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=8.095e^-3)
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

Covariate	χ²	p-value	Significance
In_3R_K	2.8182	0.0932

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1397 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
2L	11361515	2L_11361515_SNP [dm3] 2L_11361515_SNP [dm6]	A	G	1.784e^-6	0.468	INTRON salr	regulatory region REDfly_CRMs
3R	11618479	3R_11618479_SNP [dm3] 3R_15792757_SNP [dm6]	G	C	2.038e^-6	0.468	UTR_5_PRIME Acyp2 UPSTREAM c_3_G	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_disco mE1_TFBS_Ubx
3R	24217371	3R_24217371_SNP [dm3] 3R_28391649_SNP [dm6]	C	A	2.706e^-6	0.468	INTERGENIC
2L	11361516	2L_11361516_SNP [dm3] 2L_11361516_SNP [dm6]	T	C	2.753e^-6	0.468	INTRON salr	regulatory region REDfly_CRMs
3R	9151822	3R_9151822_SNP [dm3] 3R_13326100_SNP [dm6]	T	C	2.994e^-6	0.468	INTERGENIC
X	4519489	X_4519489_SNP [dm3] X_4625456_SNP [dm6]	C	T	3.702e^-6	0.468	SYNONYMOUS_CODING peb	TF binding site BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_inv
3L	14642055	3L_14642055_SNP [dm3] 3L_14648955_SNP [dm6]	A	T	5.198e^-6	0.468	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3L	14642058	3L_14642058_SNP [dm3] 3L_14648958_SNP [dm6]	G	A	5.198e^-6	0.468	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3L	14642078	3L_14642078_MNP [dm3] 3L_14648978_MNP [dm6]	GGG	AAA	5.198e^-6	0.468	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3L	13541893	3L_13541893_INS [dm3] 3L_13548793_INS [dm6]	C	CGGACAC	6.161e^-6	0.468	INTRON bru-3
3R	26119383	3R_26119383_SNP [dm3] 3R_30293661_SNP [dm6]	G	C	6.502e^-6	0.468	INTRON hdc	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	14642070	3L_14642070_SNP [dm3] 3L_14648970_SNP [dm6]	C	T	6.793e^-6	0.468	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3L	14642095	3L_14642095_SNP [dm3] 3L_14648995_SNP [dm6]	T	A	6.793e^-6	0.468	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3L	14642098	3L_14642098_SNP [dm3] 3L_14648998_SNP [dm6]	A	T	6.793e^-6	0.468	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3L	14642110	3L_14642110_SNP [dm3] 3L_14649010_SNP [dm6]	T	C	6.793e^-6	0.468	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3L	14642089	3L_14642089_SNP [dm3] 3L_14648989_SNP [dm6]	A	T	6.962e^-6	0.468	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
2R	6379235	2R_6379235_SNP [dm3] 2R_10491730_SNP [dm6]	C	T	7.089e^-6	0.468	UTR_3_PRIME lola INTRON lola
2R	6508001	2R_6508001_SNP [dm3] 2R_10620496_SNP [dm6]	A	C	7.089e^-6	0.468	INTRON CG11883
3R	25365859	3R_25365859_SNP [dm3] 3R_29540137_SNP [dm6]	T	A	7.171e^-6	0.468	INTERGENIC	TF binding site BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
2L	15343672	2L_15343672_DEL [dm3] 2L_15343672_DEL [dm6]	AAAT	A	7.204e^-6	0.468	INTERGENIC
2L	15343677	2L_15343677_SNP [dm3] 2L_15343677_SNP [dm6]	A	T	7.204e^-6	0.468	INTERGENIC
2L	15343679	2L_15343679_SNP [dm3] 2L_15343679_SNP [dm6]	T	C	7.204e^-6	0.468	INTERGENIC
2L	15343680	2L_15343680_SNP [dm3] 2L_15343680_SNP [dm6]	T	A	7.204e^-6	0.468	INTERGENIC
2L	15343689	2L_15343689_SNP [dm3] 2L_15343689_SNP [dm6]	T	A	7.204e^-6	0.468	INTERGENIC
3L	14642039	3L_14642039_SNP [dm3] 3L_14648939_SNP [dm6]	T	G	7.260e^-6	0.468	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3L	14642051	3L_14642051_SNP [dm3] 3L_14648951_SNP [dm6]	T	C	7.260e^-6	0.468	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3R	13588263	3R_13588263_INS [dm3] 3R_17762541_INS [dm6]	G	GTCG	7.375e^-6	0.468	UTR_5_PRIME TyrR UPSTREAM TyrR
2L	9507277	2L_9507277_SNP [dm3] 2L_9507277_SNP [dm6]	G	T	8.098e^-6	0.468	INTRON CG33298
3R	26119375	3R_26119375_SNP [dm3] 3R_30293653_SNP [dm6]	T	A	8.161e^-6	0.468	INTRON hdc	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	14642038	3L_14642038_SNP [dm3] 3L_14648938_SNP [dm6]	T	A	8.581e^-6	0.468	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
2L	4427850	2L_4427850_SNP [dm3] 2L_4427850_SNP [dm6]	A	G	9.461e^-6	0.468	INTRON CG15431
2R	6508615	2R_6508615_SNP [dm3] 2R_10621110_SNP [dm6]	A	G	9.503e^-6	0.468	INTRON CG11883
3R	11140143	3R_11140143_SNP [dm3] 3R_15314421_SNP [dm6]	T	C	9.503e^-6	0.468	INTRON Tm2	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
3L	12834135	3L_12834135_SNP [dm3] 3L_12841035_SNP [dm6]	G	T	1.022e^-5	0.468	INTRON CG10960	TF binding site mE1_TFBS_GATAe mE1_TFBS_HSA
3L	14642109	3L_14642109_SNP [dm3] 3L_14649009_SNP [dm6]	A	T	1.067e^-5	0.468	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3L	14642171	3L_14642171_SNP [dm3] 3L_14649071_SNP [dm6]	A	T	1.078e^-5	0.468	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
2R	11059590	2R_11059590_SNP [dm3] 2R_15172085_SNP [dm6]	T	C	1.093e^-5	0.468	INTRON igl
2R	6508603	2R_6508603_SNP [dm3] 2R_10621098_SNP [dm6]	T	G	1.093e^-5	0.468	INTRON CG11883
3R	24366641	3R_24366641_SNP [dm3] 3R_28540919_SNP [dm6]	G	A	1.134e^-5	0.468	UPSTREAM Ppn INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	15343669	2L_15343669_SNP [dm3] 2L_15343669_SNP [dm6]	A	T	1.179e^-5	0.468	INTERGENIC
2L	15343684	2L_15343684_MNP [dm3] 2L_15343684_MNP [dm6]	GTT	ACA	1.179e^-5	0.468	INTERGENIC
2L	15343691	2L_15343691_DEL [dm3] 2L_15343691_DEL [dm6]	CAC	A	1.179e^-5	0.468	INTERGENIC
3R	24807557	3R_24807557_SNP [dm3] 3R_28981835_SNP [dm6]	C	T	1.186e^-5	0.468	INTERGENIC
2L	17250611	2L_17250611_SNP [dm3] 2L_17250611_SNP [dm6]	C	T	1.209e^-5	0.468	INTRON beat-IIIc	TF binding site mE1_TFBS_HSA mE1_TFBS_run
3L	7986614	3L_7986614_SNP [dm3] 3L_7993514_SNP [dm6]	C	G	1.217e^-5	0.468	INTRON nmo	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_hb mE1_TFBS_cad mE1_TFBS_HSA
3L	9088728	3L_9088728_SNP [dm3] 3L_9095628_SNP [dm6]	C	T	1.224e^-5	0.468	DOWNSTREAM CG32032 INTERGENIC
3R	26119373	3R_26119373_SNP [dm3] 3R_30293651_SNP [dm6]	G	C	1.331e^-5	0.498	INTRON hdc	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	11360994	2L_11360994_SNP [dm3] 2L_11360994_SNP [dm6]	G	C	1.468e^-5	0.52	INTRON salr	regulatory region REDfly_CRMs
3L	14641921	3L_14641921_SNP [dm3] 3L_14648821_SNP [dm6]	A	G	1.492e^-5	0.52	INTRON dlp	TF binding site mE1_TFBS_HSA
3R	11618443	3R_11618443_SNP [dm3] 3R_15792721_SNP [dm6]	A	G	1.540e^-5	0.52	UTR_5_PRIME Acyp2 UPSTREAM c_3_G	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_Ubx
3R	16704328	3R_16704328_SNP [dm3] 3R_20878606_SNP [dm6]	T	A	1.542e^-5	0.52	DOWNSTREAM TotZ EXON CR44048
3L	14642063	3L_14642063_SNP [dm3] 3L_14648963_SNP [dm6]	T	G	1.607e^-5	0.52	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3L	970831	3L_970831_SNP [dm3] 3L_970831_SNP [dm6]	A	G	1.620e^-5	0.52	INTRON Glut1
2L	7101775	2L_7101775_SNP [dm3] 2L_7101775_SNP [dm6]	C	T	1.669e^-5	0.52	INTRON Pvf3
X	18249664	X_18249664_INS [dm3] X_18355631_INS [dm6]	G	GTAGGCGG	1.678e^-5	0.52	INTRON CG6123
2L	15740889	2L_15740889_SNP [dm3] 2L_15740889_SNP [dm6]	T	A	1.679e^-5	0.52	UTR_5_PRIME CycE INTRON CycE	regulatory region FlyBase REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	5318902	2R_5318902_INS [dm3] 2R_9431397_INS [dm6]	A	ATACA	1.686e^-5	0.52	INTRON Pdk
X	3911257	X_3911257_SNP [dm3] X_4017224_SNP [dm6]	G	A	1.730e^-5	0.524	INTERGENIC
3L	7986579	3L_7986579_MNP [dm3] 3L_7993479_MNP [dm6]	GTT	TAG	1.973e^-5	0.569	INTRON nmo	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_hb mE1_TFBS_cad mE1_TFBS_HSA
X	3911217	X_3911217_SNP [dm3] X_4017184_SNP [dm6]	C	A	1.974e^-5	0.569	INTERGENIC
X	3911229	X_3911229_SNP [dm3] X_4017196_SNP [dm6]	T	G	1.974e^-5	0.569	INTERGENIC
X	3911242	X_3911242_DEL [dm3] X_4017209_DEL [dm6]	TAATATCAGT	T	2.039e^-5	0.575	INTERGENIC
3R	16739456	3R_16739456_SNP [dm3] 3R_20913734_SNP [dm6]	C	T	2.083e^-5	0.575	UPSTREAM snoRNA:CG31191-a & 1 other DOWNSTREAM CR44106 INTRON CG31191	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
X	2794934	X_2794934_SNP [dm3] X_2900901_SNP [dm6]	A	C	2.110e^-5	0.575	INTRON kirre
3L	5376612	3L_5376612_DEL [dm3] 3L_5383512_DEL [dm6]	CTGT	A	2.139e^-5	0.575	UPSTREAM Ir64a INTERGENIC
2L	9014159	2L_9014159_SNP [dm3] 2L_9014159_SNP [dm6]	C	T	2.157e^-5	0.575	UPSTREAM Rcd-1r DOWNSTREAM CG13102 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi
3R	9151836	3R_9151836_SNP [dm3] 3R_13326114_SNP [dm6]	A	G	2.236e^-5	0.587	INTERGENIC
3L	14642130	3L_14642130_INS [dm3] 3L_14649030_INS [dm6]	T	TTGT	2.320e^-5	0.6	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3L	15737816	3L_15737816_SNP [dm3] 3L_15744716_SNP [dm6]	A	T	2.420e^-5	0.617	INTERGENIC
3R	13588248	3R_13588248_SNP [dm3] 3R_17762526_SNP [dm6]	G	A	2.506e^-5	0.622	UTR_5_PRIME TyrR UPSTREAM TyrR
X	6396781	X_6396781_SNP [dm3] X_6502748_SNP [dm6]	A	T	2.513e^-5	0.622	INTRON CG42340
3L	9088629	3L_9088629_SNP [dm3] 3L_9095529_SNP [dm6]	C	G	2.620e^-5	0.64	DOWNSTREAM CG32032 INTERGENIC
X	3911227	X_3911227_SNP [dm3] X_4017194_SNP [dm6]	A	T	2.667e^-5	0.641	INTERGENIC
3R	25365840	3R_25365840_SNP [dm3] 3R_29540118_SNP [dm6]	T	C	2.699e^-5	0.641	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3L	1605240	3L_1605240_SNP [dm3] 3L_1605240_SNP [dm6]	A	C	2.819e^-5	0.661	SYNONYMOUS_CODING CG33791 UTR_3_PRIME CG18170
3R	13626819	3R_13626819_SNP [dm3] 3R_17801097_SNP [dm6]	G	T	2.894e^-5	0.663	DOWNSTREAM CG17806 INTRON CG17803
3L	9088625	3L_9088625_SNP [dm3] 3L_9095525_SNP [dm6]	C	T	2.903e^-5	0.663	DOWNSTREAM CG32032 INTERGENIC
3L	2622009	3L_2622009_SNP [dm3] 3L_2622009_SNP [dm6]	A	T	3.151e^-5	0.71	INTRON Pxn
2R	6452247	2R_6452247_SNP [dm3] 2R_10564742_SNP [dm6]	C	T	3.262e^-5	0.726	INTRON psq	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_HSA
2L	6887132	2L_6887132_SNP [dm3] 2L_6887132_SNP [dm6]	A	G	3.427e^-5	0.744	INTRON Nlg2
2L	6887142	2L_6887142_SNP [dm3] 2L_6887142_SNP [dm6]	A	C	3.427e^-5	0.744	INTRON Nlg2
3L	8246620	3L_8246620_SNP [dm3] 3L_8253520_SNP [dm6]	A	T	3.470e^-5	0.744	INTRON Dscam4
3L	1629983	3L_1629983_SNP [dm3] 3L_1629983_SNP [dm6]	T	C	3.565e^-5	0.755	UPSTREAM GC DOWNSTREAM nSyb INTERGENIC	TF binding site mE1_TFBS_chinmo
2L	14352150	2L_14352150_SNP [dm3] 2L_14352150_SNP [dm6]	A	C	3.794e^-5	0.792	UTR_5_PRIME CG43052 UPSTREAM l_2_34Fc DOWNSTREAM l_2_34Fd
2L	4427843	2L_4427843_SNP [dm3] 2L_4427843_SNP [dm6]	G	A	4.056e^-5	0.792	INTRON CG15431
3L	19412520	3L_19412520_SNP [dm3] 3L_19419420_SNP [dm6]	G	A	4.062e^-5	0.792	INTERGENIC
3L	7061417	3L_7061417_SNP [dm3] 3L_7068317_SNP [dm6]	G	A	4.200e^-5	0.792	SYNONYMOUS_CODING CG32391 DOWNSTREAM CG14823 INTRON CG8641
3L	1383873	3L_1383873_SNP [dm3] 3L_1383873_SNP [dm6]	A	C	4.235e^-5	0.792	INTRON Ptp61F & 1 other	TF binding site mE1_TFBS_HSA
3L	16433660	3L_16433660_SNP [dm3] 3L_16440560_SNP [dm6]	A	C	4.401e^-5	0.792	INTRON CG33158 & 1 other
X	6804574	X_6804574_DEL [dm3] X_6910541_DEL [dm6]	TT	T	4.415e^-5	0.792	INTRON CG14431
2L	14359817	2L_14359817_SNP [dm3] 2L_14359817_SNP [dm6]	T	C	4.444e^-5	0.792	SYNONYMOUS_CODING Pgant35A EXON CR43463	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3R	9196104	3R_9196104_SNP [dm3] 3R_13370382_SNP [dm6]	G	A	4.461e^-5	0.792	SYNONYMOUS_CODING Lip3 DOWNSTREAM CheA87a
X	20530232	X_20530232_SNP [dm3] X_20659205_SNP [dm6]	A	G	4.483e^-5	0.792	INTRON Cyp6v1
2L	6887031	2L_6887031_SNP [dm3] 2L_6887031_SNP [dm6]	A	T	4.492e^-5	0.792	INTRON Nlg2	TF binding site BDTNP1_TFBS_twi
2L	6887035	2L_6887035_SNP [dm3] 2L_6887035_SNP [dm6]	C	T	4.492e^-5	0.792	INTRON Nlg2	TF binding site BDTNP1_TFBS_twi
2L	6887070	2L_6887070_SNP [dm3] 2L_6887070_SNP [dm6]	A	G	4.492e^-5	0.792	INTRON Nlg2
3L	14642827	3L_14642827_SNP [dm3] 3L_14649727_SNP [dm6]	G	T	4.521e^-5	0.792	INTRON dlp	TF binding site BDTNP1_TFBS_prd mE1_TFBS_HSA
3R	12384171	3R_12384171_SNP [dm3] 3R_16558449_SNP [dm6]	C	T	4.539e^-5	0.792	INTRON CG42342
2L	1460951	2L_1460951_SNP [dm3] 2L_1460951_SNP [dm6]	T	A	4.624e^-5	0.792	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cnc mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens
3L	17335883	3L_17335883_SNP [dm3] 3L_17342783_SNP [dm6]	G	A	4.700e^-5	0.792	INTRON brv2

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By genomic position
Variant impact
Gene name

daughters1 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results