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=1.470e^-8)
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

Covariate	p-value	Significance
In_3R_P	0.01639

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_3R_P	7.9519	0.0188

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2885 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

Show entries

Search:

Chromosome	Position	ID	Reference	Variant	p-value	FDR_BH	Transcript annotation	Binding site annotation
2L	5581237	2L_5581237_SNP [dm3] 2L_5581237_SNP [dm6]	T	A	1.806e^-9	0.003	UPSTREAM CG14011 INTERGENIC
2R	10621372	2R_10621372_SNP [dm3] 2R_14733867_SNP [dm6]	C	A	1.906e^-8	0.018	INTERGENIC
3R	12897470	3R_12897470_SNP [dm3] 3R_17071748_SNP [dm6]	G	A	2.318e^-7	0.109	SYNONYMOUS_CODING Ns1 UPSTREAM mRpS11	TF binding site mE1_TFBS_HSA
2R	10549501	2R_10549501_SNP [dm3] 2R_14661996_SNP [dm6]	T	G	2.711e^-7	0.109	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	10549497	2R_10549497_SNP [dm3] 2R_14661992_SNP [dm6]	T	G	2.903e^-7	0.109	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	10608749	2R_10608749_SNP [dm3] 2R_14721244_SNP [dm6]	C	G	4.076e^-7	0.127	INTERGENIC	TF binding site mE1_TFBS_inv
2L	5577797	2L_5577797_INS [dm3] 2L_5577797_INS [dm6]	A	AATAAGA	8.274e^-7	0.193	INTERGENIC
2L	5578146	2L_5578146_SNP [dm3] 2L_5578146_SNP [dm6]	A	T	8.880e^-7	0.193	INTERGENIC
2R	10608747	2R_10608747_SNP [dm3] 2R_14721242_SNP [dm6]	C	T	9.791e^-7	0.193	INTERGENIC	TF binding site mE1_TFBS_inv
2L	5577807	2L_5577807_SNP [dm3] 2L_5577807_SNP [dm6]	A	T	1.027e^-6	0.193	INTERGENIC
2L	710235	2L_710235_SNP [dm3] 2L_710235_SNP [dm6]	G	A	1.350e^-6	0.23	UPSTREAM CR44988 INTRON ds
2R	10749489	2R_10749489_SNP [dm3] 2R_14861984_SNP [dm6]	C	T	2.022e^-6	0.23	NON_SYNONYMOUS_CODING Inr-a	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	4845584	2L_4845584_SNP [dm3] 2L_4845584_SNP [dm6]	C	T	2.065e^-6	0.23	INTRON mxt	TF binding site mE1_TFBS_chinmo
2L	4845570	2L_4845570_SNP [dm3] 2L_4845570_SNP [dm6]	A	G	2.111e^-6	0.23	SYNONYMOUS_CODING mxt	TF binding site mE1_TFBS_chinmo
2R	10701426	2R_10701426_SNP [dm3] 2R_14813921_SNP [dm6]	G	A	2.486e^-6	0.23	INTERGENIC	TF binding site mE1_TFBS_Trl
2R	10294461	2R_10294461_SNP [dm3] 2R_14406956_SNP [dm6]	T	A	2.600e^-6	0.23	INTERGENIC
2L	4845602	2L_4845602_SNP [dm3] 2L_4845602_SNP [dm6]	C	A	2.735e^-6	0.23	INTRON mxt	TF binding site mE1_TFBS_chinmo
2R	12370631	2R_12370631_SNP [dm3] 2R_16483126_SNP [dm6]	G	A	2.846e^-6	0.23	INTERGENIC
2R	10589127	2R_10589127_INS [dm3] 2R_14701622_INS [dm6]	T	TT	2.923e^-6	0.23	INTRON mspo
2R	15894085	2R_15894085_SNP [dm3] 2R_20006580_SNP [dm6]	G	T	2.925e^-6	0.23	UPSTREAM CR44628 INTERGENIC
2L	7971545	2L_7971545_SNP [dm3] 2L_7971545_SNP [dm6]	G	T	2.978e^-6	0.23	INTRON Snoo
3L	10594197	3L_10594197_INS [dm3] 3L_10601097_INS [dm6]	A	AT	3.440e^-6	0.23	INTERGENIC
2R	15894108	2R_15894108_SNP [dm3] 2R_20006603_SNP [dm6]	T	C	3.487e^-6	0.23	UPSTREAM CR44628 INTERGENIC
3L	15653853	3L_15653853_SNP [dm3] 3L_15660753_SNP [dm6]	T	C	3.520e^-6	0.23	UPSTREAM Eig71Ek DOWNSTREAM Eig71Ei INTRON Eig71Ej
3L	12438191	3L_12438191_DEL [dm3] 3L_12445091_DEL [dm6]	AG	A	3.818e^-6	0.23	INTERGENIC
2L	4845583	2L_4845583_SNP [dm3] 2L_4845583_SNP [dm6]	G	A	3.859e^-6	0.23	SPLICE_SITE_REGION mxt INTRON mxt	TF binding site mE1_TFBS_chinmo
2R	10713301	2R_10713301_SNP [dm3] 2R_14825796_SNP [dm6]	T	G	4.018e^-6	0.23	INTERGENIC
3L	12438343	3L_12438343_SNP [dm3] 3L_12445243_SNP [dm6]	T	C	4.088e^-6	0.23	INTERGENIC
2L	16401064	2L_16401064_SNP [dm3] 2L_16401064_SNP [dm6]	A	G	4.261e^-6	0.23	INTRON CG5888
2R	10715639	2R_10715639_SNP [dm3] 2R_14828134_SNP [dm6]	A	T	4.278e^-6	0.23	INTERGENIC
3L	12438336	3L_12438336_SNP [dm3] 3L_12445236_SNP [dm6]	A	T	4.450e^-6	0.23	INTERGENIC
2L	710246	2L_710246_SNP [dm3] 2L_710246_SNP [dm6]	G	T	4.466e^-6	0.23	UPSTREAM CR44988 INTRON ds
2L	710247	2L_710247_SNP [dm3] 2L_710247_SNP [dm6]	T	C	4.466e^-6	0.23	UPSTREAM CR44988 INTRON ds
3L	12438344	3L_12438344_DEL [dm3] 3L_12445244_DEL [dm6]	GAT	G	4.469e^-6	0.23	INTERGENIC
2R	10705677	2R_10705677_SNP [dm3] 2R_14818172_SNP [dm6]	G	T	4.484e^-6	0.23	NON_SYNONYMOUS_CODING CG10202	TF binding site BDTNP1_TFBS_twi mE1_TFBS_sens
2R	10719564	2R_10719564_SNP [dm3] 2R_14832059_SNP [dm6]	G	A	4.484e^-6	0.23	UPSTREAM CG10205 INTERGENIC
2R	10721948	2R_10721948_SNP [dm3] 2R_14834443_SNP [dm6]	C	A	4.538e^-6	0.23	DOWNSTREAM CG10205 INTERGENIC
3R	11617750	3R_11617750_SNP [dm3] 3R_15792028_SNP [dm6]	G	A	4.718e^-6	0.233	NON_SYNONYMOUS_CODING c_3_G UPSTREAM Acyp2	TF binding site BDTNP1_TFBS_dl
2L	4845609	2L_4845609_SNP [dm3] 2L_4845609_SNP [dm6]	C	T	5.033e^-6	0.239	INTRON mxt	TF binding site mE1_TFBS_chinmo
2L	5579325	2L_5579325_SNP [dm3] 2L_5579325_SNP [dm6]	C	T	5.303e^-6	0.239	DOWNSTREAM CG14011 INTERGENIC
2L	5579341	2L_5579341_SNP [dm3] 2L_5579341_SNP [dm6]	G	A	5.303e^-6	0.239	DOWNSTREAM CG14011 INTERGENIC
2R	10371682	2R_10371682_SNP [dm3] 2R_14484177_SNP [dm6]	G	T	5.408e^-6	0.239	INTRON L	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2R	10700525	2R_10700525_SNP [dm3] 2R_14813020_SNP [dm6]	G	A	5.487e^-6	0.239	INTERGENIC	regulatory region REDfly_CRMs
3L	1871663	3L_1871663_DEL [dm3] 3L_1871663_DEL [dm6]	GG	G	5.600e^-6	0.239	UTR_3_PRIME dre4 DOWNSTREAM CG13924	TF binding site mE1_TFBS_cad
3L	12438307	3L_12438307_SNP [dm3] 3L_12445207_SNP [dm6]	A	G	5.956e^-6	0.239	INTERGENIC
2R	15894081	2R_15894081_SNP [dm3] 2R_20006576_SNP [dm6]	G	A	6.177e^-6	0.239	UPSTREAM CR44628 INTERGENIC
2R	15894055	2R_15894055_SNP [dm3] 2R_20006550_SNP [dm6]	T	C	6.299e^-6	0.239	UPSTREAM CR44628 INTERGENIC
2L	9296955	2L_9296955_SNP [dm3] 2L_9296955_SNP [dm6]	C	T	6.310e^-6	0.239	UTR_3_PRIME Ggamma30A
2L	710244	2L_710244_SNP [dm3] 2L_710244_SNP [dm6]	C	T	6.341e^-6	0.239	UPSTREAM CR44988 INTRON ds
2R	10814920	2R_10814920_SNP [dm3] 2R_14927415_SNP [dm6]	G	C	6.372e^-6	0.239	INTRON CG10249	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_Trl
2R	10702960	2R_10702960_SNP [dm3] 2R_14815455_SNP [dm6]	A	C	6.725e^-6	0.244	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv
3L	17256788	3L_17256788_SNP [dm3] 3L_17263688_SNP [dm6]	G	C	6.946e^-6	0.244	UPSTREAM CG13723 INTRON CR43870
2R	15894045	2R_15894045_SNP [dm3] 2R_20006540_SNP [dm6]	T	A	7.078e^-6	0.244	UPSTREAM CR44628 INTERGENIC
X	20291346	X_20291346_SNP [dm3] X_20420319_SNP [dm6]	G	T	7.116e^-6	0.244	DOWNSTREAM Pp4-19C INTRON Obp19d	regulatory region REDfly_CRMs TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	5578149	2L_5578149_SNP [dm3] 2L_5578149_SNP [dm6]	A	G	7.231e^-6	0.244	INTERGENIC
2L	710257	2L_710257_SNP [dm3] 2L_710257_SNP [dm6]	T	G	7.379e^-6	0.244	UPSTREAM CR44988 INTRON ds
2L	5577793	2L_5577793_SNP [dm3] 2L_5577793_SNP [dm6]	T	A	7.425e^-6	0.244	INTERGENIC
3L	12438234	3L_12438234_SNP [dm3] 3L_12445134_SNP [dm6]	A	G	7.658e^-6	0.245	INTERGENIC
3L	12502549	3L_12502549_SNP [dm3] 3L_12509449_SNP [dm6]	C	T	7.715e^-6	0.245	SYNONYMOUS_CODING sti	TF binding site mE1_TFBS_sens
3L	12405594	3L_12405594_SNP [dm3] 3L_12412494_SNP [dm6]	G	A	8.423e^-6	0.258	INTRON CG32103
2L	7777215	2L_7777215_SNP [dm3] 2L_7777215_SNP [dm6]	G	T	8.501e^-6	0.258	NON_SYNONYMOUS_CODING CG7179	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	3509585	2L_3509585_SNP [dm3] 2L_3509585_SNP [dm6]	G	A	8.518e^-6	0.258	SYNONYMOUS_CODING CG31954 DOWNSTREAM CR45299 & 2 others
X	5439660	X_5439660_INS [dm3] X_5545627_INS [dm6]	A	AA	8.665e^-6	0.258	INTRON Vsx2	TF binding site BDTNP1_TFBS_dl mE1_TFBS_eve mE1_TFBS_HSA
3L	12405591	3L_12405591_SNP [dm3] 3L_12412491_SNP [dm6]	A	G	8.807e^-6	0.258	INTRON CG32103
3L	18205448	3L_18205448_SNP [dm3] 3L_18212348_SNP [dm6]	A	T	9.294e^-6	0.26	INTERGENIC
3L	15695863	3L_15695863_SNP [dm3] 3L_15702763_SNP [dm6]	G	A	9.357e^-6	0.26	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad
2R	10676596	2R_10676596_SNP [dm3] 2R_14789091_SNP [dm6]	G	T	9.399e^-6	0.26	INTRON kn	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3L	18133280	3L_18133280_SNP [dm3] 3L_18140180_SNP [dm6]	A	G	9.470e^-6	0.26	INTRON gk	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad
2L	15920367	2L_15920367_SNP [dm3] 2L_15920367_SNP [dm6]	T	C	9.575e^-6	0.26	INTRON beat-Ib
2R	10589092	2R_10589092_SNP [dm3] 2R_14701587_SNP [dm6]	G	A	1.032e^-5	0.277	INTRON mspo
2L	7297674	2L_7297674_SNP [dm3] 2L_7297674_SNP [dm6]	G	T	1.059e^-5	0.28	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi
2L	7139978	2L_7139978_SNP [dm3] 2L_7139978_SNP [dm6]	A	G	1.095e^-5	0.285	INTRON Pvf3	TF binding site BDTNP1_TFBS_slp1
2R	10453850	2R_10453850_SNP [dm3] 2R_14566345_SNP [dm6]	T	C	1.122e^-5	0.285	INTRON ttv
3L	17256767	3L_17256767_SNP [dm3] 3L_17263667_SNP [dm6]	T	C	1.123e^-5	0.285	UPSTREAM CG13723 INTRON CR43870
2L	15886182	2L_15886182_SNP [dm3] 2L_15886182_SNP [dm6]	T	C	1.162e^-5	0.291	INTERGENIC
2R	10572638	2R_10572638_SNP [dm3] 2R_14685133_SNP [dm6]	A	G	1.189e^-5	0.293	INTRON mspo
3L	5871377	3L_5871377_SNP [dm3] 3L_5878277_SNP [dm6]	T	C	1.284e^-5	0.295	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	3512317	2R_3512317_SNP [dm3] 2R_7624812_SNP [dm6]	G	A	1.300e^-5	0.295	INTRON CG43340
2L	6587664	2L_6587664_SNP [dm3] 2L_6587664_SNP [dm6]	G	T	1.321e^-5	0.295	INTRON CG11319
2R	15893987	2R_15893987_SNP [dm3] 2R_20006482_SNP [dm6]	T	A	1.326e^-5	0.295	UPSTREAM CR44628 INTERGENIC
2R	14991593	2R_14991593_SNP [dm3] 2R_19104088_SNP [dm6]	A	T	1.328e^-5	0.295	INTRON 5-HT1A
2L	15919085	2L_15919085_SNP [dm3] 2L_15919085_SNP [dm6]	C	T	1.329e^-5	0.295	INTRON beat-Ib
2R	10705422	2R_10705422_SNP [dm3] 2R_14817917_SNP [dm6]	A	C	1.350e^-5	0.295	UTR_3_PRIME CG10202	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	5796045	2L_5796045_SNP [dm3] 2L_5796045_SNP [dm6]	T	C	1.371e^-5	0.295	INTRON CG9171
3R	12335764	3R_12335764_SNP [dm3] 3R_16510042_SNP [dm6]	C	G	1.393e^-5	0.295	INTRON CG42342
2R	3527972	2R_3527972_SNP [dm3] 2R_7640467_SNP [dm6]	C	A	1.401e^-5	0.295	NON_SYNONYMOUS_CODING CG43340	TF binding site mE1_TFBS_cad
3L	18205426	3L_18205426_SNP [dm3] 3L_18212326_SNP [dm6]	A	G	1.413e^-5	0.295	INTERGENIC	TF binding site mE1_TFBS_cnc
2L	13923741	2L_13923741_SNP [dm3] 2L_13923741_SNP [dm6]	G	A	1.463e^-5	0.295	UPSTREAM CG16886 INTRON Ance-3	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	7087674	3R_7087674_SNP [dm3] 3R_11261952_SNP [dm6]	C	G	1.471e^-5	0.295	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	13563248	2R_13563248_SNP [dm3] 2R_17675743_SNP [dm6]	G	A	1.472e^-5	0.295	SYNONYMOUS_CODING Sema-1b	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	18135219	3L_18135219_SNP [dm3] 3L_18142119_SNP [dm6]	A	G	1.493e^-5	0.295	INTRON gk
3L	5909643	3L_5909643_SNP [dm3] 3L_5916543_SNP [dm6]	T	C	1.509e^-5	0.295	INTRON CG13288
2R	15894067	2R_15894067_SNP [dm3] 2R_20006562_SNP [dm6]	T	A	1.509e^-5	0.295	UPSTREAM CR44628 INTERGENIC
3L	12443140	3L_12443140_INS [dm3] 3L_12450040_INS [dm6]	A	AT	1.511e^-5	0.295	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi
2R	10585509	2R_10585509_SNP [dm3] 2R_14698004_SNP [dm6]	G	T	1.515e^-5	0.295	INTRON mspo
2R	15894034	2R_15894034_SNP [dm3] 2R_20006529_SNP [dm6]	T	C	1.521e^-5	0.295	UPSTREAM CR44628 INTERGENIC
3L	7063942	3L_7063942_SNP [dm3] 3L_7070842_SNP [dm6]	G	A	1.524e^-5	0.295	INTRON CG8641
2L	7139984	2L_7139984_SNP [dm3] 2L_7139984_SNP [dm6]	T	G	1.545e^-5	0.296	INTRON Pvf3
2L	10208831	2L_10208831_SNP [dm3] 2L_10208831_SNP [dm6]	T	G	1.590e^-5	0.301	UPSTREAM CR44845 INTRON CG5731 EXON CR44845	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_Trl
3L	12438260	3L_12438260_SNP [dm3] 3L_12445160_SNP [dm6]	T	C	1.624e^-5	0.305	INTERGENIC

Showing 1 to 100 of 1,000 entries

Previous1 2 3 4 5…10Next

By genomic position
Variant impact
Gene name

Delta_Death.at.48h Experience 4 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results