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=2.477e^-1)
Null hypothesis is not rejected (p>0.05).
Interpretation: 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_2L_t	0.002733
In_2R_NS	0.011209

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1940 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
3L	7315308	3L_7315308_SNP [dm3] 3L_7322208_SNP [dm6]	A	G	1.412e^-6	0.724	SYNONYMOUS_CODING RhoGEF4 DOWNSTREAM CG8607	TF binding site mE1_TFBS_sens
3L	10092496	3L_10092496_SNP [dm3] 3L_10099396_SNP [dm6]	T	C	1.580e^-6	0.724	SYNONYMOUS_CODING CG42826 INTRON dpr6
2L	4048482	2L_4048482_SNP [dm3] 2L_4048482_SNP [dm6]	C	A	2.581e^-6	0.724	INTRON ed
2R	16713076	2R_16713076_SNP [dm3] 2R_20825571_SNP [dm6]	A	G	3.405e^-6	0.724	INTRON insc	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3R	20313081	3R_20313081_SNP [dm3] 3R_24487359_SNP [dm6]	A	G	3.892e^-6	0.724	INTRON nAChRalpha2
3L	7314757	3L_7314757_SNP [dm3] 3L_7321657_SNP [dm6]	G	A	4.300e^-6	0.724	SYNONYMOUS_CODING RhoGEF4 DOWNSTREAM CG8607
2L	7787792	2L_7787792_DEL [dm3] 2L_7787792_DEL [dm6]	AA	A	4.468e^-6	0.724	INTRON CG7149
3R	12509066	3R_12509066_SNP [dm3] 3R_16683344_SNP [dm6]	A	T	4.597e^-6	0.724	INTRON Ubx	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
3L	7314852	3L_7314852_SNP [dm3] 3L_7321752_SNP [dm6]	C	T	4.706e^-6	0.724	NON_SYNONYMOUS_CODING RhoGEF4 DOWNSTREAM CG8607
X	15436386	X_15436386_DEL [dm3] X_15542353_DEL [dm6]	CC	C	4.766e^-6	0.724	INTRON Ac13E
2R	9907704	2R_9907704_SNP [dm3] 2R_14020199_SNP [dm6]	A	G	5.218e^-6	0.724	INTRON mam
3R	12509069	3R_12509069_SNP [dm3] 3R_16683347_SNP [dm6]	T	C	5.537e^-6	0.724	INTRON Ubx	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
2R	14495551	2R_14495551_SNP [dm3] 2R_18608046_SNP [dm6]	T	C	5.909e^-6	0.724	INTRON GEFmeso	TF binding site mE1_TFBS_cad
2L	1419970	2L_1419970_SNP [dm3] 2L_1419970_SNP [dm6]	C	A	6.126e^-6	0.724	NON_SYNONYMOUS_CODING lea	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_tll BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_disco mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_sens
3L	15233361	3L_15233361_SNP [dm3] 3L_15240261_SNP [dm6]	G	T	6.490e^-6	0.724	UTR_3_PRIME Tollo	TF binding site mE1_TFBS_cad
3L	10904778	3L_10904778_SNP [dm3] 3L_10911678_SNP [dm6]	C	T	6.500e^-6	0.724	INTERGENIC
3L	7314774	3L_7314774_SNP [dm3] 3L_7321674_SNP [dm6]	G	A	6.565e^-6	0.724	NON_SYNONYMOUS_CODING RhoGEF4 DOWNSTREAM CG8607
2L	16614407	2L_16614407_SNP [dm3] 2L_16614407_SNP [dm6]	C	T	7.093e^-6	0.739	INTRON CG42389
2L	7287410	2L_7287410_SNP [dm3] 2L_7287410_SNP [dm6]	A	G	7.802e^-6	0.758	INTERGENIC
X	19084978	X_19084978_SNP [dm3] X_19190945_SNP [dm6]	A	C	8.086e^-6	0.758	UTR_3_PRIME HP1D3csd DOWNSTREAM Mec2	TF binding site BDTNP1_TFBS_twi mE1_TFBS_h
2R	14124537	2R_14124537_SNP [dm3] 2R_18237032_SNP [dm6]	T	C	8.490e^-6	0.758	DOWNSTREAM fj INTERGENIC	TF binding site BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
X	4315136	X_4315136_SNP [dm3] X_4421103_SNP [dm6]	T	C	1.006e^-5	0.83	INTRON CR32773 & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_inv
3R	18855266	3R_18855266_SNP [dm3] 3R_23029544_SNP [dm6]	C	T	1.018e^-5	0.83	INTERGENIC	regulatory region REDfly_CRMs
2L	16613556	2L_16613556_SNP [dm3] 2L_16613556_SNP [dm6]	C	T	1.084e^-5	0.846	INTRON CG42389
2L	8210242	2L_8210242_SNP [dm3] 2L_8210242_SNP [dm6]	G	A	1.281e^-5	0.867	DOWNSTREAM CG8419 INTRON Su_var_205	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	7315263	3L_7315263_SNP [dm3] 3L_7322163_SNP [dm6]	G	A	1.291e^-5	0.867	SYNONYMOUS_CODING RhoGEF4 DOWNSTREAM CG8607	TF binding site mE1_TFBS_sens
3L	15233343	3L_15233343_SNP [dm3] 3L_15240243_SNP [dm6]	A	T	1.352e^-5	0.867	UTR_3_PRIME Tollo	TF binding site mE1_TFBS_cad
2L	16600466	2L_16600466_SNP [dm3] 2L_16600466_SNP [dm6]	T	A	1.361e^-5	0.867	INTRON CG42389	TF binding site mE1_TFBS_Trl
3L	19461403	3L_19461403_SNP [dm3] 3L_19468303_SNP [dm6]	C	T	1.410e^-5	0.867	DOWNSTREAM CG32214 INTERGENIC	transposable element FlyBase
3L	1371369	3L_1371369_SNP [dm3] 3L_1371369_SNP [dm6]	C	G	1.435e^-5	0.867	INTRON Ptp61F & 1 other	TF binding site mE1_TFBS_HSA
3L	1371371	3L_1371371_SNP [dm3] 3L_1371371_SNP [dm6]	C	T	1.435e^-5	0.867	INTRON Ptp61F & 1 other	TF binding site mE1_TFBS_HSA
3R	19360525	3R_19360525_SNP [dm3] 3R_23534803_SNP [dm6]	A	T	1.507e^-5	0.883	UPSTREAM CG10170 DOWNSTREAM CG16732 INTERGENIC
3L	15233355	3L_15233355_SNP [dm3] 3L_15240255_SNP [dm6]	C	T	1.571e^-5	0.892	UTR_3_PRIME Tollo	TF binding site mE1_TFBS_cad
2L	16694865	2L_16694865_SNP [dm3] 2L_16694865_SNP [dm6]	T	A	1.778e^-5	0.952	UPSTREAM grp INTRON grp
2L	16696824	2L_16696824_SNP [dm3] 2L_16696824_SNP [dm6]	A	C	1.778e^-5	0.952	DOWNSTREAM CR44975 INTRON grp	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	2200126	2L_2200126_SNP [dm3] 2L_2200126_SNP [dm6]	A	G	1.841e^-5	0.955	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Trl
2L	7963140	2L_7963140_SNP [dm3] 2L_7963140_SNP [dm6]	A	G	1.920e^-5	0.955	INTRON Snoo
3R	18855268	3R_18855268_SNP [dm3] 3R_23029546_SNP [dm6]	A	G	2.012e^-5	0.955	INTERGENIC	regulatory region REDfly_CRMs
3R	12509139	3R_12509139_SNP [dm3] 3R_16683417_SNP [dm6]	C	T	2.018e^-5	0.955	INTRON Ubx	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb mE1_TFBS_cad
2L	16627790	2L_16627790_SNP [dm3] 2L_16627790_SNP [dm6]	A	G	2.128e^-5	0.955	DOWNSTREAM CR44151 INTRON CG42389	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA
2L	2019278	2L_2019278_SNP [dm3] 2L_2019278_SNP [dm6]	G	A	2.156e^-5	0.955	INTRON CG4238	TF binding site BDTNP1_TFBS_da
3L	14285553	3L_14285553_SNP [dm3] 3L_14292453_SNP [dm6]	A	G	2.180e^-5	0.955	INTRON fz
3L	19461417	3L_19461417_SNP [dm3] 3L_19468317_SNP [dm6]	A	C	2.428e^-5	0.955	DOWNSTREAM CG32214 INTERGENIC	transposable element FlyBase
2R	15785665	2R_15785665_SNP [dm3] 2R_19898160_SNP [dm6]	A	C	2.457e^-5	0.955	EXON CR44572
3L	23811220	3L_23811220_SNP [dm3] 3L_23818120_SNP [dm6]	A	T	2.520e^-5	0.955	INTERGENIC	transposable element FlyBase
3L	6916636	3L_6916636_SNP [dm3] 3L_6923536_SNP [dm6]	A	G	2.609e^-5	0.955	INTERGENIC
3R	22306209	3R_22306209_SNP [dm3] 3R_26480487_SNP [dm6]	T	A	2.670e^-5	0.955	INTRON plum
3R	25344717	3R_25344717_SNP [dm3] 3R_29518995_SNP [dm6]	A	G	2.683e^-5	0.955	INTERGENIC
2R	10679272	2R_10679272_SNP [dm3] 2R_14791767_SNP [dm6]	C	T	2.704e^-5	0.955	INTRON kn	TF binding site BDTNP1_TFBS_dl
2L	7963090	2L_7963090_SNP [dm3] 2L_7963090_SNP [dm6]	A	T	2.723e^-5	0.955	INTRON Snoo
X	2464028	X_2464028_SNP [dm3] X_2569995_SNP [dm6]	C	T	2.853e^-5	0.955	INTRON Pdfr
3R	14342228	3R_14342228_SNP [dm3] 3R_18516506_SNP [dm6]	A	T	2.898e^-5	0.955	INTRON fru	TF binding site BDTNP1_TFBS_twi
3L	11142079	3L_11142079_SNP [dm3] 3L_11148979_SNP [dm6]	A	G	2.934e^-5	0.955	DOWNSTREAM CG6216 INTRON CG32082
2L	2195638	2L_2195638_SNP [dm3] 2L_2195638_SNP [dm6]	T	G	2.935e^-5	0.955	INTRON CG34172	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_D mE1_TFBS_GATAe mE1_TFBS_HSA
3L	21324115	3L_21324115_SNP [dm3] 3L_21331015_SNP [dm6]	C	G	3.005e^-5	0.955	INTRON Rab26
2L	18529151	2L_18529151_SNP [dm3] 2L_18529151_SNP [dm6]	T	C	3.057e^-5	0.955	SYNONYMOUS_CODING CG10211	TF binding site mE1_TFBS_cad
2L	8209898	2L_8209898_SNP [dm3] 2L_8209898_SNP [dm6]	G	A	3.169e^-5	0.955	SYNONYMOUS_CODING Su_var_205 DOWNSTREAM CG8419	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv
2L	16578088	2L_16578088_SNP [dm3] 2L_16578088_SNP [dm6]	A	G	3.219e^-5	0.955	INTRON CG42389
2R	16686743	2R_16686743_SNP [dm3] 2R_20799238_SNP [dm6]	A	G	3.375e^-5	0.955	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	10103234	3L_10103234_SNP [dm3] 3L_10110134_SNP [dm6]	A	G	3.496e^-5	0.955	INTRON dpr6	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	10092492	3L_10092492_SNP [dm3] 3L_10099392_SNP [dm6]	G	C	3.499e^-5	0.955	NON_SYNONYMOUS_CODING CG42826 INTRON dpr6
2L	15896700	2L_15896700_SNP [dm3] 2L_15896700_SNP [dm6]	A	G	3.541e^-5	0.955	INTRON CG31735
X	9009579	X_9009579_SNP [dm3] X_9115546_SNP [dm6]	C	T	3.634e^-5	0.955	SYNONYMOUS_CODING AP-1gamma
2L	3981132	2L_3981132_SNP [dm3] 2L_3981132_SNP [dm6]	C	A	3.887e^-5	0.955	INTRON fred
3L	2375522	3L_2375522_SNP [dm3] 3L_2375522_SNP [dm6]	G	C	3.980e^-5	0.955	SYNONYMOUS_CODING CG9004 DOWNSTREAM CG15877	TF binding site mE1_TFBS_sens
2L	16665443	2L_16665443_SNP [dm3] 2L_16665443_SNP [dm6]	C	T	4.028e^-5	0.955	NON_SYNONYMOUS_CODING Trpgamma	TF binding site mE1_TFBS_cad
2R	15990623	2R_15990623_SNP [dm3] 2R_20103118_SNP [dm6]	A	G	4.058e^-5	0.955	INTERGENIC	enhancer mE1_CBP_Enhancers regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3L	1371362	3L_1371362_SNP [dm3] 3L_1371362_SNP [dm6]	C	A	4.061e^-5	0.955	INTRON Ptp61F & 1 other	TF binding site mE1_TFBS_HSA
3R	14675485	3R_14675485_SNP [dm3] 3R_18849763_SNP [dm6]	A	G	4.074e^-5	0.955	UPSTREAM CG18208 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
2L	16653973	2L_16653973_SNP [dm3] 2L_16653973_SNP [dm6]	G	A	4.201e^-5	0.955	INTRON CG42389	TF binding site mE1_TFBS_inv
2L	7787974	2L_7787974_SNP [dm3] 2L_7787974_SNP [dm6]	A	G	4.211e^-5	0.955	SYNONYMOUS_CODING CG7149
3R	25349798	3R_25349798_SNP [dm3] 3R_29524076_SNP [dm6]	C	G	4.356e^-5	0.955	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	3102565	2L_3102565_SNP [dm3] 2L_3102565_SNP [dm6]	C	A	4.385e^-5	0.955	INTRON toc
2L	2198421	2L_2198421_SNP [dm3] 2L_2198421_SNP [dm6]	G	T	4.393e^-5	0.955	UPSTREAM CG34172 INTERGENIC	TF binding site BDTNP1_TFBS_dl
2L	2204992	2L_2204992_SNP [dm3] 2L_2204992_SNP [dm6]	G	A	4.412e^-5	0.955	SYNONYMOUS_CODING CG31668	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2L	1031394	2L_1031394_SNP [dm3] 2L_1031394_SNP [dm6]	A	T	4.437e^-5	0.955	INTRON IA-2
2R	7342643	2R_7342643_SNP [dm3] 2R_11455138_SNP [dm6]	C	T	4.467e^-5	0.955	SYNONYMOUS_CODING E_Pc_	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	15874811	2R_15874811_SNP [dm3] 2R_19987306_SNP [dm6]	A	T	4.481e^-5	0.955	INTERGENIC
3R	22309643	3R_22309643_SNP [dm3] 3R_26483921_SNP [dm6]	T	C	4.546e^-5	0.955	INTRON plum
3L	15233346	3L_15233346_SNP [dm3] 3L_15240246_SNP [dm6]	A	G	4.619e^-5	0.955	UTR_3_PRIME Tollo	TF binding site mE1_TFBS_cad
3L	14907435	3L_14907435_SNP [dm3] 3L_14914335_SNP [dm6]	T	A	4.640e^-5	0.955	INTRON DCX-EMAP
2L	7787341	2L_7787341_DEL [dm3] 2L_7787341_DEL [dm6]	AA	A	4.646e^-5	0.955	INTRON CG7149
2L	16629127	2L_16629127_SNP [dm3] 2L_16629127_SNP [dm6]	A	T	4.684e^-5	0.955	INTRON CG42389 EXON CR44151
3L	18426856	3L_18426856_MNP [dm3] 3L_18433756_MNP [dm6]	TTC	AAG	4.708e^-5	0.955	INTERGENIC
2R	15782343	2R_15782343_SNP [dm3] 2R_19894838_SNP [dm6]	G	A	4.743e^-5	0.955	INTERGENIC
2L	2195572	2L_2195572_SNP [dm3] 2L_2195572_SNP [dm6]	T	C	4.784e^-5	0.955	INTRON CG34172	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_sens
2L	16677922	2L_16677922_SNP [dm3] 2L_16677922_SNP [dm6]	T	A	4.986e^-5	0.955	NON_SYNONYMOUS_CODING her UPSTREAM mir-2497	TF binding site mE1_TFBS_sens
2L	2189255	2L_2189255_SNP [dm3] 2L_2189255_SNP [dm6]	C	A	5.028e^-5	0.955	UPSTREAM CR44065 DOWNSTREAM CG10874 INTRON CR45290	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	6308908	3L_6308908_SNP [dm3] 3L_6315808_SNP [dm6]	G	A	5.031e^-5	0.955	INTERGENIC
3R	25349132	3R_25349132_DEL [dm3] 3R_29523410_DEL [dm6]	ATGTC	A	5.121e^-5	0.955	INTERGENIC	TF binding site mE1_TFBS_sens
2L	2195621	2L_2195621_DEL [dm3] 2L_2195621_DEL [dm6]	AT	G	5.121e^-5	0.955	INTRON CG34172	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_D mE1_TFBS_GATAe mE1_TFBS_HSA
2R	9907828	2R_9907828_SNP [dm3] 2R_14020323_SNP [dm6]	T	A	5.224e^-5	0.955	INTRON mam
3L	19461284	3L_19461284_SNP [dm3] 3L_19468184_SNP [dm6]	T	G	5.254e^-5	0.955	DOWNSTREAM CG32214 INTERGENIC
2L	8209514	2L_8209514_SNP [dm3] 2L_8209514_SNP [dm6]	C	T	5.310e^-5	0.955	UTR_3_PRIME CG8419 DOWNSTREAM Su_var_205	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv
3R	11082148	3R_11082148_SNP [dm3] 3R_15256426_SNP [dm6]	A	G	5.379e^-5	0.955	UTR_3_PRIME CG42404
2L	6377011	2L_6377011_SNP [dm3] 2L_6377011_SNP [dm6]	A	G	5.384e^-5	0.955	SYNONYMOUS_CODING slam DOWNSTREAM CG42368	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_chinmo mE1_TFBS_HSA
3R	24632711	3R_24632711_SNP [dm3] 3R_28806989_SNP [dm6]	G	C	5.388e^-5	0.955	DOWNSTREAM wdn INTRON CheB98a
2L	3725386	2L_3725386_SNP [dm3] 2L_3725386_SNP [dm6]	C	A	5.471e^-5	0.955	INTRON Shaw
3L	3891736	3L_3891736_SNP [dm3] 3L_3891736_SNP [dm6]	A	C	5.511e^-5	0.955	UPSTREAM Fie EXON CR45422
2L	2199923	2L_2199923_SNP [dm3] 2L_2199923_SNP [dm6]	G	A	5.615e^-5	0.955	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb mE1_TFBS_inv mE1_TFBS_Trl

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Phenotype distribution and association to known covariates

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GWAS results