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=2.640e^-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
No significant result.

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1304 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	1068382	2L_1068382_SNP [dm3] 2L_1068382_SNP [dm6]	G	A	1.256e^-6	0.896	INTRON S	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_kni BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_eve mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3L	13541893	3L_13541893_INS [dm3] 3L_13548793_INS [dm6]	C	CGGACAC	1.621e^-6	0.896	INTRON bru-3
X	18249664	X_18249664_INS [dm3] X_18355631_INS [dm6]	G	GTAGGCGG	2.843e^-6	0.896	INTRON CG6123
2R	13993156	2R_13993156_SNP [dm3] 2R_18105651_SNP [dm6]	T	G	4.815e^-6	0.896	INTRON CG5756
X	2730005	X_2730005_SNP [dm3] X_2835972_SNP [dm6]	T	C	4.832e^-6	0.896	INTRON kirre
3R	927064	3R_927064_SNP [dm3] 3R_5101342_SNP [dm6]	G	T	7.720e^-6	0.896	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	11253610	3L_11253610_SNP [dm3] 3L_11260510_SNP [dm6]	C	T	7.797e^-6	0.896	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_zfh1
3R	25365859	3R_25365859_SNP [dm3] 3R_29540137_SNP [dm6]	T	A	9.235e^-6	0.896	INTERGENIC	TF binding site BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
X	20530232	X_20530232_SNP [dm3] X_20659205_SNP [dm6]	A	G	1.020e^-5	0.896	INTRON Cyp6v1
2L	13983795	2L_13983795_SNP [dm3] 2L_13983795_SNP [dm6]	T	G	1.086e^-5	0.896	SPLICE_SITE_REGION rk DOWNSTREAM NimC2 INTRON rk	TF binding site mE1_TFBS_chinmo
2R	20188889	2R_20188889_SNP [dm3] 2R_24301366_SNP [dm6]	T	G	1.297e^-5	0.896	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	15343672	2L_15343672_DEL [dm3] 2L_15343672_DEL [dm6]	AAAT	A	1.338e^-5	0.896	INTERGENIC
2L	15343677	2L_15343677_SNP [dm3] 2L_15343677_SNP [dm6]	A	T	1.338e^-5	0.896	INTERGENIC
2L	15343679	2L_15343679_SNP [dm3] 2L_15343679_SNP [dm6]	T	C	1.338e^-5	0.896	INTERGENIC
2L	15343680	2L_15343680_SNP [dm3] 2L_15343680_SNP [dm6]	T	A	1.338e^-5	0.896	INTERGENIC
2L	15343689	2L_15343689_SNP [dm3] 2L_15343689_SNP [dm6]	T	A	1.338e^-5	0.896	INTERGENIC
3R	10603796	3R_10603796_SNP [dm3] 3R_14778074_SNP [dm6]	C	T	1.577e^-5	0.896	INTRON jvl
3R	9151822	3R_9151822_SNP [dm3] 3R_13326100_SNP [dm6]	T	C	1.667e^-5	0.896	INTERGENIC
X	20530224	X_20530224_SNP [dm3] X_20659197_SNP [dm6]	A	G	1.706e^-5	0.896	INTRON Cyp6v1
3R	14423644	3R_14423644_SNP [dm3] 3R_18597922_SNP [dm6]	G	C	1.877e^-5	0.896	UPSTREAM CG14305 INTRON qin & 1 other	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	1051015	2L_1051015_SNP [dm3] 2L_1051015_SNP [dm6]	T	A	1.970e^-5	0.896	UTR_3_PRIME S DOWNSTREAM S
2L	1650899	2L_1650899_DEL [dm3] 2L_1650899_DEL [dm6]	CC	C	2.129e^-5	0.896	UPSTREAM chinmo INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
2L	15343669	2L_15343669_SNP [dm3] 2L_15343669_SNP [dm6]	A	T	2.190e^-5	0.896	INTERGENIC
2L	15343684	2L_15343684_MNP [dm3] 2L_15343684_MNP [dm6]	GTT	ACA	2.190e^-5	0.896	INTERGENIC
2L	15343691	2L_15343691_DEL [dm3] 2L_15343691_DEL [dm6]	CAC	A	2.190e^-5	0.896	INTERGENIC
2L	1050940	2L_1050940_SNP [dm3] 2L_1050940_SNP [dm6]	G	T	2.217e^-5	0.896	UTR_3_PRIME S DOWNSTREAM S
2L	1050942	2L_1050942_SNP [dm3] 2L_1050942_SNP [dm6]	A	T	2.217e^-5	0.896	UTR_3_PRIME S DOWNSTREAM S
X	17167501	X_17167501_SNP [dm3] X_17273468_SNP [dm6]	A	G	2.291e^-5	0.896	INTRON f	TF binding site mE1_TFBS_cad
3L	14642070	3L_14642070_SNP [dm3] 3L_14648970_SNP [dm6]	C	T	2.568e^-5	0.896	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3L	14642095	3L_14642095_SNP [dm3] 3L_14648995_SNP [dm6]	T	A	2.568e^-5	0.896	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3L	14642098	3L_14642098_SNP [dm3] 3L_14648998_SNP [dm6]	A	T	2.568e^-5	0.896	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3L	14642110	3L_14642110_SNP [dm3] 3L_14649010_SNP [dm6]	T	C	2.568e^-5	0.896	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3R	11618443	3R_11618443_SNP [dm3] 3R_15792721_SNP [dm6]	A	G	2.613e^-5	0.896	UTR_5_PRIME Acyp2 UPSTREAM c_3_G	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_Ubx
3L	2627277	3L_2627277_SNP [dm3] 3L_2627277_SNP [dm6]	A	G	2.636e^-5	0.896	INTRON Pxn
3L	11513577	3L_11513577_DEL [dm3] 3L_11520477_DEL [dm6]	TTTATT	T	2.765e^-5	0.896	DOWNSTREAM CG11714 INTRON Fuca
X	20534979	X_20534979_INS [dm3] X_20663952_INS [dm6]	G	GGTCG	2.824e^-5	0.896	INTRON CG1835	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Kr
2L	13321376	2L_13321376_SNP [dm3] 2L_13321376_SNP [dm6]	A	T	2.971e^-5	0.896	INTRON CG43778
2L	12807907	2L_12807907_SNP [dm3] 2L_12807907_SNP [dm6]	A	G	3.031e^-5	0.896	EXON CR43818
3L	2998162	3L_2998162_SNP [dm3] 3L_2998162_SNP [dm6]	A	T	3.206e^-5	0.896	INTERGENIC
3L	14642039	3L_14642039_SNP [dm3] 3L_14648939_SNP [dm6]	T	G	3.431e^-5	0.896	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3L	14642051	3L_14642051_SNP [dm3] 3L_14648951_SNP [dm6]	T	C	3.431e^-5	0.896	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3R	24366641	3R_24366641_SNP [dm3] 3R_28540919_SNP [dm6]	G	A	3.573e^-5	0.896	UPSTREAM Ppn INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	12290341	3L_12290341_INS [dm3] 3L_12297241_INS [dm6]	T	TCCCAGTCCACTTT...	3.597e^-5	0.896	INTERGENIC
2L	11361516	2L_11361516_SNP [dm3] 2L_11361516_SNP [dm6]	T	C	3.708e^-5	0.896	INTRON salr	regulatory region REDfly_CRMs
3L	14642109	3L_14642109_SNP [dm3] 3L_14649009_SNP [dm6]	A	T	3.866e^-5	0.896	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3L	14642171	3L_14642171_SNP [dm3] 3L_14649071_SNP [dm6]	A	T	3.892e^-5	0.896	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
2L	9585406	2L_9585406_SNP [dm3] 2L_9585406_SNP [dm6]	C	G	3.894e^-5	0.896	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
2L	7944635	2L_7944635_SNP [dm3] 2L_7944635_SNP [dm6]	C	T	4.139e^-5	0.896	INTRON Snoo
3L	14642038	3L_14642038_SNP [dm3] 3L_14648938_SNP [dm6]	T	A	4.139e^-5	0.896	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
X	20529187	X_20529187_SNP [dm3] X_20658160_SNP [dm6]	T	C	4.249e^-5	0.896	UTR_5_PRIME Cyp6v1 UPSTREAM CR45466
X	20528986	X_20528986_SNP [dm3] X_20657959_SNP [dm6]	G	C	4.432e^-5	0.896	UTR_5_PRIME Cyp6v1 UPSTREAM CR45466
3R	9751978	3R_9751978_SNP [dm3] 3R_13926256_SNP [dm6]	A	G	4.473e^-5	0.896	INTERGENIC
2R	2463585	2R_2463585_SNP [dm3] 2R_6576080_SNP [dm6]	C	A	4.481e^-5	0.896	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
3L	10219833	3L_10219833_SNP [dm3] 3L_10226733_SNP [dm6]	A	C	4.591e^-5	0.896	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	10219855	3L_10219855_SNP [dm3] 3L_10226755_SNP [dm6]	G	T	4.591e^-5	0.896	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	25365840	3R_25365840_SNP [dm3] 3R_29540118_SNP [dm6]	T	C	4.633e^-5	0.896	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3L	14642055	3L_14642055_SNP [dm3] 3L_14648955_SNP [dm6]	A	T	4.827e^-5	0.896	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3L	14642058	3L_14642058_SNP [dm3] 3L_14648958_SNP [dm6]	G	A	4.827e^-5	0.896	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3L	14642078	3L_14642078_MNP [dm3] 3L_14648978_MNP [dm6]	GGG	AAA	4.827e^-5	0.896	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3L	3039454	3L_3039454_SNP [dm3] 3L_3039454_SNP [dm6]	T	C	4.871e^-5	0.896	SYNONYMOUS_CODING CG2162	TF binding site BDTNP1_TFBS_dl mE1_TFBS_sens
2L	3714053	2L_3714053_SNP [dm3] 2L_3714053_SNP [dm6]	G	C	4.892e^-5	0.896	UPSTREAM CG31955 & 1 other INTRON CG2818	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
3R	24477152	3R_24477152_SNP [dm3] 3R_28651430_SNP [dm6]	G	A	4.939e^-5	0.896	UPSTREAM CG31050 INTERGENIC
3R	24477187	3R_24477187_SNP [dm3] 3R_28651465_SNP [dm6]	A	T	4.939e^-5	0.896	UPSTREAM CG31050 INTERGENIC
3R	24477204	3R_24477204_SNP [dm3] 3R_28651482_SNP [dm6]	T	A	4.939e^-5	0.896	INTERGENIC
3R	24477211	3R_24477211_SNP [dm3] 3R_28651489_SNP [dm6]	T	A	4.939e^-5	0.896	INTERGENIC
3R	24477212	3R_24477212_SNP [dm3] 3R_28651490_SNP [dm6]	C	T	4.939e^-5	0.896	INTERGENIC
2R	6379235	2R_6379235_SNP [dm3] 2R_10491730_SNP [dm6]	C	T	4.993e^-5	0.896	UTR_3_PRIME lola INTRON lola
2R	6508001	2R_6508001_SNP [dm3] 2R_10620496_SNP [dm6]	A	C	4.993e^-5	0.896	INTRON CG11883
3R	12048597	3R_12048597_SNP [dm3] 3R_16222875_SNP [dm6]	C	G	5.026e^-5	0.896	UPSTREAM CR45643 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl mE1_TFBS_zfh1
3L	9088728	3L_9088728_SNP [dm3] 3L_9095628_SNP [dm6]	C	T	5.044e^-5	0.896	DOWNSTREAM CG32032 INTERGENIC
X	16082234	X_16082234_SNP [dm3] X_16188201_SNP [dm6]	T	C	5.104e^-5	0.896	INTERGENIC	TF binding site mE1_TFBS_hkb mE1_TFBS_HSA
2L	1650910	2L_1650910_SNP [dm3] 2L_1650910_SNP [dm6]	G	A	5.321e^-5	0.896	UPSTREAM chinmo INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
2R	11471496	2R_11471496_SNP [dm3] 2R_15583991_SNP [dm6]	T	A	5.347e^-5	0.896	INTERGENIC
3R	14423609	3R_14423609_SNP [dm3] 3R_18597887_SNP [dm6]	T	G	5.373e^-5	0.896	UPSTREAM CG14305 INTRON qin & 1 other	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	14642063	3L_14642063_SNP [dm3] 3L_14648963_SNP [dm6]	T	G	5.863e^-5	0.896	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
2R	12408082	2R_12408082_SNP [dm3] 2R_16520577_SNP [dm6]	T	G	5.885e^-5	0.896	INTRON Sema-2a	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi
3R	11618479	3R_11618479_SNP [dm3] 3R_15792757_SNP [dm6]	G	C	6.095e^-5	0.896	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
3L	957055	3L_957055_SNP [dm3] 3L_957055_SNP [dm6]	A	G	6.121e^-5	0.896	INTRON Glut1
X	20529036	X_20529036_SNP [dm3] X_20658009_SNP [dm6]	G	T	6.377e^-5	0.896	UTR_5_PRIME Cyp6v1 UPSTREAM CR45466
3L	14642089	3L_14642089_SNP [dm3] 3L_14648989_SNP [dm6]	A	T	6.437e^-5	0.896	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3L	970831	3L_970831_SNP [dm3] 3L_970831_SNP [dm6]	A	G	6.450e^-5	0.896	INTRON Glut1
3R	25024503	3R_25024503_SNP [dm3] 3R_29198781_SNP [dm6]	G	A	6.519e^-5	0.896	INTRON CG14515
X	5591823	X_5591823_SNP [dm3] X_5697790_SNP [dm6]	A	G	6.567e^-5	0.896	UPSTREAM CG4096 DOWNSTREAM CR42794 INTERGENIC	TF binding site BDTNP1_TFBS_dl
2R	12408099	2R_12408099_SNP [dm3] 2R_16520594_SNP [dm6]	C	T	6.648e^-5	0.896	INTRON Sema-2a	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi
2R	6508615	2R_6508615_SNP [dm3] 2R_10621110_SNP [dm6]	A	G	6.664e^-5	0.896	INTRON CG11883
3R	11140143	3R_11140143_SNP [dm3] 3R_15314421_SNP [dm6]	T	C	6.664e^-5	0.896	INTRON Tm2	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
X	21910607	X_21910607_SNP [dm3] X_22508771_SNP [dm6]	C	A	6.741e^-5	0.896	DOWNSTREAM l_1_G0196 INTERGENIC	TF binding site BDTNP1_TFBS_dl
X	20527032	X_20527032_SNP [dm3] X_20656005_SNP [dm6]	T	G	6.749e^-5	0.896	DOWNSTREAM CR45466 INTERGENIC	TF binding site BDTNP1_TFBS_dl
2L	11361515	2L_11361515_SNP [dm3] 2L_11361515_SNP [dm6]	A	G	6.751e^-5	0.896	INTRON salr	regulatory region REDfly_CRMs
2R	19685444	2R_19685444_SNP [dm3] 2R_23797921_SNP [dm6]	C	T	6.908e^-5	0.896	UTR_5_PRIME CG9850	TF binding site mE1_TFBS_HSA
3L	17925410	3L_17925410_SNP [dm3] 3L_17932310_SNP [dm6]	C	T	6.933e^-5	0.896	INTERGENIC
2L	11921294	2L_11921294_SNP [dm3] 2L_11921294_SNP [dm6]	T	C	7.009e^-5	0.896	INTRON Pde1c
2R	11059590	2R_11059590_SNP [dm3] 2R_15172085_SNP [dm6]	T	C	7.017e^-5	0.896	INTRON igl
2R	6508603	2R_6508603_SNP [dm3] 2R_10621098_SNP [dm6]	T	G	7.017e^-5	0.896	INTRON CG11883
3R	18357577	3R_18357577_SNP [dm3] 3R_22531855_SNP [dm6]	A	G	7.116e^-5	0.896	NON_SYNONYMOUS_CODING CG33093 DOWNSTREAM CG5326
X	9790622	X_9790622_SNP [dm3] X_9896589_SNP [dm6]	G	A	7.197e^-5	0.896	INTRON CG15249
3R	10604335	3R_10604335_SNP [dm3] 3R_14778613_SNP [dm6]	G	A	7.218e^-5	0.896	INTRON jvl
2L	7329612	2L_7329612_SNP [dm3] 2L_7329612_SNP [dm6]	C	G	7.473e^-5	0.896	UPSTREAM CR45304 INTERGENIC
2L	11920331	2L_11920331_SNP [dm3] 2L_11920331_SNP [dm6]	G	T	7.518e^-5	0.896	INTRON Pde1c
2L	11920411	2L_11920411_SNP [dm3] 2L_11920411_SNP [dm6]	T	C	7.518e^-5	0.896	INTRON Pde1c

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By genomic position
Variant impact
Gene name

daughtersTotal phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results