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=7.095e^-15)
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

2852 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
3R	21914567	3R_21914567_SNP [dm3] 3R_26088845_SNP [dm6]	T	C	1.259e^-7	0.087	INTRON dys	regulatory region REDfly_CRMs
3R	21914466	3R_21914466_INS [dm3] 3R_26088744_INS [dm6]	A	AAAA	1.284e^-7	0.087	INTRON dys	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl
2R	8154731	2R_8154731_SNP [dm3] 2R_12267226_SNP [dm6]	A	T	1.399e^-7	0.087	INTRON Cam
3L	6321402	3L_6321402_SNP [dm3] 3L_6328302_SNP [dm6]	A	G	5.847e^-7	0.176	NON_SYNONYMOUS_CODING Or65c
3R	9248835	3R_9248835_SNP [dm3] 3R_13423113_SNP [dm6]	T	G	6.905e^-7	0.176	SYNONYMOUS_CODING Ir87a
3R	23976724	3R_23976724_SNP [dm3] 3R_28151002_SNP [dm6]	G	T	7.107e^-7	0.176	INTRON CG34354	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	9248864	3R_9248864_SNP [dm3] 3R_13423142_SNP [dm6]	A	G	7.918e^-7	0.176	DOWNSTREAM Ir87a INTERGENIC
3L	12765716	3L_12765716_SNP [dm3] 3L_12772616_SNP [dm6]	G	A	8.166e^-7	0.176	INTRON Hip1
3R	9238940	3R_9238940_SNP [dm3] 3R_13413218_SNP [dm6]	G	A	9.388e^-7	0.176	INTRON yellow-e	TF binding site BDTNP1_TFBS_prd
X	15422572	X_15422572_SNP [dm3] X_15528539_SNP [dm6]	G	T	9.466e^-7	0.176	INTRON Ac13E
2R	2430161	2R_2430161_SNP [dm3] 2R_6542656_SNP [dm6]	C	A	1.157e^-6	0.176	INTRON jing	TF binding site mE1_TFBS_chinmo
2L	19185700	2L_19185700_SNP [dm3] 2L_19185700_SNP [dm6]	A	C	1.208e^-6	0.176	START_GAINED gammaTub37C UTR_5_PRIME gammaTub37C UPSTREAM pigeon	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
3L	218584	3L_218584_SNP [dm3] 3L_218584_SNP [dm6]	T	C	1.326e^-6	0.176	SYNONYMOUS_CODING CG13877 UTR_3_PRIME pyx DOWNSTREAM Kaz1-ORFB
3L	176565	3L_176565_SNP [dm3] 3L_176565_SNP [dm6]	A	T	1.327e^-6	0.176	UTR_3_PRIME Vdup1 UPSTREAM CG7049	TF binding site mE1_TFBS_cad
3R	21914468	3R_21914468_SNP [dm3] 3R_26088746_SNP [dm6]	T	A	1.530e^-6	0.18	INTRON dys	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl
3R	3045532	3R_3045532_SNP [dm3] 3R_7219810_SNP [dm6]	T	A	1.657e^-6	0.18	UPSTREAM CG14605 INTERGENIC
3R	3045257	3R_3045257_SNP [dm3] 3R_7219535_SNP [dm6]	G	A	1.688e^-6	0.18	SPLICE_SITE_REGION CG14605 START_GAINED CG14605 UTR_5_PRIME CG14605
3L	52959	3L_52959_DEL [dm3] 3L_52959_DEL [dm6]	AATTTAAGATCTACCTA...	A	1.754e^-6	0.18	DOWNSTREAM CG43149 INTERGENIC
3R	21914562	3R_21914562_SNP [dm3] 3R_26088840_SNP [dm6]	T	G	1.850e^-6	0.18	INTRON dys	regulatory region REDfly_CRMs
3L	12765727	3L_12765727_SNP [dm3] 3L_12772627_SNP [dm6]	G	A	1.983e^-6	0.18	INTRON Hip1
3L	191741	3L_191741_SNP [dm3] 3L_191741_SNP [dm6]	G	C	2.049e^-6	0.18	SYNONYMOUS_CODING rno	TF binding site mE1_TFBS_cad
3R	3084496	3R_3084496_SNP [dm3] 3R_7258774_SNP [dm6]	C	A	2.134e^-6	0.18	INTRON Gld
2R	10993803	2R_10993803_SNP [dm3] 2R_15106298_SNP [dm6]	C	T	2.517e^-6	0.189	INTERGENIC
2L	13753488	2L_13753488_SNP [dm3] 2L_13753488_SNP [dm6]	A	G	2.588e^-6	0.189	INTRON CR44846 & 1 other EXON CR44846
2R	8150334	2R_8150334_SNP [dm3] 2R_12262829_SNP [dm6]	C	A	2.697e^-6	0.189	INTRON Cam
3L	2707530	3L_2707530_SNP [dm3] 3L_2707530_SNP [dm6]	A	C	2.738e^-6	0.189	INTRON Fife
3R	21914537	3R_21914537_SNP [dm3] 3R_26088815_SNP [dm6]	A	C	2.748e^-6	0.189	INTRON dys	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl
X	7615605	X_7615605_SNP [dm3] X_7721572_SNP [dm6]	T	C	3.282e^-6	0.218	UPSTREAM Hira INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
X	18908535	X_18908535_SNP [dm3] X_19014502_SNP [dm6]	G	A	4.227e^-6	0.268	INTRON CG43759
2R	8133354	2R_8133354_SNP [dm3] 2R_12245849_SNP [dm6]	G	C	4.394e^-6	0.268	DOWNSTREAM CR44315 INTERGENIC
3L	3910427	3L_3910427_SNP [dm3] 3L_3910427_SNP [dm6]	G	T	4.465e^-6	0.268	UTR_3_PRIME Eip63F-1 UPSTREAM mge
2R	17879836	2R_17879836_SNP [dm3] 2R_21992331_SNP [dm6]	G	A	4.798e^-6	0.279	INTRON CG34370
3L	7173824	3L_7173824_SNP [dm3] 3L_7180724_SNP [dm6]	T	C	5.209e^-6	0.28	INTRON Dscam2	TF binding site mE1_TFBS_inv
2R	2424244	2R_2424244_SNP [dm3] 2R_6536739_SNP [dm6]	T	C	5.371e^-6	0.28	INTRON jing
3L	8844892	3L_8844892_SNP [dm3] 3L_8851792_SNP [dm6]	A	G	5.691e^-6	0.28	INTRON dally	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA mE1_TFBS_sens
3R	18871721	3R_18871721_SNP [dm3] 3R_23045999_SNP [dm6]	G	A	5.710e^-6	0.28	INTRON CG17121
2R	15105556	2R_15105556_SNP [dm3] 2R_19218051_SNP [dm6]	C	T	5.794e^-6	0.28	INTRON hppy
3L	2465323	3L_2465323_SNP [dm3] 3L_2465323_SNP [dm6]	C	T	5.899e^-6	0.28	SYNONYMOUS_CODING CG45186 DOWNSTREAM CG45186
X	9606267	X_9606267_SNP [dm3] X_9712234_SNP [dm6]	T	C	6.040e^-6	0.28	INTERGENIC
2R	10997432	2R_10997432_SNP [dm3] 2R_15109927_SNP [dm6]	C	T	6.151e^-6	0.28	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	15404864	2R_15404864_SNP [dm3] 2R_19517359_SNP [dm6]	A	C	6.524e^-6	0.28	DOWNSTREAM sm INTERGENIC
2R	2424254	2R_2424254_SNP [dm3] 2R_6536749_SNP [dm6]	G	C	6.610e^-6	0.28	INTRON jing
2L	8006567	2L_8006567_SNP [dm3] 2L_8006567_SNP [dm6]	C	T	6.621e^-6	0.28	NON_SYNONYMOUS_CODING Spn28Dc	TF binding site BDTNP1_TFBS_da mE1_TFBS_chinmo mE1_TFBS_HSA
X	7777246	X_7777246_SNP [dm3] X_7883213_SNP [dm6]	C	G	7.221e^-6	0.28	NON_SYNONYMOUS_CODING Ir7f	TF binding site mE1_TFBS_chinmo
X	7647215	X_7647215_SNP [dm3] X_7753182_SNP [dm6]	T	C	7.265e^-6	0.28	INTERGENIC
2R	10986796	2R_10986796_SNP [dm3] 2R_15099291_SNP [dm6]	G	T	7.420e^-6	0.28	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi
2L	17799009	2L_17799009_SNP [dm3] 2L_17799009_SNP [dm6]	G	A	8.028e^-6	0.28	SYNONYMOUS_CODING CadN2	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3L	13489957	3L_13489957_SNP [dm3] 3L_13496857_SNP [dm6]	G	C	8.129e^-6	0.28	INTRON Tgi	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	21914508	3R_21914508_SNP [dm3] 3R_26088786_SNP [dm6]	A	T	8.232e^-6	0.28	INTRON dys	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl
2R	7379615	2R_7379615_SNP [dm3] 2R_11492110_SNP [dm6]	A	T	8.299e^-6	0.28	INTRON inv	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
X	7618329	X_7618329_SNP [dm3] X_7724296_SNP [dm6]	T	A	8.426e^-6	0.28	INTRON Hira
2L	16695275	2L_16695275_SNP [dm3] 2L_16695275_SNP [dm6]	G	A	8.466e^-6	0.28	UPSTREAM grp INTRON grp
2R	16735844	2R_16735844_SNP [dm3] 2R_20848339_SNP [dm6]	A	C	8.679e^-6	0.28	SYNONYMOUS_CODING CG17999	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3R	9320751	3R_9320751_SNP [dm3] 3R_13495029_SNP [dm6]	C	T	8.686e^-6	0.28	INTERGENIC
3R	20574544	3R_20574544_SNP [dm3] 3R_24748822_SNP [dm6]	C	G	8.967e^-6	0.28	UTR_3_PRIME tok UPSTREAM tld	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	7379616	2R_7379616_SNP [dm3] 2R_11492111_SNP [dm6]	A	T	9.191e^-6	0.28	INTRON inv	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	17879809	2R_17879809_SNP [dm3] 2R_21992304_SNP [dm6]	G	T	9.372e^-6	0.28	INTRON CG34370
3L	11924803	3L_11924803_SNP [dm3] 3L_11931703_SNP [dm6]	G	A	9.646e^-6	0.28	INTRON CG44837 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	9320744	3R_9320744_SNP [dm3] 3R_13495022_SNP [dm6]	G	C	9.985e^-6	0.28	INTERGENIC
X	8937127	X_8937127_SNP [dm3] X_9043094_SNP [dm6]	T	C	1.015e^-5	0.28	INTRON CR43836 & 1 other	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
3R	5464367	3R_5464367_SNP [dm3] 3R_9638645_SNP [dm6]	G	C	1.029e^-5	0.28	INTRON Dh44
3L	8894717	3L_8894717_SNP [dm3] 3L_8901617_SNP [dm6]	G	C	1.049e^-5	0.28	NON_SYNONYMOUS_CODING TrpA1 INTRON TrpA1
2L	2912498	2L_2912498_SNP [dm3] 2L_2912498_SNP [dm6]	A	G	1.058e^-5	0.28	INTRON lilli
2R	7670634	2R_7670634_INS [dm3] 2R_11783129_INS [dm6]	T	TCATATT	1.062e^-5	0.28	INTRON ths
3L	10641161	3L_10641161_SNP [dm3] 3L_10648061_SNP [dm6]	C	T	1.099e^-5	0.28	INTRON CG32066
3R	21914470	3R_21914470_SNP [dm3] 3R_26088748_SNP [dm6]	A	T	1.145e^-5	0.28	INTRON dys	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl
3R	21914476	3R_21914476_SNP [dm3] 3R_26088754_SNP [dm6]	T	C	1.145e^-5	0.28	INTRON dys	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl
3R	21914481	3R_21914481_SNP [dm3] 3R_26088759_SNP [dm6]	G	T	1.145e^-5	0.28	INTRON dys	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl
3R	21914484	3R_21914484_SNP [dm3] 3R_26088762_SNP [dm6]	T	A	1.145e^-5	0.28	INTRON dys	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl
3L	2757981	3L_2757981_SNP [dm3] 3L_2757981_SNP [dm6]	G	A	1.156e^-5	0.28	INTRON Mrtf	TF binding site BDTNP1_TFBS_twi
3R	3041234	3R_3041234_SNP [dm3] 3R_7215512_SNP [dm6]	C	T	1.176e^-5	0.28	SYNONYMOUS_CODING CG14606
3R	9248912	3R_9248912_SNP [dm3] 3R_13423190_SNP [dm6]	C	T	1.188e^-5	0.28	DOWNSTREAM Ir87a INTERGENIC
2L	7227674	2L_7227674_DEL [dm3] 2L_7227674_DEL [dm6]	AGCC	A	1.202e^-5	0.28	UPSTREAM CG43799 INTRON Ndae1	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3L	12407305	3L_12407305_SNP [dm3] 3L_12414205_SNP [dm6]	C	T	1.202e^-5	0.28	DOWNSTREAM ArfGAP1 INTRON CG32103	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
3L	5597698	3L_5597698_INS [dm3] 3L_5604598_INS [dm6]	A	AAAAGAA	1.224e^-5	0.28	UPSTREAM mthl2 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_run
3L	18380848	3L_18380848_SNP [dm3] 3L_18387748_SNP [dm6]	T	C	1.232e^-5	0.28	INTERGENIC
2L	15742509	2L_15742509_SNP [dm3] 2L_15742509_SNP [dm6]	T	A	1.237e^-5	0.28	INTRON CycE	regulatory region FlyBase REDfly_CRMs TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_shn BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad
2L	6642887	2L_6642887_SNP [dm3] 2L_6642887_SNP [dm6]	A	T	1.251e^-5	0.28	INTRON CG31635	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3L	12765672	3L_12765672_SNP [dm3] 3L_12772572_SNP [dm6]	C	T	1.252e^-5	0.28	SYNONYMOUS_CODING Hip1 UTR_5_PRIME Hip1
3L	12765698	3L_12765698_SNP [dm3] 3L_12772598_SNP [dm6]	A	T	1.252e^-5	0.28	INTRON Hip1
3L	5498963	3L_5498963_SNP [dm3] 3L_5505863_SNP [dm6]	G	A	1.267e^-5	0.28	INTRON CG34342
3L	13129113	3L_13129113_SNP [dm3] 3L_13136013_SNP [dm6]	G	C	1.273e^-5	0.28	UPSTREAM CG33262 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	5726459	3R_5726459_SNP [dm3] 3R_9900737_SNP [dm6]	C	T	1.291e^-5	0.28	INTRON Glut4EF
3L	7024457	3L_7024457_SNP [dm3] 3L_7031357_SNP [dm6]	G	T	1.313e^-5	0.28	INTRON Mp
X	12353312	X_12353312_SNP [dm3] X_12459279_SNP [dm6]	G	T	1.317e^-5	0.28	DOWNSTREAM Rab40 INTERGENIC
3R	21914480	3R_21914480_SNP [dm3] 3R_26088758_SNP [dm6]	A	T	1.320e^-5	0.28	INTRON dys	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl
3R	11137045	3R_11137045_SNP [dm3] 3R_15311323_SNP [dm6]	T	G	1.349e^-5	0.28	UPSTREAM Tm2 INTRON Tm2	regulatory region REDfly_CRMs
3L	12371920	3L_12371920_SNP [dm3] 3L_12378820_SNP [dm6]	A	T	1.369e^-5	0.28	INTRON Ncc69
X	18633968	X_18633968_SNP [dm3] X_18739935_SNP [dm6]	T	G	1.375e^-5	0.28	UPSTREAM CG6873 INTERGENIC
3R	5726392	3R_5726392_DEL [dm3] 3R_9900670_DEL [dm6]	TAGTT	T	1.391e^-5	0.28	INTRON Glut4EF
2R	5222747	2R_5222747_SNP [dm3] 2R_9335242_SNP [dm6]	T	A	1.405e^-5	0.28	INTRON CG13954 & 1 other	TF binding site mE1_TFBS_HSA
2L	19185807	2L_19185807_SNP [dm3] 2L_19185807_SNP [dm6]	T	C	1.416e^-5	0.28	UPSTREAM pigeon & 1 other INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
3R	9231536	3R_9231536_SNP [dm3] 3R_13405814_SNP [dm6]	C	T	1.429e^-5	0.28	SYNONYMOUS_CODING yellow-e2 UPSTREAM yellow-e3	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	9248882	3R_9248882_SNP [dm3] 3R_13423160_SNP [dm6]	G	T	1.429e^-5	0.28	DOWNSTREAM Ir87a INTERGENIC
3R	9258009	3R_9258009_SNP [dm3] 3R_13432287_SNP [dm6]	G	A	1.429e^-5	0.28	SYNONYMOUS_CODING yrt
3L	71116	3L_71116_SNP [dm3] 3L_71116_SNP [dm6]	A	G	1.456e^-5	0.28	SYNONYMOUS_CODING CG43150 UPSTREAM CR44511
2L	4233665	2L_4233665_SNP [dm3] 2L_4233665_SNP [dm6]	T	C	1.460e^-5	0.28	INTERGENIC
X	21435103	X_21435103_SNP [dm3] X_21564076_SNP [dm6]	T	A	1.516e^-5	0.288	INTERGENIC
3L	5591211	3L_5591211_SNP [dm3] 3L_5598111_SNP [dm6]	T	G	1.571e^-5	0.292	DOWNSTREAM CG5150 & 1 other INTERGENIC
X	12283913	X_12283913_INS [dm3] X_12389880_INS [dm6]	C	CCATGTAGCTCC...	1.604e^-5	0.292	INTERGENIC

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By genomic position
Variant impact
Gene name

Microbiota_OTU027 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results