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=3.827e^-17)
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	0.0219

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2R_NS	5.4914	0.0642
In_3R_P	7.3994	0.0247

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2364 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	12710777	3L_12710777_SNP [dm3] 3L_12717677_SNP [dm6]	G	T	1.923e^-8	0.029	INTERGENIC
3L	12710782	3L_12710782_SNP [dm3] 3L_12717682_SNP [dm6]	G	A	4.522e^-8	0.029	INTERGENIC
2R	10621372	2R_10621372_SNP [dm3] 2R_14733867_SNP [dm6]	C	A	4.679e^-8	0.029	INTERGENIC
2R	10152761	2R_10152761_SNP [dm3] 2R_14265256_SNP [dm6]	A	T	1.758e^-7	0.082	INTRON CG8547
2R	10549497	2R_10549497_SNP [dm3] 2R_14661992_SNP [dm6]	T	G	2.602e^-7	0.092	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	10151361	2R_10151361_SNP [dm3] 2R_14263856_SNP [dm6]	A	C	3.627e^-7	0.092	SPLICE_SITE_REGION CG8547 INTRON CG8547	TF binding site mE1_TFBS_cad
2R	10151451	2R_10151451_SNP [dm3] 2R_14263946_SNP [dm6]	A	G	3.702e^-7	0.092	SYNONYMOUS_CODING CG8547	TF binding site mE1_TFBS_cad
2R	10701426	2R_10701426_SNP [dm3] 2R_14813921_SNP [dm6]	G	A	4.048e^-7	0.092	INTERGENIC	TF binding site mE1_TFBS_Trl
3L	18147174	3L_18147174_SNP [dm3] 3L_18154074_SNP [dm6]	C	T	4.393e^-7	0.092	DOWNSTREAM CG7330 & 1 other INTERGENIC	insulator Insulator_Class_II.mE01 TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	10151358	2R_10151358_SNP [dm3] 2R_14263853_SNP [dm6]	T	C	5.036e^-7	0.094	INTRON CG8547	TF binding site mE1_TFBS_cad
2R	10549501	2R_10549501_SNP [dm3] 2R_14661996_SNP [dm6]	T	G	5.532e^-7	0.094	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	10749489	2R_10749489_SNP [dm3] 2R_14861984_SNP [dm6]	C	T	7.665e^-7	0.107	NON_SYNONYMOUS_CODING Inr-a	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2R	10715639	2R_10715639_SNP [dm3] 2R_14828134_SNP [dm6]	A	T	8.237e^-7	0.107	INTERGENIC
2R	10705677	2R_10705677_SNP [dm3] 2R_14818172_SNP [dm6]	G	T	8.870e^-7	0.107	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	8.870e^-7	0.107	UPSTREAM CG10205 INTERGENIC
3L	1604325	3L_1604325_SNP [dm3] 3L_1604325_SNP [dm6]	A	C	9.446e^-7	0.107	NON_SYNONYMOUS_CODING CG18170 UTR_5_PRIME CG33791 UPSTREAM CG33791
2R	10713301	2R_10713301_SNP [dm3] 2R_14825796_SNP [dm6]	T	G	9.738e^-7	0.107	INTERGENIC
2R	10721948	2R_10721948_SNP [dm3] 2R_14834443_SNP [dm6]	C	A	1.033e^-6	0.108	DOWNSTREAM CG10205 INTERGENIC
2R	10700525	2R_10700525_SNP [dm3] 2R_14813020_SNP [dm6]	G	A	1.120e^-6	0.109	INTERGENIC	regulatory region REDfly_CRMs
2R	7475070	2R_7475070_SNP [dm3] 2R_11587565_SNP [dm6]	A	T	1.166e^-6	0.109	SYNONYMOUS_CODING tou DOWNSTREAM snoRNA:Psi28S-1936 INTRON tou
2L	1305304	2L_1305304_SNP [dm3] 2L_1305304_SNP [dm6]	G	A	1.388e^-6	0.122	INTERGENIC
2R	10151359	2R_10151359_SNP [dm3] 2R_14263854_SNP [dm6]	G	T	1.448e^-6	0.122	INTRON CG8547	TF binding site mE1_TFBS_cad
2R	12972020	2R_12972020_SNP [dm3] 2R_17084515_SNP [dm6]	G	T	1.502e^-6	0.122	INTRON CG30460	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	15863357	2R_15863357_SNP [dm3] 2R_19975852_SNP [dm6]	G	A	1.593e^-6	0.125	INTERGENIC
2R	10368189	2R_10368189_SNP [dm3] 2R_14480684_SNP [dm6]	G	C	1.986e^-6	0.133	UPSTREAM L INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_bab1
2R	12971953	2R_12971953_SNP [dm3] 2R_17084448_SNP [dm6]	C	G	1.997e^-6	0.133	INTRON CG30460	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	562444	2L_562444_SNP [dm3] 2L_562444_SNP [dm6]	C	A	2.011e^-6	0.133	SYNONYMOUS_CODING CG11835	TF binding site mE1_TFBS_chinmo
2R	10366370	2R_10366370_SNP [dm3] 2R_14478865_SNP [dm6]	T	C	2.036e^-6	0.133	DOWNSTREAM CR44462 INTERGENIC	TF binding site mE1_TFBS_cad
2R	7474501	2R_7474501_SNP [dm3] 2R_11586996_SNP [dm6]	G	A	2.050e^-6	0.133	SYNONYMOUS_CODING tou
2R	10787494	2R_10787494_SNP [dm3] 2R_14899989_SNP [dm6]	C	T	2.173e^-6	0.133	SYNONYMOUS_CODING Cyp317a1	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
2L	562738	2L_562738_SNP [dm3] 2L_562738_SNP [dm6]	A	G	2.192e^-6	0.133	SYNONYMOUS_CODING CG11835	TF binding site mE1_TFBS_chinmo
2R	10151602	2R_10151602_SNP [dm3] 2R_14264097_SNP [dm6]	C	T	2.463e^-6	0.144	INTRON CG8547	TF binding site mE1_TFBS_cad
2L	562744	2L_562744_SNP [dm3] 2L_562744_SNP [dm6]	A	C	2.783e^-6	0.155	SYNONYMOUS_CODING CG11835	TF binding site mE1_TFBS_chinmo
2R	10153923	2R_10153923_INS [dm3] 2R_14266418_INS [dm6]	A	AATCG	2.801e^-6	0.155	INTRON CG8547
2R	7475262	2R_7475262_SNP [dm3] 2R_11587757_SNP [dm6]	C	A	2.918e^-6	0.156	DOWNSTREAM snoRNA:Psi28S-1936 INTRON tou
2R	17268226	2R_17268226_SNP [dm3] 2R_21380721_SNP [dm6]	G	T	3.051e^-6	0.159	INTERGENIC	TF binding site mE1_TFBS_sens
2R	10151270	2R_10151270_SNP [dm3] 2R_14263765_SNP [dm6]	C	T	3.289e^-6	0.166	SYNONYMOUS_CODING CG8547	TF binding site mE1_TFBS_cad
2R	10294461	2R_10294461_SNP [dm3] 2R_14406956_SNP [dm6]	T	A	3.365e^-6	0.166	INTERGENIC
2L	562762	2L_562762_SNP [dm3] 2L_562762_SNP [dm6]	G	A	3.552e^-6	0.169	SYNONYMOUS_CODING CG11835	TF binding site mE1_TFBS_chinmo
2L	562662	2L_562662_SNP [dm3] 2L_562662_SNP [dm6]	T	C	3.600e^-6	0.169	NON_SYNONYMOUS_CODING CG11835	TF binding site mE1_TFBS_chinmo
2L	3338964	2L_3338964_SNP [dm3] 2L_3338964_SNP [dm6]	T	C	3.777e^-6	0.171	INTRON E23	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Trl mE1_TFBS_zfh1
2R	7474789	2R_7474789_SNP [dm3] 2R_11587284_SNP [dm6]	G	A	3.834e^-6	0.171	DOWNSTREAM snoRNA:Psi28S-1936 INTRON tou
2L	4576819	2L_4576819_SNP [dm3] 2L_4576819_SNP [dm6]	A	G	4.335e^-6	0.189	DOWNSTREAM HP6 INTRON dp	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Kr
2L	17923262	2L_17923262_SNP [dm3] 2L_17923262_SNP [dm6]	G	C	4.660e^-6	0.199	INTERGENIC
2L	18912293	2L_18912293_SNP [dm3] 2L_18912293_SNP [dm6]	C	T	5.223e^-6	0.213	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2R	10153715	2R_10153715_SNP [dm3] 2R_14266210_SNP [dm6]	A	T	5.227e^-6	0.213	INTRON CG8547
2R	10721104	2R_10721104_SNP [dm3] 2R_14833599_SNP [dm6]	G	A	5.568e^-6	0.222	NON_SYNONYMOUS_CODING CG10205 UTR_3_PRIME CG10205
3R	14869673	3R_14869673_SNP [dm3] 3R_19043951_SNP [dm6]	G	T	5.867e^-6	0.225	NON_SYNONYMOUS_CODING CG6026 DOWNSTREAM cdi	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_sens
2R	10788315	2R_10788315_SNP [dm3] 2R_14900810_SNP [dm6]	G	A	5.880e^-6	0.225	NON_SYNONYMOUS_CODING Cyp317a1 DOWNSTREAM CG10249	TF binding site mE1_TFBS_sens
2R	17712723	2R_17712723_SNP [dm3] 2R_21825218_SNP [dm6]	C	T	6.488e^-6	0.243	SYNONYMOUS_CODING CG13492	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_sens
2R	10787579	2R_10787579_SNP [dm3] 2R_14900074_SNP [dm6]	T	C	6.716e^-6	0.247	SYNONYMOUS_CODING Cyp317a1	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	2991541	3L_2991541_SNP [dm3] 3L_2991541_SNP [dm6]	T	A	6.989e^-6	0.251	INTERGENIC
2R	10460322	2R_10460322_SNP [dm3] 2R_14572817_SNP [dm6]	C	A	7.100e^-6	0.251	SYNONYMOUS_CODING LamC INTRON ttv
2R	10688949	2R_10688949_SNP [dm3] 2R_14801444_SNP [dm6]	C	A	7.479e^-6	0.26	INTRON kn	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	17923288	2L_17923288_SNP [dm3] 2L_17923288_SNP [dm6]	T	A	7.853e^-6	0.268	INTERGENIC
2L	18731011	2L_18731011_INS [dm3] 2L_18731011_INS [dm6]	G	GTTG	8.200e^-6	0.275	UTR_5_PRIME CG10348
X	14228810	X_14228810_SNP [dm3] X_14334777_SNP [dm6]	G	C	9.446e^-6	0.311	INTRON dpr8
2R	10608747	2R_10608747_SNP [dm3] 2R_14721242_SNP [dm6]	C	T	1.012e^-5	0.314	INTERGENIC	TF binding site mE1_TFBS_inv
2R	7475118	2R_7475118_SNP [dm3] 2R_11587613_SNP [dm6]	G	T	1.065e^-5	0.314	DOWNSTREAM snoRNA:Psi28S-1936 INTRON tou
2L	20561362	2L_20561362_SNP [dm3] 2L_20561362_SNP [dm6]	G	T	1.067e^-5	0.314	UPSTREAM CR45347 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
2L	20599455	2L_20599455_SNP [dm3] 2L_20599455_SNP [dm6]	G	A	1.078e^-5	0.314	INTRON CR44909	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	10674472	2R_10674472_SNP [dm3] 2R_14786967_SNP [dm6]	A	G	1.086e^-5	0.314	INTRON kn	TF binding site BDTNP1_TFBS_dl
2R	10675354	2R_10675354_SNP [dm3] 2R_14787849_SNP [dm6]	C	A	1.086e^-5	0.314	INTRON kn	TF binding site BDTNP1_TFBS_da
2R	10616116	2R_10616116_SNP [dm3] 2R_14728611_SNP [dm6]	G	A	1.116e^-5	0.314	INTERGENIC
3L	12242272	3L_12242272_SNP [dm3] 3L_12249172_SNP [dm6]	T	A	1.134e^-5	0.314	INTRON app	TF binding site mE1_TFBS_cad
2R	10453850	2R_10453850_SNP [dm3] 2R_14566345_SNP [dm6]	T	C	1.144e^-5	0.314	INTRON ttv
2R	15159014	2R_15159014_SNP [dm3] 2R_19271509_SNP [dm6]	G	T	1.148e^-5	0.314	INTRON rib	enhancer mE1_CBP_Enhancers TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad
2R	10153763	2R_10153763_SNP [dm3] 2R_14266258_SNP [dm6]	A	G	1.152e^-5	0.314	INTRON CG8547
2L	20226409	2L_20226409_SNP [dm3] 2L_20226409_SNP [dm6]	G	C	1.161e^-5	0.314	INTERGENIC	TF binding site mE1_TFBS_hkb mE1_TFBS_HSA
2R	10154268	2R_10154268_SNP [dm3] 2R_14266763_SNP [dm6]	T	C	1.171e^-5	0.314	INTRON CG8547
2R	10151413	2R_10151413_SNP [dm3] 2R_14263908_SNP [dm6]	C	T	1.192e^-5	0.314	SYNONYMOUS_CODING CG8547	TF binding site mE1_TFBS_cad
2R	12693123	2R_12693123_SNP [dm3] 2R_16805618_SNP [dm6]	T	A	1.206e^-5	0.314	INTERGENIC
2R	10516851	2R_10516851_SNP [dm3] 2R_14629346_SNP [dm6]	T	C	1.285e^-5	0.33	UPSTREAM CG10131 INTERGENIC
2R	10666534	2R_10666534_SNP [dm3] 2R_14779029_SNP [dm6]	G	A	1.320e^-5	0.33	INTRON kn
2R	7464443	2R_7464443_SNP [dm3] 2R_11576938_SNP [dm6]	G	A	1.320e^-5	0.33	DOWNSTREAM tou INTERGENIC
2R	10517407	2R_10517407_SNP [dm3] 2R_14629902_SNP [dm6]	T	C	1.337e^-5	0.33	UPSTREAM CG10131 INTERGENIC	TF binding site mE1_TFBS_cad
3R	3405376	3R_3405376_SNP [dm3] 3R_7579654_SNP [dm6]	T	G	1.367e^-5	0.333	INTRON CG34127
2R	17183061	2R_17183061_SNP [dm3] 2R_21295556_SNP [dm6]	G	A	1.426e^-5	0.337	UTR_5_PRIME CG9752 UPSTREAM CG42672	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_GATAe mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Ubx
2R	10186537	2R_10186537_SNP [dm3] 2R_14299032_SNP [dm6]	C	A	1.431e^-5	0.337	UTR_3_PRIME Ih DOWNSTREAM Ih
2R	10154275	2R_10154275_SNP [dm3] 2R_14266770_SNP [dm6]	A	G	1.450e^-5	0.337	INTRON CG8547
2R	11741984	2R_11741984_SNP [dm3] 2R_15854479_SNP [dm6]	T	A	1.456e^-5	0.337	UTR_3_PRIME tun DOWNSTREAM tun
2R	15159096	2R_15159096_SNP [dm3] 2R_19271591_SNP [dm6]	G	C	1.503e^-5	0.344	INTRON rib	enhancer mE1_CBP_Enhancers TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad
3L	21153405	3L_21153405_SNP [dm3] 3L_21160305_SNP [dm6]	C	T	1.542e^-5	0.346	INTRON Ac78C
2R	9647502	2R_9647502_SNP [dm3] 2R_13759997_SNP [dm6]	C	T	1.566e^-5	0.346	INTERGENIC
2L	17054282	2L_17054282_SNP [dm3] 2L_17054282_SNP [dm6]	A	T	1.598e^-5	0.346	INTERGENIC
2L	6296972	2L_6296972_SNP [dm3] 2L_6296972_SNP [dm6]	G	A	1.603e^-5	0.346	INTRON Ddr
3R	26762888	3R_26762888_SNP [dm3] 3R_30937166_SNP [dm6]	A	C	1.603e^-5	0.346	UPSTREAM CG15549 & 1 other INTERGENIC	TF binding site mE1_TFBS_chinmo
2R	15159019	2R_15159019_SNP [dm3] 2R_19271514_SNP [dm6]	A	T	1.634e^-5	0.348	INTRON rib	enhancer mE1_CBP_Enhancers TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad
2L	714027	2L_714027_SNP [dm3] 2L_714027_SNP [dm6]	A	G	1.655e^-5	0.349	INTRON ds & 1 other	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	13075547	2R_13075547_SNP [dm3] 2R_17188042_SNP [dm6]	C	A	1.673e^-5	0.349	UPSTREAM CR44388 DOWNSTREAM CR44389 INTERGENIC
2L	17060671	2L_17060671_SNP [dm3] 2L_17060671_SNP [dm6]	G	A	1.731e^-5	0.356	INTERGENIC
2L	17924068	2L_17924068_SNP [dm3] 2L_17924068_SNP [dm6]	A	C	1.746e^-5	0.356	INTERGENIC
2R	7315395	2R_7315395_SNP [dm3] 2R_11427890_SNP [dm6]	A	G	1.780e^-5	0.359	UPSTREAM Drip INTRON Drip
X	17176368	X_17176368_SNP [dm3] X_17282335_SNP [dm6]	T	C	1.830e^-5	0.365	NON_SYNONYMOUS_CODING CG8664 UPSTREAM CG5445	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_inv
2R	10608749	2R_10608749_SNP [dm3] 2R_14721244_SNP [dm6]	C	G	1.930e^-5	0.379	INTERGENIC	TF binding site mE1_TFBS_inv
3L	11617001	3L_11617001_SNP [dm3] 3L_11623901_SNP [dm6]	C	A	1.938e^-5	0.379	UPSTREAM CG6084 DOWNSTREAM CG6083 INTRON CG6084
2L	3272656	2L_3272656_INS [dm3] 2L_3272656_INS [dm6]	T	TTATCTTATTACCGCGT...	1.978e^-5	0.383	DOWNSTREAM CG3347 INTERGENIC
2R	7315344	2R_7315344_SNP [dm3] 2R_11427839_SNP [dm6]	G	T	2.022e^-5	0.386	UPSTREAM Drip INTRON Drip
2R	17254946	2R_17254946_SNP [dm3] 2R_21367441_SNP [dm6]	G	A	2.053e^-5	0.386	INTRON cv-2	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_kni BDTNP1_TFBS_Mad 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_eve mE1_TFBS_HSA
2R	17185532	2R_17185532_SNP [dm3] 2R_21298027_SNP [dm6]	A	T	2.056e^-5	0.386	UTR_5_PRIME CG42672 INTRON CG42672 EXON CR44724

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By genomic position
Variant impact
Gene name

Delta_Alive.at.48h Experience 4 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results