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=3.051e^-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	2.8192	0.0931

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1850 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
X	5806121	X_5806121_SNP [dm3] X_5912088_SNP [dm6]	C	T	8.257e^-7	0.921	DOWNSTREAM CG12236 & 1 other INTRON CG12236	TF binding site mE1_TFBS_Trl
X	21906166	X_21906166_SNP [dm3] X_22504330_SNP [dm6]	A	G	2.198e^-6	0.921	UTR_3_PRIME l_1_G0196 DOWNSTREAM l_1_G0196 INTRON l_1_G0196
2L	15093700	2L_15093700_SNP [dm3] 2L_15093700_SNP [dm6]	C	G	2.473e^-6	0.921	INTRON CG15270
2L	15093713	2L_15093713_SNP [dm3] 2L_15093713_SNP [dm6]	A	T	2.473e^-6	0.921	INTRON CG15270
3L	17296210	3L_17296210_SNP [dm3] 3L_17303110_SNP [dm6]	C	G	4.441e^-6	0.921	INTERGENIC
3L	1937583	3L_1937583_SNP [dm3] 3L_1937583_SNP [dm6]	G	A	4.459e^-6	0.921	INTRON CG5687
2R	16400241	2R_16400241_SNP [dm3] 2R_20512736_SNP [dm6]	G	T	4.916e^-6	0.921	UTR_3_PRIME CG13426 DOWNSTREAM CR44649
3R	10956114	3R_10956114_DEL [dm3] 3R_15130392_DEL [dm6]	AT	C	5.799e^-6	0.921	DOWNSTREAM mir-2493 INTRON CG42788
X	5019812	X_5019812_SNP [dm3] X_5125779_SNP [dm6]	A	C	7.038e^-6	0.921	INTRON rg & 1 other
3L	14151102	3L_14151102_SNP [dm3] 3L_14158002_SNP [dm6]	T	A	7.585e^-6	0.921	INTERGENIC	regulatory region REDfly_CRMs
2L	772437	2L_772437_SNP [dm3] 2L_772437_SNP [dm6]	C	T	8.196e^-6	0.921	UPSTREAM CR44614 INTERGENIC
X	6786988	X_6786988_SNP [dm3] X_6892955_SNP [dm6]	T	G	8.828e^-6	0.921	INTERGENIC
3L	9087349	3L_9087349_SNP [dm3] 3L_9094249_SNP [dm6]	A	T	9.968e^-6	0.921	INTRON CG32032
3L	2669602	3L_2669602_SNP [dm3] 3L_2669602_SNP [dm6]	A	G	1.025e^-5	0.921	INTRON Fife
2R	20206041	2R_20206041_SNP [dm3] 2R_24318518_SNP [dm6]	G	T	1.030e^-5	0.921	INTERGENIC
2L	769955	2L_769955_SNP [dm3] 2L_769955_SNP [dm6]	A	T	1.128e^-5	0.921	INTERGENIC
2R	10348270	2R_10348270_SNP [dm3] 2R_14460765_SNP [dm6]	A	G	1.219e^-5	0.921	INTRON Oaz	TF binding site mE1_TFBS_cad
2L	3816876	2L_3816876_SNP [dm3] 2L_3816876_SNP [dm6]	T	C	1.284e^-5	0.921	UPSTREAM CR44077 DOWNSTREAM CR44076 INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_hb BDTNP1_TFBS_twi
X	18806907	X_18806907_SNP [dm3] X_18912874_SNP [dm6]	G	A	1.358e^-5	0.921	DOWNSTREAM CR44708 INTERGENIC
3R	15093894	3R_15093894_SNP [dm3] 3R_19268172_SNP [dm6]	T	C	1.377e^-5	0.921	INTERGENIC
2L	16222318	2L_16222318_SNP [dm3] 2L_16222318_SNP [dm6]	A	G	1.445e^-5	0.921	INTERGENIC
2R	12407045	2R_12407045_SNP [dm3] 2R_16519540_SNP [dm6]	C	A	1.466e^-5	0.921	INTRON Sema-2a	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv
2L	4460926	2L_4460926_SNP [dm3] 2L_4460926_SNP [dm6]	T	G	1.569e^-5	0.921	SYNONYMOUS_CODING CG15435 DOWNSTREAM CG15443	TF binding site mE1_TFBS_sens
2L	769970	2L_769970_SNP [dm3] 2L_769970_SNP [dm6]	A	G	1.600e^-5	0.921	INTERGENIC
2R	20209968	2R_20209968_SNP [dm3] 2R_24322445_SNP [dm6]	T	A	1.601e^-5	0.921	INTERGENIC
2L	769925	2L_769925_SNP [dm3] 2L_769925_SNP [dm6]	C	T	1.662e^-5	0.921	INTERGENIC
2L	769928	2L_769928_SNP [dm3] 2L_769928_SNP [dm6]	A	G	1.662e^-5	0.921	INTERGENIC
2L	769946	2L_769946_SNP [dm3] 2L_769946_SNP [dm6]	A	C	1.662e^-5	0.921	INTERGENIC
2L	769951	2L_769951_SNP [dm3] 2L_769951_SNP [dm6]	T	A	1.662e^-5	0.921	INTERGENIC
2L	769958	2L_769958_SNP [dm3] 2L_769958_SNP [dm6]	G	T	1.662e^-5	0.921	INTERGENIC
3L	7771687	3L_7771687_SNP [dm3] 3L_7778587_SNP [dm6]	C	T	1.779e^-5	0.921	SYNONYMOUS_CODING CG32369	TF binding site mE1_TFBS_chinmo
2L	3815753	2L_3815753_SNP [dm3] 2L_3815753_SNP [dm6]	G	A	1.936e^-5	0.921	EXON CR44076	regulatory region REDfly_CRMs
3L	1937584	3L_1937584_SNP [dm3] 3L_1937584_SNP [dm6]	A	G	2.030e^-5	0.921	INTRON CG5687
X	14260616	X_14260616_SNP [dm3] X_14366583_SNP [dm6]	A	T	2.123e^-5	0.921	INTRON dpr8
3R	11612115	3R_11612115_SNP [dm3] 3R_15786393_SNP [dm6]	T	C	2.203e^-5	0.921	UPSTREAM CG9590 INTERGENIC
2R	20210450	2R_20210450_INS [dm3] 2R_24322927_INS [dm6]	T	TT	2.204e^-5	0.921	INTERGENIC	TF binding site mE1_TFBS_inv
3L	9046152	3L_9046152_SNP [dm3] 3L_9053052_SNP [dm6]	C	T	2.243e^-5	0.921	INTRON Argk	TF binding site mE1_TFBS_HSA
2R	20209952	2R_20209952_SNP [dm3] 2R_24322429_SNP [dm6]	G	A	2.254e^-5	0.921	INTERGENIC
X	14260187	X_14260187_SNP [dm3] X_14366154_SNP [dm6]	A	G	2.344e^-5	0.921	INTRON dpr8
2L	6730043	2L_6730043_SNP [dm3] 2L_6730043_SNP [dm6]	A	G	2.347e^-5	0.921	SPLICE_SITE_REGION Liprin-alpha INTRON Liprin-alpha
2L	7785317	2L_7785317_SNP [dm3] 2L_7785317_SNP [dm6]	G	A	2.378e^-5	0.921	NON_SYNONYMOUS_CODING CG7154 DOWNSTREAM CG7149	TF binding site mE1_TFBS_cad mE1_TFBS_sens
X	10809083	X_10809083_SNP [dm3] X_10915050_SNP [dm6]	G	A	2.642e^-5	0.921	INTRON CG43901
3L	18166679	3L_18166679_SNP [dm3] 3L_18173579_SNP [dm6]	T	C	2.799e^-5	0.921	INTRON W	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	7835242	3L_7835242_SNP [dm3] 3L_7842142_SNP [dm6]	A	T	2.806e^-5	0.921	INTRON Pdp1	regulatory region REDfly_CRMs TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2L	17545065	2L_17545065_SNP [dm3] 2L_17545065_SNP [dm6]	A	T	2.983e^-5	0.921	INTERGENIC
3L	18168486	3L_18168486_SNP [dm3] 3L_18175386_SNP [dm6]	T	A	3.011e^-5	0.921	INTRON W	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	15971164	3R_15971164_SNP [dm3] 3R_20145442_SNP [dm6]	A	G	3.130e^-5	0.921	INTERGENIC
2L	2782693	2L_2782693_SNP [dm3] 2L_2782693_SNP [dm6]	A	G	3.310e^-5	0.921	UTR_3_PRIME Syt1
2L	1364571	2L_1364571_SNP [dm3] 2L_1364571_SNP [dm6]	C	T	3.358e^-5	0.921	INTERGENIC
2L	1364502	2L_1364502_INS [dm3] 2L_1364502_INS [dm6]	T	TGCTGT	3.504e^-5	0.921	INTERGENIC
2R	7075296	2R_7075296_SNP [dm3] 2R_11187791_SNP [dm6]	G	C	3.929e^-5	0.921	INTRON shn	TF binding site BDTNP1_TFBS_twi
3R	17186726	3R_17186726_SNP [dm3] 3R_21361004_SNP [dm6]	C	A	4.035e^-5	0.921	SYNONYMOUS_CODING pre-mod_mdg4_-T UTR_5_PRIME pre-mod_mdg4_-Z INTRON mod_mdg4_
X	18807060	X_18807060_SNP [dm3] X_18913027_SNP [dm6]	A	G	4.068e^-5	0.921	DOWNSTREAM CR44708 INTERGENIC
3L	2657947	3L_2657947_SNP [dm3] 3L_2657947_SNP [dm6]	T	C	4.080e^-5	0.921	INTRON Fife	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_ftz BDTNP1_TFBS_Med BDTNP1_TFBS_prd mE1_TFBS_chinmo mE1_TFBS_HSA
2L	3122711	2L_3122711_SNP [dm3] 2L_3122711_SNP [dm6]	A	C	4.237e^-5	0.921	INTRON toc
2L	1055199	2L_1055199_SNP [dm3] 2L_1055199_SNP [dm6]	C	T	4.261e^-5	0.921	INTRON S	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
X	15502775	X_15502775_DEL [dm3] X_15608742_DEL [dm6]	AC	A	4.309e^-5	0.921	INTRON sog	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3L	7834801	3L_7834801_SNP [dm3] 3L_7841701_SNP [dm6]	G	A	4.567e^-5	0.921	INTRON Pdp1	regulatory region REDfly_CRMs TF binding site mE1_TFBS_cad
X	18806982	X_18806982_SNP [dm3] X_18912949_SNP [dm6]	C	A	4.727e^-5	0.921	DOWNSTREAM CR44708 INTERGENIC
2R	13923938	2R_13923938_SNP [dm3] 2R_18036433_SNP [dm6]	C	T	4.736e^-5	0.921	INTERGENIC
2L	17533554	2L_17533554_SNP [dm3] 2L_17533554_SNP [dm6]	A	G	4.814e^-5	0.921	INTERGENIC
3R	16891998	3R_16891998_SNP [dm3] 3R_21066276_SNP [dm6]	T	A	4.860e^-5	0.921	INTRON AnxB9	TF binding site mE1_TFBS_Trl
2R	10893903	2R_10893903_SNP [dm3] 2R_15006398_SNP [dm6]	A	G	4.870e^-5	0.921	INTERGENIC
2L	12575800	2L_12575800_SNP [dm3] 2L_12575800_SNP [dm6]	G	A	5.037e^-5	0.921	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Kr
X	21906190	X_21906190_SNP [dm3] X_22504354_SNP [dm6]	A	T	5.059e^-5	0.921	UTR_3_PRIME l_1_G0196 DOWNSTREAM l_1_G0196 INTRON l_1_G0196
2R	16115203	2R_16115203_SNP [dm3] 2R_20227698_SNP [dm6]	T	A	5.357e^-5	0.921	INTERGENIC
2L	3815739	2L_3815739_SNP [dm3] 2L_3815739_SNP [dm6]	C	G	5.382e^-5	0.921	EXON CR44076	regulatory region REDfly_CRMs
3L	3039454	3L_3039454_SNP [dm3] 3L_3039454_SNP [dm6]	T	C	5.436e^-5	0.921	SYNONYMOUS_CODING CG2162	TF binding site BDTNP1_TFBS_dl mE1_TFBS_sens
3L	12969385	3L_12969385_SNP [dm3] 3L_12976285_SNP [dm6]	A	T	5.553e^-5	0.921	INTERGENIC
X	10021062	X_10021062_SNP [dm3] X_10127029_SNP [dm6]	A	C	5.613e^-5	0.921	INTRON CR44894 & 1 other
3R	9151836	3R_9151836_SNP [dm3] 3R_13326114_SNP [dm6]	A	G	5.637e^-5	0.921	INTERGENIC
2L	2125859	2L_2125859_SNP [dm3] 2L_2125859_SNP [dm6]	G	T	5.670e^-5	0.921	INTERGENIC
3L	3147910	3L_3147910_SNP [dm3] 3L_3147910_SNP [dm6]	G	A	5.699e^-5	0.921	SYNONYMOUS_CODING CG12082 UPSTREAM BtbVII	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_sens
2L	15021856	2L_15021856_SNP [dm3] 2L_15021856_SNP [dm6]	C	T	5.737e^-5	0.921	INTRON GABA-B-R1
2L	1364507	2L_1364507_SNP [dm3] 2L_1364507_SNP [dm6]	G	C	5.789e^-5	0.921	INTERGENIC
2L	1364682	2L_1364682_SNP [dm3] 2L_1364682_SNP [dm6]	C	A	5.789e^-5	0.921	INTERGENIC
2L	1364687	2L_1364687_SNP [dm3] 2L_1364687_SNP [dm6]	C	A	5.789e^-5	0.921	INTERGENIC
3R	15971158	3R_15971158_SNP [dm3] 3R_20145436_SNP [dm6]	A	T	5.851e^-5	0.921	INTERGENIC
3R	16892077	3R_16892077_SNP [dm3] 3R_21066355_SNP [dm6]	C	G	5.861e^-5	0.921	INTRON AnxB9	TF binding site mE1_TFBS_Trl
X	7514597	X_7514597_SNP [dm3] X_7620564_SNP [dm6]	C	T	5.947e^-5	0.921	INTRON ct	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	15327816	2R_15327816_SNP [dm3] 2R_19440311_SNP [dm6]	T	C	6.011e^-5	0.921	SYNONYMOUS_CODING Spt5	TF binding site mE1_TFBS_sens
3L	10895087	3L_10895087_INS [dm3] 3L_10901987_INS [dm6]	C	CTATAGATTCA...	6.049e^-5	0.921	INTERGENIC
X	11076656	X_11076656_SNP [dm3] X_11182623_SNP [dm6]	T	A	6.082e^-5	0.921	UPSTREAM CG15200 INTERGENIC
2L	1364487	2L_1364487_SNP [dm3] 2L_1364487_SNP [dm6]	C	T	6.191e^-5	0.921	INTERGENIC
3L	3171832	3L_3171832_SNP [dm3] 3L_3171832_SNP [dm6]	C	G	6.336e^-5	0.921	NON_SYNONYMOUS_CODING CG14963 DOWNSTREAM CG32281 & 2 others
3R	13485692	3R_13485692_SNP [dm3] 3R_17659970_SNP [dm6]	C	A	6.496e^-5	0.921	INTRON CG14322
2R	18845660	2R_18845660_SNP [dm3] 2R_22958137_SNP [dm6]	A	C	6.537e^-5	0.921	UPSTREAM CR44780 INTERGENIC
2L	7911801	2L_7911801_SNP [dm3] 2L_7911801_SNP [dm6]	C	T	6.543e^-5	0.921	INTRON Snoo
3L	6586109	3L_6586109_SNP [dm3] 3L_6593009_SNP [dm6]	A	T	6.616e^-5	0.921	UTR_3_PRIME CG18769 DOWNSTREAM CG18769 & 1 other	transposable element FlyBase
X	20528986	X_20528986_SNP [dm3] X_20657959_SNP [dm6]	G	C	6.680e^-5	0.921	UTR_5_PRIME Cyp6v1 UPSTREAM CR45466
2L	3629942	2L_3629942_SNP [dm3] 2L_3629942_SNP [dm6]	C	T	6.687e^-5	0.921	INTRON for
X	19224666	X_19224666_SNP [dm3] X_19330633_SNP [dm6]	G	A	6.802e^-5	0.921	INTRON nAChRalpha7	transposable element FlyBase
2L	15114292	2L_15114292_SNP [dm3] 2L_15114292_SNP [dm6]	C	T	6.805e^-5	0.921	SPLICE_SITE_REGION stc INTRON stc	TF binding site BDTNP1_TFBS_dl mE1_TFBS_sens
2L	6244360	2L_6244360_SNP [dm3] 2L_6244360_SNP [dm6]	T	A	6.853e^-5	0.921	INTERGENIC
3L	4740113	3L_4740113_SNP [dm3] 3L_4740113_SNP [dm6]	G	T	6.876e^-5	0.921	INTRON RhoGEF64C	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
X	14302410	X_14302410_SNP [dm3] X_14408377_SNP [dm6]	A	T	6.876e^-5	0.921	INTRON dpr8
X	5554035	X_5554035_SNP [dm3] X_5660002_SNP [dm6]	A	C	6.974e^-5	0.921	INTRON CG42265
3L	10184720	3L_10184720_SNP [dm3] 3L_10191620_SNP [dm6]	A	G	7.116e^-5	0.921	SYNONYMOUS_CODING ect
3R	9610534	3R_9610534_SNP [dm3] 3R_13784812_SNP [dm6]	C	T	7.248e^-5	0.921	SYNONYMOUS_CODING Dip-B DOWNSTREAM CR45590	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
X	12237355	X_12237355_SNP [dm3] X_12343322_SNP [dm6]	G	A	7.268e^-5	0.921	INTERGENIC

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By genomic position
Variant impact
Gene name

Larvae phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results