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=3.218e^-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
No significant result.

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

910 significant hits at p-value < 0.001.

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	3178812	3L_3178812_INS [dm3] 3L_3178812_INS [dm6]	G	AAAAAA	7.069e^-6	0.948	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	7.069e^-6	0.948	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
X	15888696	X_15888696_SNP [dm3] X_15994663_SNP [dm6]	A	G	8.727e^-6	0.948	INTRON exd	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
X	17727386	X_17727386_SNP [dm3] X_17833353_SNP [dm6]	C	A	9.693e^-6	0.948	INTRON CG6398	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_z mE1_TFBS_sens
3R	4905271	3R_4905271_SNP [dm3] 3R_9079549_SNP [dm6]	C	A	1.165e^-5	0.948	INTRON pum
X	2831946	X_2831946_SNP [dm3] X_2937913_SNP [dm6]	G	A	1.245e^-5	0.948	SYNONYMOUS_CODING CG3598 UPSTREAM CG14420 INTRON kirre
3L	3179264	3L_3179264_SNP [dm3] 3L_3179264_SNP [dm6]	A	G	1.467e^-5	0.948	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	17728100	X_17728100_SNP [dm3] X_17834067_SNP [dm6]	C	T	1.914e^-5	0.948	INTRON CG6398	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z
X	4099086	X_4099086_SNP [dm3] X_4205053_SNP [dm6]	C	T	1.914e^-5	0.948	INTRON Fas2	TF binding site BDTNP1_TFBS_dl
3L	3178662	3L_3178662_SNP [dm3] 3L_3178662_SNP [dm6]	C	A	2.213e^-5	0.948	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
3R	4905273	3R_4905273_SNP [dm3] 3R_9079551_SNP [dm6]	G	T	2.486e^-5	0.948	INTRON pum
3R	4905278	3R_4905278_SNP [dm3] 3R_9079556_SNP [dm6]	T	C	2.486e^-5	0.948	INTRON pum
3R	4905280	3R_4905280_SNP [dm3] 3R_9079558_SNP [dm6]	T	G	2.486e^-5	0.948	INTRON pum
3R	4905296	3R_4905296_SNP [dm3] 3R_9079574_SNP [dm6]	A	G	2.486e^-5	0.948	INTRON pum
3L	18594882	3L_18594882_SNP [dm3] 3L_18601782_SNP [dm6]	T	G	2.827e^-5	0.948	NON_SYNONYMOUS_CODING CG4174 UTR_3_PRIME CG13380
2R	3174379	2R_3174379_SNP [dm3] 2R_7286874_SNP [dm6]	C	A	2.834e^-5	0.948	INTRON pwn
3L	3173799	3L_3173799_SNP [dm3] 3L_3173799_SNP [dm6]	G	T	3.095e^-5	0.948	NON_SYNONYMOUS_CODING CG14964	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	4812700	2L_4812700_SNP [dm3] 2L_4812700_SNP [dm6]	A	C	3.306e^-5	0.948	UPSTREAM CR45297 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_h
3L	15229037	3L_15229037_SNP [dm3] 3L_15235937_SNP [dm6]	G	C	3.372e^-5	0.948	UTR_5_PRIME Tollo	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_Trl
2L	19112145	2L_19112145_SNP [dm3] 2L_19112145_SNP [dm6]	G	A	3.415e^-5	0.948	NON_SYNONYMOUS_CODING amd INTRON amd	TF binding site BDTNP1_TFBS_prd mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3L	3179317	3L_3179317_SNP [dm3] 3L_3179317_SNP [dm6]	C	T	3.816e^-5	0.948	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
3L	3178137	3L_3178137_SNP [dm3] 3L_3178137_SNP [dm6]	C	A	4.049e^-5	0.948	UPSTREAM Girdin INTRON CG14964	TF binding site BDTNP1_TFBS_dl
3R	18684565	3R_18684565_SNP [dm3] 3R_22858843_SNP [dm6]	T	G	4.062e^-5	0.948	INTERGENIC
3L	13351852	3L_13351852_SNP [dm3] 3L_13358752_SNP [dm6]	C	T	4.105e^-5	0.948	INTERGENIC	TF binding site BDTNP1_TFBS_twi
2R	10088262	2R_10088262_SNP [dm3] 2R_14200757_SNP [dm6]	G	A	4.149e^-5	0.948	UTR_5_PRIME VGAT DOWNSTREAM Sox15	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
X	7951688	X_7951688_SNP [dm3] X_8057655_SNP [dm6]	C	T	4.154e^-5	0.948	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
X	14324269	X_14324269_SNP [dm3] X_14430236_SNP [dm6]	T	A	4.200e^-5	0.948	INTRON dpr8
3L	3181290	3L_3181290_SNP [dm3] 3L_3181290_SNP [dm6]	G	T	4.458e^-5	0.948	NON_SYNONYMOUS_CODING Girdin
2R	14427637	2R_14427637_SNP [dm3] 2R_18540132_SNP [dm6]	G	C	4.490e^-5	0.948	UTR_5_PRIME Rgk2 DOWNSTREAM Pepck & 1 other	TF binding site mE1_TFBS_chinmo
3L	9726657	3L_9726657_INS [dm3] 3L_9733557_INS [dm6]	G	AA	4.636e^-5	0.948	DOWNSTREAM mir-4986 & 1 other INTRON CG6749
3L	9726673	3L_9726673_SNP [dm3] 3L_9733573_SNP [dm6]	T	C	4.636e^-5	0.948	DOWNSTREAM mir-4986 & 1 other INTRON CG6749
X	4099096	X_4099096_SNP [dm3] X_4205063_SNP [dm6]	C	A	5.000e^-5	0.948	INTRON Fas2	TF binding site BDTNP1_TFBS_dl
3R	17882203	3R_17882203_INS [dm3] 3R_22056481_INS [dm6]	T	TAT	5.029e^-5	0.948	INTRON how
3L	1870616	3L_1870616_SNP [dm3] 3L_1870616_SNP [dm6]	G	C	5.100e^-5	0.948	SYNONYMOUS_CODING CG13924 DOWNSTREAM dre4	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3L	9726588	3L_9726588_SNP [dm3] 3L_9733488_SNP [dm6]	G	A	5.302e^-5	0.948	DOWNSTREAM mir-4986 & 1 other INTRON CG6749
3L	3177647	3L_3177647_SNP [dm3] 3L_3177647_SNP [dm6]	T	A	5.310e^-5	0.948	SYNONYMOUS_CODING CG14964
X	15887848	X_15887848_SNP [dm3] X_15993815_SNP [dm6]	C	A	5.387e^-5	0.948	INTRON exd
X	15887867	X_15887867_SNP [dm3] X_15993834_SNP [dm6]	T	A	5.387e^-5	0.948	INTRON exd
X	15887905	X_15887905_SNP [dm3] X_15993872_SNP [dm6]	A	G	5.387e^-5	0.948	INTRON exd
X	15887907	X_15887907_SNP [dm3] X_15993874_SNP [dm6]	T	C	5.387e^-5	0.948	INTRON exd
X	15887911	X_15887911_SNP [dm3] X_15993878_SNP [dm6]	T	G	5.387e^-5	0.948	INTRON exd
X	15888744	X_15888744_SNP [dm3] X_15994711_SNP [dm6]	C	T	5.387e^-5	0.948	SYNONYMOUS_CODING exd	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	4222956	2L_4222956_SNP [dm3] 2L_4222956_SNP [dm6]	C	T	6.349e^-5	0.948	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med
2R	13728096	2R_13728096_SNP [dm3] 2R_17840591_SNP [dm6]	C	A	6.493e^-5	0.948	INTRON grh
X	20337874	X_20337874_SNP [dm3] X_20466847_SNP [dm6]	T	C	6.587e^-5	0.948	UTR_3_PRIME CG32506 UPSTREAM GstT3 DOWNSTREAM CG32506
3L	13351836	3L_13351836_SNP [dm3] 3L_13358736_SNP [dm6]	T	G	6.814e^-5	0.948	INTERGENIC	TF binding site BDTNP1_TFBS_twi
3L	13351858	3L_13351858_SNP [dm3] 3L_13358758_SNP [dm6]	T	A	6.814e^-5	0.948	INTERGENIC	TF binding site BDTNP1_TFBS_twi
X	19414527	X_19414527_SNP [dm3] X_19520494_SNP [dm6]	C	A	7.201e^-5	0.948	INTRON l_1_G0156	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
2L	4226977	2L_4226977_SNP [dm3] 2L_4226977_SNP [dm6]	A	C	7.262e^-5	0.948	UTR_5_PRIME CG3702 UPSTREAM RpL40	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_Kr
3L	855962	3L_855962_SNP [dm3] 3L_855962_SNP [dm6]	C	G	7.428e^-5	0.948	INTRON dpr20
3L	855963	3L_855963_SNP [dm3] 3L_855963_SNP [dm6]	A	C	7.428e^-5	0.948	INTRON dpr20
3L	855969	3L_855969_SNP [dm3] 3L_855969_SNP [dm6]	A	C	7.428e^-5	0.948	INTRON dpr20
X	5252796	X_5252796_SNP [dm3] X_5358763_SNP [dm6]	A	T	7.708e^-5	0.948	INTRON SK
2R	10962841	2R_10962841_SNP [dm3] 2R_15075336_SNP [dm6]	C	G	7.828e^-5	0.948	INTERGENIC
X	19868563	X_19868563_INS [dm3] X_19974530_INS [dm6]	A	ACACAGTGT	8.229e^-5	0.948	INTERGENIC
2R	16702805	2R_16702805_DEL [dm3] 2R_20815300_DEL [dm6]	ACTTAACTT	A	8.554e^-5	0.948	INTERGENIC
2R	16702836	2R_16702836_SNP [dm3] 2R_20815331_SNP [dm6]	T	A	8.554e^-5	0.948	INTERGENIC
2L	8484977	2L_8484977_SNP [dm3] 2L_8484977_SNP [dm6]	C	G	8.937e^-5	0.948	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	8.937e^-5	0.948	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	8.937e^-5	0.948	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	8.937e^-5	0.948	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	8.937e^-5	0.948	UPSTREAM unsRNA:d-a INTRON d
2L	8485535	2L_8485535_SNP [dm3] 2L_8485535_SNP [dm6]	A	T	8.937e^-5	0.948	UPSTREAM unsRNA:d-a INTRON d
2L	8485546	2L_8485546_SNP [dm3] 2L_8485546_SNP [dm6]	G	T	8.937e^-5	0.948	UPSTREAM unsRNA:d-a INTRON d
2L	8485549	2L_8485549_SNP [dm3] 2L_8485549_SNP [dm6]	G	A	8.937e^-5	0.948	UPSTREAM unsRNA:d-a INTRON d
2L	8485561	2L_8485561_SNP [dm3] 2L_8485561_SNP [dm6]	C	A	8.937e^-5	0.948	UPSTREAM unsRNA:d-a INTRON d
2L	8485573	2L_8485573_SNP [dm3] 2L_8485573_SNP [dm6]	T	A	8.937e^-5	0.948	UPSTREAM unsRNA:d-a INTRON d
2L	8485592	2L_8485592_SNP [dm3] 2L_8485592_SNP [dm6]	T	C	8.937e^-5	0.948	UPSTREAM unsRNA:d-a INTRON d
2L	8485610	2L_8485610_SNP [dm3] 2L_8485610_SNP [dm6]	A	T	8.937e^-5	0.948	UPSTREAM unsRNA:d-a INTRON d
2L	8485629	2L_8485629_SNP [dm3] 2L_8485629_SNP [dm6]	C	T	8.937e^-5	0.948	UPSTREAM unsRNA:d-a INTRON d
2L	8485644	2L_8485644_SNP [dm3] 2L_8485644_SNP [dm6]	A	T	8.937e^-5	0.948	UPSTREAM unsRNA:d-a INTRON d
2L	8485649	2L_8485649_SNP [dm3] 2L_8485649_SNP [dm6]	C	A	8.937e^-5	0.948	UPSTREAM unsRNA:d-a INTRON d
2L	8485724	2L_8485724_SNP [dm3] 2L_8485724_SNP [dm6]	T	C	8.937e^-5	0.948	UPSTREAM unsRNA:d-a INTRON d
2L	8485991	2L_8485991_SNP [dm3] 2L_8485991_SNP [dm6]	T	A	8.937e^-5	0.948	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	8.937e^-5	0.948	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	8.937e^-5	0.948	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	8.937e^-5	0.948	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	8.937e^-5	0.948	SYNONYMOUS_CODING d DOWNSTREAM unsRNA:d-a	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
X	4877667	X_4877667_SNP [dm3] X_4983634_SNP [dm6]	G	A	8.942e^-5	0.948	INTRON CR44833	regulatory region REDfly_CRMs
X	4877751	X_4877751_SNP [dm3] X_4983718_SNP [dm6]	A	G	8.942e^-5	0.948	INTRON CR44833	regulatory region REDfly_CRMs
2L	3301249	2L_3301249_SNP [dm3] 2L_3301249_SNP [dm6]	T	G	9.225e^-5	0.948	NON_SYNONYMOUS_CODING CG9663	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2L	3260094	2L_3260094_SNP [dm3] 2L_3260094_SNP [dm6]	A	G	9.962e^-5	0.948	DOWNSTREAM CR45337 INTERGENIC
2R	12478014	2R_12478014_SNP [dm3] 2R_16590509_SNP [dm6]	C	G	9.990e^-5	0.948	SYNONYMOUS_CODING CG8306	TF binding site mE1_TFBS_sens
3R	4905303	3R_4905303_DEL [dm3] 3R_9079581_DEL [dm6]	ATATGCCA	A	9.991e^-5	0.948	INTRON pum
3R	4905320	3R_4905320_SNP [dm3] 3R_9079598_SNP [dm6]	T	A	9.991e^-5	0.948	INTRON pum
2R	12968500	2R_12968500_SNP [dm3] 2R_17080995_SNP [dm6]	A	T	1.008e^-4	0.948	INTRON CG30460
2R	12968503	2R_12968503_SNP [dm3] 2R_17080998_SNP [dm6]	T	A	1.008e^-4	0.948	INTRON CG30460
2R	12968515	2R_12968515_SNP [dm3] 2R_17081010_SNP [dm6]	A	G	1.008e^-4	0.948	INTRON CG30460
2R	12968528	2R_12968528_SNP [dm3] 2R_17081023_SNP [dm6]	T	C	1.008e^-4	0.948	INTRON CG30460
2L	13705071	2L_13705071_SNP [dm3] 2L_13705071_SNP [dm6]	A	T	1.032e^-4	0.948	INTRON CG31814	TF binding site BDTNP1_TFBS_twi
2R	16229998	2R_16229998_SNP [dm3] 2R_20342493_SNP [dm6]	T	A	1.055e^-4	0.948	INTRON CG16739
2R	16230018	2R_16230018_SNP [dm3] 2R_20342513_SNP [dm6]	G	T	1.055e^-4	0.948	SPLICE_SITE_REGION CG16739 SYNONYMOUS_CODING CG16739
X	19414662	X_19414662_SNP [dm3] X_19520629_SNP [dm6]	C	A	1.055e^-4	0.948	INTRON l_1_G0156	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad
2L	10253187	2L_10253187_SNP [dm3] 2L_10253187_SNP [dm6]	A	G	1.068e^-4	0.948	SYNONYMOUS_CODING Ror
3R	4905328	3R_4905328_SNP [dm3] 3R_9079606_SNP [dm6]	T	G	1.077e^-4	0.948	INTRON pum
3R	4905329	3R_4905329_SNP [dm3] 3R_9079607_SNP [dm6]	T	C	1.077e^-4	0.948	INTRON pum
2R	16701450	2R_16701450_SNP [dm3] 2R_20813945_SNP [dm6]	G	C	1.078e^-4	0.948	INTERGENIC
2R	16701877	2R_16701877_SNP [dm3] 2R_20814372_SNP [dm6]	G	A	1.078e^-4	0.948	INTERGENIC
X	4877676	X_4877676_SNP [dm3] X_4983643_SNP [dm6]	G	A	1.084e^-4	0.948	INTRON CR44833	regulatory region REDfly_CRMs
2R	14318431	2R_14318431_INS [dm3] 2R_18430926_INS [dm6]	A	AATTTGAGAA	1.095e^-4	0.948	UTR_3_PRIME CG30118 DOWNSTREAM CG12263 INTRON CG30118

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DAControl phenotype

Phenotype distribution and association to known covariates

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GWAS results