CG12263 INTRON CG30118
2R	17856409	2R_17856409_SNP [dm3] 2R_21968904_SNP [dm6]	G	A	7.767e^-5	0.959	INTRON ppk9
X	5252892	X_5252892_SNP [dm3] X_5358859_SNP [dm6]	G	T	7.858e^-5	0.959	INTRON SK
2R	9199357	2R_9199357_SNP [dm3] 2R_13311852_SNP [dm6]	C	A	7.992e^-5	0.959	INTERGENIC
2L	4226977	2L_4226977_SNP [dm3] 2L_4226977_SNP [dm6]	A	C	8.195e^-5	0.959	UTR_5_PRIME CG3702 UPSTREAM RpL40	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_Kr
2L	4239948	2L_4239948_SNP [dm3] 2L_4239948_SNP [dm6]	A	G	8.302e^-5	0.959	DOWNSTREAM CR45720 INTERGENIC
X	7951007	X_7951007_SNP [dm3] X_8056974_SNP [dm6]	T	A	8.351e^-5	0.959	UPSTREAM fs_1_h INTRON fs_1_h	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_Trl mE1_TFBS_zfh1
2L	8486078	2L_8486078_SNP [dm3] 2L_8486078_SNP [dm6]	T	C	8.382e^-5	0.959	SYNONYMOUS_CODING d DOWNSTREAM unsRNA:d-a	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	8486228	2L_8486228_SNP [dm3] 2L_8486228_SNP [dm6]	T	C	8.382e^-5	0.959	SYNONYMOUS_CODING d DOWNSTREAM unsRNA:d-a	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	4222956	2L_4222956_SNP [dm3] 2L_4222956_SNP [dm6]	C	T	8.531e^-5	0.959	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med
2R	16229998	2R_16229998_SNP [dm3] 2R_20342493_SNP [dm6]	T	A	8.706e^-5	0.959	INTRON CG16739
2R	16230018	2R_16230018_SNP [dm3] 2R_20342513_SNP [dm6]	G	T	8.706e^-5	0.959	SPLICE_SITE_REGION CG16739 SYNONYMOUS_CODING CG16739
X	19414662	X_19414662_SNP [dm3] X_19520629_SNP [dm6]	C	A	8.706e^-5	0.959	INTRON l_1_G0156	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad
3R	22583111	3R_22583111_SNP [dm3] 3R_26757389_SNP [dm6]	G	T	8.708e^-5	0.959	EXON CR45562
2L	8485611	2L_8485611_SNP [dm3] 2L_8485611_SNP [dm6]	A	T	8.813e^-5	0.959	UPSTREAM unsRNA:d-a INTRON d
3L	11304738	3L_11304738_SNP [dm3] 3L_11311638_SNP [dm6]	A	G	8.894e^-5	0.959	UPSTREAM CG7573 INTERGENIC
2R	16701450	2R_16701450_SNP [dm3] 2R_20813945_SNP [dm6]	G	C	8.944e^-5	0.959	INTERGENIC
2R	16701877	2R_16701877_SNP [dm3] 2R_20814372_SNP [dm6]	G	A	8.944e^-5	0.959	INTERGENIC
2L	18983860	2L_18983860_INS [dm3] 2L_18983860_INS [dm6]	T	TTGACTT	9.167e^-5	0.959	INTRON Swip-1
X	19414527	X_19414527_SNP [dm3] X_19520494_SNP [dm6]	C	A	9.266e^-5	0.959	INTRON l_1_G0156	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
2R	19389831	2R_19389831_SNP [dm3] 2R_23502308_SNP [dm6]	T	C	9.275e^-5	0.959	UPSTREAM CG13559 INTERGENIC	TF binding site mE1_TFBS_inv
3R	24115383	3R_24115383_SNP [dm3] 3R_28289661_SNP [dm6]	C	T	9.377e^-5	0.959	INTERGENIC
3R	24115387	3R_24115387_DEL [dm3] 3R_28289665_DEL [dm6]	TT	T	9.377e^-5	0.959	INTERGENIC
3R	24115395	3R_24115395_SNP [dm3] 3R_28289673_SNP [dm6]	A	T	9.377e^-5	0.959	INTERGENIC
2R	14427637	2R_14427637_SNP [dm3] 2R_18540132_SNP [dm6]	G	C	9.961e^-5	0.959	UTR_5_PRIME Rgk2 DOWNSTREAM Pepck & 1 other	TF binding site mE1_TFBS_chinmo
3L	9726588	3L_9726588_SNP [dm3] 3L_9733488_SNP [dm6]	G	A	1.004e^-4	0.959	DOWNSTREAM mir-4986 & 1 other INTRON CG6749
X	2831946	X_2831946_SNP [dm3] X_2937913_SNP [dm6]	G	A	1.053e^-4	0.959	SYNONYMOUS_CODING CG3598 UPSTREAM CG14420 INTRON kirre
X	5253158	X_5253158_SNP [dm3] X_5359125_SNP [dm6]	T	C	1.070e^-4	0.959	INTRON SK
X	5253159	X_5253159_SNP [dm3] X_5359126_SNP [dm6]	G	A	1.070e^-4	0.959	INTRON SK
2L	20750617	2L_20750617_SNP [dm3] 2L_20750617_SNP [dm6]	G	A	1.070e^-4	0.959	UTR_3_PRIME Fs_2_Ket DOWNSTREAM CG9319	TF binding site mE1_TFBS_sens
2L	1111598	2L_1111598_SNP [dm3] 2L_1111598_SNP [dm6]	C	T	1.074e^-4	0.959	SYNONYMOUS_CODING CG14339
X	17728100	X_17728100_SNP [dm3] X_17834067_SNP [dm6]	C	T	1.086e^-4	0.959	INTRON CG6398	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z
X	4099086	X_4099086_SNP [dm3] X_4205053_SNP [dm6]	C	T	1.086e^-4	0.959	INTRON Fas2	TF binding site BDTNP1_TFBS_dl
X	8607067	X_8607067_SNP [dm3] X_8713034_SNP [dm6]	C	T	1.119e^-4	0.959	NON_SYNONYMOUS_CODING CG2004 DOWNSTREAM Hexo2
X	8607069	X_8607069_SNP [dm3] X_8713036_SNP [dm6]	T	C	1.119e^-4	0.959	SYNONYMOUS_CODING CG2004 DOWNSTREAM Hexo2
X	1146474	X_1146474_SNP [dm3] X_1252441_SNP [dm6]	A	C	1.126e^-4	0.959	INTRON Atf3
2L	3301249	2L_3301249_SNP [dm3] 2L_3301249_SNP [dm6]	T	G	1.143e^-4	0.959	NON_SYNONYMOUS_CODING CG9663	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	18597854	3L_18597854_SNP [dm3] 3L_18604754_SNP [dm6]	G	A	1.146e^-4	0.959	SYNONYMOUS_CODING CG18234 UPSTREAM CG18233 INTRON CG4174 & 1 other
3L	9719888	3L_9719888_SNP [dm3] 3L_9726788_SNP [dm6]	A	T	1.146e^-4	0.959	UPSTREAM Naa60 DOWNSTREAM defl INTERGENIC	TF binding site mE1_TFBS_HSA
3L	17929828	3L_17929828_SNP [dm3] 3L_17936728_SNP [dm6]	C	A	1.162e^-4	0.959	INTRON CG43174
2R	14087695	2R_14087695_SNP [dm3] 2R_18200190_SNP [dm6]	A	C	1.163e^-4	0.959	INTERGENIC
X	21231603	X_21231603_SNP [dm3] X_21360576_SNP [dm6]	C	T	1.163e^-4	0.959	INTRON Sep1	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
X	15887848	X_15887848_SNP [dm3] X_15993815_SNP [dm6]	C	A	1.170e^-4	0.959	INTRON exd
X	15887867	X_15887867_SNP [dm3] X_15993834_SNP [dm6]	T	A	1.170e^-4	0.959	INTRON exd
X	15887905	X_15887905_SNP [dm3] X_15993872_SNP [dm6]	A	G	1.170e^-4	0.959	INTRON exd
X	15887907	X_15887907_SNP [dm3] X_15993874_SNP [dm6]	T	C	1.170e^-4	0.959	INTRON exd
X	15887911	X_15887911_SNP [dm3] X_15993878_SNP [dm6]	T	G	1.170e^-4	0.959	INTRON exd
X	15888744	X_15888744_SNP [dm3] X_15994711_SNP [dm6]	C	T	1.170e^-4	0.959	SYNONYMOUS_CODING exd	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	10253187	2L_10253187_SNP [dm3] 2L_10253187_SNP [dm6]	A	G	1.194e^-4	0.959	SYNONYMOUS_CODING Ror

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By genomic position
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ParaquatDA phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results