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=7.640e^-4)
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
wolba	3.3893	0.0656

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1878 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	12281534	3L_12281534_SNP [dm3] 3L_12288434_SNP [dm6]	G	A	7.859e^-7	0.535	DOWNSTREAM CR45658 INTERGENIC	TF binding site BDTNP1_TFBS_twi
3L	12281536	3L_12281536_SNP [dm3] 3L_12288436_SNP [dm6]	A	G	7.859e^-7	0.535	DOWNSTREAM CR45658 INTERGENIC	TF binding site BDTNP1_TFBS_twi
3L	6224210	3L_6224210_SNP [dm3] 3L_6231110_SNP [dm6]	G	A	3.243e^-6	0.535	DOWNSTREAM CG13299 INTERGENIC
3R	13895519	3R_13895519_SNP [dm3] 3R_18069797_SNP [dm6]	C	T	3.310e^-6	0.535	INTERGENIC
3L	12277874	3L_12277874_SNP [dm3] 3L_12284774_SNP [dm6]	G	T	4.080e^-6	0.535	INTERGENIC
3R	13895471	3R_13895471_SNP [dm3] 3R_18069749_SNP [dm6]	T	A	4.450e^-6	0.535	INTERGENIC
X	11152349	X_11152349_SNP [dm3] X_11258316_SNP [dm6]	T	G	5.060e^-6	0.535	INTRON CG44422
2L	16937946	2L_16937946_SNP [dm3] 2L_16937946_SNP [dm6]	C	A	7.341e^-6	0.535	INTERGENIC
X	18401895	X_18401895_SNP [dm3] X_18507862_SNP [dm6]	G	A	7.964e^-6	0.535	SYNONYMOUS_CODING Ggt-1	TF binding site BDTNP1_TFBS_sna mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
X	2877161	X_2877161_SNP [dm3] X_2983128_SNP [dm6]	A	T	8.249e^-6	0.535	INTRON kirre	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_Trl
3L	8759370	3L_8759370_SNP [dm3] 3L_8766270_SNP [dm6]	T	C	8.392e^-6	0.535	UPSTREAM Fhos INTRON Fhos	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
3L	4487449	3L_4487449_SNP [dm3] 3L_4487449_SNP [dm6]	T	G	8.435e^-6	0.535	SYNONYMOUS_CODING CG13722
3L	8759403	3L_8759403_SNP [dm3] 3L_8766303_SNP [dm6]	C	G	8.803e^-6	0.535	UPSTREAM Fhos INTRON Fhos	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
3L	8752483	3L_8752483_SNP [dm3] 3L_8759383_SNP [dm6]	T	G	9.209e^-6	0.535	SPLICE_SITE_REGION Fhos INTRON Fhos
3L	8752504	3L_8752504_SNP [dm3] 3L_8759404_SNP [dm6]	A	C	9.209e^-6	0.535	INTRON Fhos
X	2877195	X_2877195_SNP [dm3] X_2983162_SNP [dm6]	T	C	9.356e^-6	0.535	INTRON kirre	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_Trl
2R	18022014	2R_18022014_SNP [dm3] 2R_22134509_SNP [dm6]	G	A	1.050e^-5	0.535	INTERGENIC
3L	7991987	3L_7991987_SNP [dm3] 3L_7998887_SNP [dm6]	C	A	1.080e^-5	0.535	INTRON nmo
3L	8754057	3L_8754057_SNP [dm3] 3L_8760957_SNP [dm6]	T	C	1.118e^-5	0.535	SYNONYMOUS_CODING Fhos UPSTREAM Fhos
3L	8752611	3L_8752611_SNP [dm3] 3L_8759511_SNP [dm6]	C	T	1.133e^-5	0.535	SYNONYMOUS_CODING Fhos
3L	8760238	3L_8760238_SNP [dm3] 3L_8767138_SNP [dm6]	G	C	1.133e^-5	0.535	INTRON Fhos	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3L	8760309	3L_8760309_SNP [dm3] 3L_8767209_SNP [dm6]	C	A	1.133e^-5	0.535	INTRON Fhos	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3L	8760421	3L_8760421_SNP [dm3] 3L_8767321_SNP [dm6]	G	A	1.133e^-5	0.535	INTRON Fhos	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
3L	8755197	3L_8755197_SNP [dm3] 3L_8762097_SNP [dm6]	C	A	1.166e^-5	0.535	SYNONYMOUS_CODING Fhos	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv
3L	8756429	3L_8756429_SNP [dm3] 3L_8763329_SNP [dm6]	T	C	1.166e^-5	0.535	INTRON Fhos
3L	8756459	3L_8756459_SNP [dm3] 3L_8763359_SNP [dm6]	T	A	1.166e^-5	0.535	INTRON Fhos
3L	8756461	3L_8756461_SNP [dm3] 3L_8763361_SNP [dm6]	T	C	1.166e^-5	0.535	INTRON Fhos
3L	8756462	3L_8756462_SNP [dm3] 3L_8763362_SNP [dm6]	T	A	1.166e^-5	0.535	INTRON Fhos
3L	8756484	3L_8756484_SNP [dm3] 3L_8763384_SNP [dm6]	T	C	1.166e^-5	0.535	INTRON Fhos
3L	8756485	3L_8756485_SNP [dm3] 3L_8763385_SNP [dm6]	G	T	1.166e^-5	0.535	INTRON Fhos
3L	8756498	3L_8756498_SNP [dm3] 3L_8763398_SNP [dm6]	A	G	1.166e^-5	0.535	INTRON Fhos
3L	8756512	3L_8756512_SNP [dm3] 3L_8763412_SNP [dm6]	A	T	1.166e^-5	0.535	INTRON Fhos
3L	8758245	3L_8758245_SNP [dm3] 3L_8765145_SNP [dm6]	T	A	1.166e^-5	0.535	INTRON Fhos
3L	8758246	3L_8758246_SNP [dm3] 3L_8765146_SNP [dm6]	A	T	1.166e^-5	0.535	INTRON Fhos
3L	8758817	3L_8758817_SNP [dm3] 3L_8765717_SNP [dm6]	A	G	1.166e^-5	0.535	UPSTREAM Fhos INTRON Fhos	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
3L	8759284	3L_8759284_SNP [dm3] 3L_8766184_SNP [dm6]	T	G	1.166e^-5	0.535	UPSTREAM Fhos INTRON Fhos	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
3L	8759325	3L_8759325_SNP [dm3] 3L_8766225_SNP [dm6]	A	T	1.166e^-5	0.535	UPSTREAM Fhos INTRON Fhos	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
3L	8759326	3L_8759326_SNP [dm3] 3L_8766226_SNP [dm6]	G	A	1.166e^-5	0.535	UPSTREAM Fhos INTRON Fhos	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
2L	13286109	2L_13286109_SNP [dm3] 2L_13286109_SNP [dm6]	C	T	1.173e^-5	0.535	UPSTREAM Uvrag INTRON Drep-4 EXON CR44083	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad mE1_TFBS_HSA
3L	4487448	3L_4487448_SNP [dm3] 3L_4487448_SNP [dm6]	T	G	1.178e^-5	0.535	NON_SYNONYMOUS_CODING CG13722
2R	19109550	2R_19109550_SNP [dm3] 2R_23222027_SNP [dm6]	C	T	1.280e^-5	0.565	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	16931983	2R_16931983_SNP [dm3] 2R_21044478_SNP [dm6]	C	A	1.306e^-5	0.565	INTERGENIC
X	11152348	X_11152348_SNP [dm3] X_11258315_SNP [dm6]	G	A	1.374e^-5	0.577	INTRON CG44422
2R	18022102	2R_18022102_SNP [dm3] 2R_22134597_SNP [dm6]	G	A	1.404e^-5	0.577	INTERGENIC
3R	21449047	3R_21449047_SNP [dm3] 3R_25623325_SNP [dm6]	G	A	1.430e^-5	0.577	SYNONYMOUS_CODING Npl4	TF binding site mE1_TFBS_sens
3L	8761259	3L_8761259_SNP [dm3] 3L_8768159_SNP [dm6]	A	G	1.472e^-5	0.581	INTRON Fhos
3R	7957332	3R_7957332_SNP [dm3] 3R_12131610_SNP [dm6]	T	A	1.736e^-5	0.662	DOWNSTREAM tRNA:K5:87BC INTERGENIC
2R	7113939	2R_7113939_SNP [dm3] 2R_11226434_SNP [dm6]	A	T	1.771e^-5	0.662	UTR_3_PRIME CG7737 DOWNSTREAM metro
3L	10115037	3L_10115037_SNP [dm3] 3L_10121937_SNP [dm6]	C	T	1.786e^-5	0.662	INTRON dpr6
3R	5128994	3R_5128994_SNP [dm3] 3R_9303272_SNP [dm6]	T	A	2.003e^-5	0.684	INTRON CG8861
3L	20652707	3L_20652707_SNP [dm3] 3L_20659607_SNP [dm6]	T	A	2.104e^-5	0.684	INTERGENIC	transposable element FlyBase
X	2877199	X_2877199_SNP [dm3] X_2983166_SNP [dm6]	T	C	2.133e^-5	0.684	INTRON kirre	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_Trl
3L	8756444	3L_8756444_MNP [dm3] 3L_8763344_MNP [dm6]	CAT	TCA	2.145e^-5	0.684	INTRON Fhos
3L	8756448	3L_8756448_SNP [dm3] 3L_8763348_SNP [dm6]	C	A	2.145e^-5	0.684	INTRON Fhos
3L	8756451	3L_8756451_SNP [dm3] 3L_8763351_SNP [dm6]	T	A	2.145e^-5	0.684	INTRON Fhos
3L	8756455	3L_8756455_SNP [dm3] 3L_8763355_SNP [dm6]	T	A	2.145e^-5	0.684	INTRON Fhos
3L	8756457	3L_8756457_SNP [dm3] 3L_8763357_SNP [dm6]	T	A	2.145e^-5	0.684	INTRON Fhos
3R	11995909	3R_11995909_SNP [dm3] 3R_16170187_SNP [dm6]	G	A	2.220e^-5	0.695	SYNONYMOUS_CODING CG6006	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	3794161	3L_3794161_SNP [dm3] 3L_3794161_SNP [dm6]	T	A	2.411e^-5	0.742	INTRON CG32264
2R	18024827	2R_18024827_SNP [dm3] 2R_22137322_SNP [dm6]	T	C	2.470e^-5	0.748	UPSTREAM a INTRON a	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_run mE1_TFBS_Trl
3L	18916749	3L_18916749_SNP [dm3] 3L_18923649_SNP [dm6]	T	C	2.704e^-5	0.768	UTR_3_PRIME CG32204	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2L	14712875	2L_14712875_SNP [dm3] 2L_14712875_SNP [dm6]	C	T	2.738e^-5	0.768	SYNONYMOUS_CODING CG15282 UPSTREAM CG34165
2R	12168670	2R_12168670_SNP [dm3] 2R_16281165_SNP [dm6]	T	C	2.744e^-5	0.768	SYNONYMOUS_CODING CG15705 DOWNSTREAM CG15704 & 1 other
2R	15967566	2R_15967566_SNP [dm3] 2R_20080061_SNP [dm6]	A	G	2.838e^-5	0.768	INTERGENIC
3L	1080045	3L_1080045_SNP [dm3] 3L_1080045_SNP [dm6]	C	G	2.876e^-5	0.768	INTRON bab1	TF binding site mE1_TFBS_chinmo
3L	1080134	3L_1080134_SNP [dm3] 3L_1080134_SNP [dm6]	T	C	2.876e^-5	0.768	INTRON bab1	TF binding site mE1_TFBS_chinmo
3L	18915960	3L_18915960_SNP [dm3] 3L_18922860_SNP [dm6]	G	T	2.876e^-5	0.768	UTR_3_PRIME CG32204 UPSTREAM CG3819
X	4842920	X_4842920_SNP [dm3] X_4948887_SNP [dm6]	A	T	2.876e^-5	0.768	INTRON Ptp4E	TF binding site mE1_TFBS_cad
2L	1371431	2L_1371431_SNP [dm3] 2L_1371431_SNP [dm6]	G	A	2.971e^-5	0.777	INTERGENIC	TF binding site BDTNP1_TFBS_Med mE1_TFBS_HSA
2R	397477	2R_397477_SNP [dm3] 2R_4509972_SNP [dm6]	C	T	2.995e^-5	0.777	INTERGENIC	transposable element FlyBase
2L	4325651	2L_4325651_SNP [dm3] 2L_4325651_SNP [dm6]	A	G	3.144e^-5	0.805	INTRON CG16857
2R	16931982	2R_16931982_SNP [dm3] 2R_21044477_SNP [dm6]	C	A	3.402e^-5	0.847	INTERGENIC
2L	1371353	2L_1371353_SNP [dm3] 2L_1371353_SNP [dm6]	T	G	3.438e^-5	0.847	INTERGENIC	TF binding site BDTNP1_TFBS_Med
2L	13128536	2L_13128536_SNP [dm3] 2L_13128536_SNP [dm6]	G	T	3.508e^-5	0.847	INTERGENIC
3L	3630320	3L_3630320_SNP [dm3] 3L_3630320_SNP [dm6]	T	C	3.577e^-5	0.847	INTRON dar1
3L	11693323	3L_11693323_SNP [dm3] 3L_11700223_SNP [dm6]	A	T	3.578e^-5	0.847	UTR_3_PRIME CG11658 UPSTREAM CG6053
2R	289852	2R_289852_SNP [dm3] 2R_4402347_SNP [dm6]	C	A	3.644e^-5	0.847	INTRON Gprk1
3L	15859526	3L_15859526_SNP [dm3] 3L_15866426_SNP [dm6]	T	A	3.674e^-5	0.847	INTRON pHCl
3L	3630330	3L_3630330_SNP [dm3] 3L_3630330_SNP [dm6]	G	A	3.715e^-5	0.847	INTRON dar1
X	17180521	X_17180521_DEL [dm3] X_17286488_DEL [dm6]	AA	A	3.958e^-5	0.847	UTR_3_PRIME Fim INTRON CG5445	TF binding site mE1_TFBS_HSA
2R	13363677	2R_13363677_SNP [dm3] 2R_17476172_SNP [dm6]	G	A	4.030e^-5	0.847	UTR_5_PRIME CG6520 UPSTREAM CG6520	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_inv mE1_TFBS_Trl
2L	9140024	2L_9140024_SNP [dm3] 2L_9140024_SNP [dm6]	G	A	4.050e^-5	0.847	INTRON CG32982
2R	18427191	2R_18427191_SNP [dm3] 2R_22539686_SNP [dm6]	T	C	4.092e^-5	0.847	INTRON px
2R	19709329	2R_19709329_SNP [dm3] 2R_23821806_SNP [dm6]	G	A	4.218e^-5	0.847	INTRON CG5549	TF binding site mE1_TFBS_chinmo
2L	9447238	2L_9447238_SNP [dm3] 2L_9447238_SNP [dm6]	T	C	4.267e^-5	0.847	INTRON numb	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_Trl
3L	10732027	3L_10732027_SNP [dm3] 3L_10738927_SNP [dm6]	T	C	4.333e^-5	0.847	INTERGENIC	TF binding site BDTNP1_TFBS_dl
2L	12486790	2L_12486790_SNP [dm3] 2L_12486790_SNP [dm6]	A	G	4.350e^-5	0.847	INTRON bun
2L	3011965	2L_3011965_SNP [dm3] 2L_3011965_SNP [dm6]	G	A	4.457e^-5	0.847	INTRON CG17265	TF binding site mE1_TFBS_inv
2L	13082911	2L_13082911_SNP [dm3] 2L_13082911_SNP [dm6]	A	G	4.494e^-5	0.847	INTERGENIC
2R	10732438	2R_10732438_SNP [dm3] 2R_14844933_SNP [dm6]	G	A	4.534e^-5	0.847	SYNONYMOUS_CODING NaPi-T	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	1372594	2L_1372594_SNP [dm3] 2L_1372594_SNP [dm6]	C	T	4.546e^-5	0.847	INTERGENIC
3L	20652991	3L_20652991_SNP [dm3] 3L_20659891_SNP [dm6]	A	C	4.584e^-5	0.847	INTERGENIC
3L	7814988	3L_7814988_SNP [dm3] 3L_7821888_SNP [dm6]	T	C	4.625e^-5	0.847	INTRON Pdp1
3L	11866202	3L_11866202_SNP [dm3] 3L_11873102_SNP [dm6]	C	A	4.642e^-5	0.847	INTRON CG44837
3L	6133022	3L_6133022_SNP [dm3] 3L_6139922_SNP [dm6]	T	C	4.740e^-5	0.847	START_GAINED Cpr65Av UTR_5_PRIME Cpr65Av
3L	8756057	3L_8756057_SNP [dm3] 3L_8762957_SNP [dm6]	C	T	4.790e^-5	0.847	INTRON Fhos	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	6954857	3L_6954857_SNP [dm3] 3L_6961757_SNP [dm6]	T	A	4.819e^-5	0.847	INTRON sgl
2R	16381467	2R_16381467_SNP [dm3] 2R_20493962_SNP [dm6]	C	T	4.827e^-5	0.847	INTERGENIC	TF binding site BDTNP1_TFBS_twi
3L	5072426	3L_5072426_SNP [dm3] 3L_5072426_SNP [dm6]	C	T	4.894e^-5	0.847	INTRON Con
3L	5072432	3L_5072432_DEL [dm3] 3L_5072432_DEL [dm6]	CAACTATGCGATGCAGGATT...	C	4.894e^-5	0.847	INTRON Con

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Missing results

By genomic position
Variant impact
Gene name

pc_KP_PElem_HS phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results