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=1.072e^-12)
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	0.09131

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_3R_P	5.2055	0.0741

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

3233 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
2R	10608749	2R_10608749_SNP [dm3] 2R_14721244_SNP [dm6]	C	G	1.496e^-8	0.025	INTERGENIC	TF binding site mE1_TFBS_inv
2R	10621372	2R_10621372_SNP [dm3] 2R_14733867_SNP [dm6]	C	A	5.121e^-8	0.025	INTERGENIC
2R	10608747	2R_10608747_SNP [dm3] 2R_14721242_SNP [dm6]	C	T	6.435e^-8	0.025	INTERGENIC	TF binding site mE1_TFBS_inv
2R	10721948	2R_10721948_SNP [dm3] 2R_14834443_SNP [dm6]	C	A	7.742e^-8	0.025	DOWNSTREAM CG10205 INTERGENIC
2R	10705677	2R_10705677_SNP [dm3] 2R_14818172_SNP [dm6]	G	T	1.033e^-7	0.025	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	1.033e^-7	0.025	UPSTREAM CG10205 INTERGENIC
2R	10715639	2R_10715639_SNP [dm3] 2R_14828134_SNP [dm6]	A	T	1.074e^-7	0.025	INTERGENIC
2R	10713301	2R_10713301_SNP [dm3] 2R_14825796_SNP [dm6]	T	G	1.121e^-7	0.025	INTERGENIC
2L	8390046	2L_8390046_SNP [dm3] 2L_8390046_SNP [dm6]	G	A	1.229e^-7	0.025	UTR_3_PRIME CG42820 UPSTREAM CG42819 DOWNSTREAM snRNA:U6atac:29B	TF binding site BDTNP1_TFBS_twi
2R	10700525	2R_10700525_SNP [dm3] 2R_14813020_SNP [dm6]	G	A	1.349e^-7	0.025	INTERGENIC	regulatory region REDfly_CRMs
2L	8390177	2L_8390177_SNP [dm3] 2L_8390177_SNP [dm6]	T	G	1.627e^-7	0.028	SYNONYMOUS_CODING CG42820 UPSTREAM CG42819 DOWNSTREAM snRNA:U6atac:29B	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	10749489	2R_10749489_SNP [dm3] 2R_14861984_SNP [dm6]	C	T	2.236e^-7	0.035	NON_SYNONYMOUS_CODING Inr-a	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	8390049	2L_8390049_SNP [dm3] 2L_8390049_SNP [dm6]	C	T	2.982e^-7	0.043	UTR_3_PRIME CG42820 UPSTREAM CG42819 DOWNSTREAM snRNA:U6atac:29B	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	10368189	2R_10368189_SNP [dm3] 2R_14480684_SNP [dm6]	G	C	3.485e^-7	0.047	UPSTREAM L INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_bab1
2R	10676596	2R_10676596_SNP [dm3] 2R_14789091_SNP [dm6]	G	T	4.645e^-7	0.058	INTRON kn	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
2R	7475070	2R_7475070_SNP [dm3] 2R_11587565_SNP [dm6]	A	T	5.137e^-7	0.059	SYNONYMOUS_CODING tou DOWNSTREAM snoRNA:Psi28S-1936 INTRON tou
2L	8390166	2L_8390166_SNP [dm3] 2L_8390166_SNP [dm6]	A	G	5.415e^-7	0.059	SYNONYMOUS_CODING CG42820 UPSTREAM CG42819 DOWNSTREAM snRNA:U6atac:29B	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	15863357	2R_15863357_SNP [dm3] 2R_19975852_SNP [dm6]	G	A	5.712e^-7	0.059	INTERGENIC
2R	10460322	2R_10460322_SNP [dm3] 2R_14572817_SNP [dm6]	C	A	6.171e^-7	0.059	SYNONYMOUS_CODING LamC INTRON ttv
2R	15861441	2R_15861441_SNP [dm3] 2R_19973936_SNP [dm6]	A	G	6.264e^-7	0.059	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2R	10608696	2R_10608696_SNP [dm3] 2R_14721191_SNP [dm6]	G	A	7.969e^-7	0.071	INTERGENIC
2R	10701426	2R_10701426_SNP [dm3] 2R_14813921_SNP [dm6]	G	A	9.595e^-7	0.081	INTERGENIC	TF binding site mE1_TFBS_Trl
2L	8363433	2L_8363433_DEL [dm3] 2L_8363433_DEL [dm6]	CC	C	9.918e^-7	0.081	UPSTREAM CG7627 DOWNSTREAM RpS13 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z
2R	10674472	2R_10674472_SNP [dm3] 2R_14786967_SNP [dm6]	A	G	1.255e^-6	0.086	INTRON kn	TF binding site BDTNP1_TFBS_dl
2R	10675354	2R_10675354_SNP [dm3] 2R_14787849_SNP [dm6]	C	A	1.255e^-6	0.086	INTRON kn	TF binding site BDTNP1_TFBS_da
2L	10870068	2L_10870068_SNP [dm3] 2L_10870068_SNP [dm6]	C	T	1.265e^-6	0.086	UPSTREAM CG12517 & 1 other INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2R	10585509	2R_10585509_SNP [dm3] 2R_14698004_SNP [dm6]	G	T	1.274e^-6	0.086	INTRON mspo
2R	10616116	2R_10616116_SNP [dm3] 2R_14728611_SNP [dm6]	G	A	1.281e^-6	0.086	INTERGENIC
2R	12245315	2R_12245315_SNP [dm3] 2R_16357810_SNP [dm6]	G	A	1.353e^-6	0.087	DOWNSTREAM CR45322 EXON CR43416
2R	10294461	2R_10294461_SNP [dm3] 2R_14406956_SNP [dm6]	T	A	1.432e^-6	0.09	INTERGENIC
2L	9621407	2L_9621407_SNP [dm3] 2L_9621407_SNP [dm6]	C	T	1.553e^-6	0.094	SYNONYMOUS_CODING GlcAT-S
3R	14345446	3R_14345446_SNP [dm3] 3R_18519724_SNP [dm6]	T	G	1.607e^-6	0.094	INTRON fru
2R	10608610	2R_10608610_SNP [dm3] 2R_14721105_SNP [dm6]	C	G	1.814e^-6	0.103	INTERGENIC
2R	10585511	2R_10585511_SNP [dm3] 2R_14698006_SNP [dm6]	T	A	2.029e^-6	0.111	INTRON mspo
2L	12141445	2L_12141445_SNP [dm3] 2L_12141445_SNP [dm6]	C	T	2.155e^-6	0.111	INTERGENIC
2R	10622250	2R_10622250_SNP [dm3] 2R_14734745_SNP [dm6]	A	T	2.178e^-6	0.111	INTERGENIC
3L	18746778	3L_18746778_SNP [dm3] 3L_18753678_SNP [dm6]	A	T	2.210e^-6	0.111	INTRON ftz-f1
2R	7475262	2R_7475262_SNP [dm3] 2R_11587757_SNP [dm6]	C	A	2.272e^-6	0.111	DOWNSTREAM snoRNA:Psi28S-1936 INTRON tou
2R	10153979	2R_10153979_SNP [dm3] 2R_14266474_SNP [dm6]	A	G	2.307e^-6	0.111	INTRON CG8547
2L	10869985	2L_10869985_SNP [dm3] 2L_10869985_SNP [dm6]	C	G	2.442e^-6	0.112	UPSTREAM CG12517 & 1 other INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2R	10549501	2R_10549501_SNP [dm3] 2R_14661996_SNP [dm6]	T	G	2.525e^-6	0.112	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	10702960	2R_10702960_SNP [dm3] 2R_14815455_SNP [dm6]	A	C	2.536e^-6	0.112	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
2R	10721104	2R_10721104_SNP [dm3] 2R_14833599_SNP [dm6]	G	A	2.569e^-6	0.112	NON_SYNONYMOUS_CODING CG10205 UTR_3_PRIME CG10205
2R	7475118	2R_7475118_SNP [dm3] 2R_11587613_SNP [dm6]	G	T	2.723e^-6	0.116	DOWNSTREAM snoRNA:Psi28S-1936 INTRON tou
2R	10549497	2R_10549497_SNP [dm3] 2R_14661992_SNP [dm6]	T	G	2.910e^-6	0.121	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	12370631	2R_12370631_SNP [dm3] 2R_16483126_SNP [dm6]	G	A	3.089e^-6	0.123	INTERGENIC
2R	10676540	2R_10676540_SNP [dm3] 2R_14789035_SNP [dm6]	C	T	3.092e^-6	0.123	INTRON kn	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
2L	17054282	2L_17054282_SNP [dm3] 2L_17054282_SNP [dm6]	A	T	3.337e^-6	0.13	INTERGENIC
3L	3024694	3L_3024694_SNP [dm3] 3L_3024694_SNP [dm6]	G	A	3.407e^-6	0.13	SYNONYMOUS_CODING aly
2R	10151361	2R_10151361_SNP [dm3] 2R_14263856_SNP [dm6]	A	C	4.160e^-6	0.155	SPLICE_SITE_REGION CG8547 INTRON CG8547	TF binding site mE1_TFBS_cad
X	4561087	X_4561087_SNP [dm3] X_4667054_SNP [dm6]	C	G	4.206e^-6	0.155	UPSTREAM CG3009 DOWNSTREAM rap INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_disco mE1_TFBS_HSA
3R	14345445	3R_14345445_SNP [dm3] 3R_18519723_SNP [dm6]	T	A	4.528e^-6	0.16	INTRON fru
3L	10921255	3L_10921255_SNP [dm3] 3L_10928155_SNP [dm6]	T	C	4.529e^-6	0.16	INTERGENIC
3L	19770694	3L_19770694_SNP [dm3] 3L_19777594_SNP [dm6]	A	T	4.784e^-6	0.164	INTRON CG42637 & 1 other
2R	10676788	2R_10676788_SNP [dm3] 2R_14789283_SNP [dm6]	C	T	4.797e^-6	0.164	INTRON kn	TF binding site mE1_TFBS_inv mE1_TFBS_sens
2R	10688949	2R_10688949_SNP [dm3] 2R_14801444_SNP [dm6]	C	A	4.931e^-6	0.165	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
2R	10622258	2R_10622258_SNP [dm3] 2R_14734753_SNP [dm6]	T	C	5.072e^-6	0.167	INTERGENIC
2L	11710313	2L_11710313_SNP [dm3] 2L_11710313_SNP [dm6]	G	T	5.209e^-6	0.168	INTERGENIC
3L	14980603	3L_14980603_SNP [dm3] 3L_14987503_SNP [dm6]	C	A	5.452e^-6	0.173	UTR_5_PRIME mnd INTRON mnd	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
2L	4376521	2L_4376521_SNP [dm3] 2L_4376521_SNP [dm6]	A	T	5.614e^-6	0.175	INTRON Traf4	TF binding site mE1_TFBS_cad
2R	10004495	2R_10004495_SNP [dm3] 2R_14116990_SNP [dm6]	T	A	5.992e^-6	0.184	INTRON Prosap
X	4561091	X_4561091_SNP [dm3] X_4667058_SNP [dm6]	C	A	6.171e^-6	0.184	UPSTREAM CG3009 DOWNSTREAM rap INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_disco mE1_TFBS_HSA
2R	8918212	2R_8918212_SNP [dm3] 2R_13030707_SNP [dm6]	A	T	6.199e^-6	0.184	INTERGENIC	TF binding site mE1_TFBS_sens
2L	9304036	2L_9304036_SNP [dm3] 2L_9304036_SNP [dm6]	C	T	6.331e^-6	0.184	DOWNSTREAM CR42844 INTERGENIC
2R	8587821	2R_8587821_SNP [dm3] 2R_12700316_SNP [dm6]	A	T	6.458e^-6	0.184	NON_SYNONYMOUS_CODING wuc
2R	10704614	2R_10704614_SNP [dm3] 2R_14817109_SNP [dm6]	G	A	6.479e^-6	0.184	DOWNSTREAM CG10202 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	10154658	2R_10154658_SNP [dm3] 2R_14267153_SNP [dm6]	A	G	6.631e^-6	0.186	INTRON CG8547	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	21094572	3L_21094572_SNP [dm3] 3L_21101472_SNP [dm6]	C	T	6.852e^-6	0.189	INTRON ko	regulatory region REDfly_CRMs
2R	10171174	2R_10171174_SNP [dm3] 2R_14283669_SNP [dm6]	G	A	7.124e^-6	0.191	INTRON Ih
X	16131982	X_16131982_SNP [dm3] X_16237949_SNP [dm6]	T	A	7.143e^-6	0.191	INTERGENIC
2R	10366370	2R_10366370_SNP [dm3] 2R_14478865_SNP [dm6]	T	C	7.324e^-6	0.193	DOWNSTREAM CR44462 INTERGENIC	TF binding site mE1_TFBS_cad
3R	15620180	3R_15620180_SNP [dm3] 3R_19794458_SNP [dm6]	C	G	7.486e^-6	0.194	DOWNSTREAM bnl INTRON bnl
3L	20757697	3L_20757697_SNP [dm3] 3L_20764597_SNP [dm6]	C	T	7.544e^-6	0.194	INTERGENIC
2R	10188073	2R_10188073_SNP [dm3] 2R_14300568_SNP [dm6]	C	A	8.168e^-6	0.205	NON_SYNONYMOUS_CODING tej DOWNSTREAM Ih
2R	10585346	2R_10585346_SNP [dm3] 2R_14697841_SNP [dm6]	C	T	8.199e^-6	0.205	INTRON mspo
X	21054778	X_21054778_SNP [dm3] X_21183751_SNP [dm6]	T	C	8.522e^-6	0.207	INTERGENIC
3R	12874837	3R_12874837_SNP [dm3] 3R_17049115_SNP [dm6]	T	G	8.565e^-6	0.207	DOWNSTREAM Patr-1 INTERGENIC
X	9986149	X_9986149_SNP [dm3] X_10092116_SNP [dm6]	C	T	8.699e^-6	0.207	INTRON RhoU	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	12972020	2R_12972020_SNP [dm3] 2R_17084515_SNP [dm6]	G	T	8.710e^-6	0.207	INTRON CG30460	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	7474864	2R_7474864_SNP [dm3] 2R_11587359_SNP [dm6]	C	T	8.926e^-6	0.209	DOWNSTREAM snoRNA:Psi28S-1936 INTRON tou
2R	7475985	2R_7475985_SNP [dm3] 2R_11588480_SNP [dm6]	G	T	9.023e^-6	0.209	SYNONYMOUS_CODING tou UPSTREAM snoRNA:Psi28S-1936	TF binding site mE1_TFBS_cad
3R	9398434	3R_9398434_SNP [dm3] 3R_13572712_SNP [dm6]	A	C	9.821e^-6	0.225	INTERGENIC
3R	5641700	3R_5641700_SNP [dm3] 3R_9815978_SNP [dm6]	G	T	1.036e^-5	0.23	UTR_3_PRIME CG16904 DOWNSTREAM eloF	TF binding site BDTNP1_TFBS_da
3L	10726178	3L_10726178_SNP [dm3] 3L_10733078_SNP [dm6]	A	G	1.037e^-5	0.23	INTERGENIC
2R	10154655	2R_10154655_INS [dm3] 2R_14267150_INS [dm6]	A	AATTTCCGA	1.040e^-5	0.23	INTRON CG8547	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	12710782	3L_12710782_SNP [dm3] 3L_12717682_SNP [dm6]	G	A	1.091e^-5	0.238	INTERGENIC
2L	6525314	2L_6525314_SNP [dm3] 2L_6525314_SNP [dm6]	A	C	1.127e^-5	0.243	INTRON CG31637
2R	10151270	2R_10151270_SNP [dm3] 2R_14263765_SNP [dm6]	C	T	1.145e^-5	0.243	SYNONYMOUS_CODING CG8547	TF binding site mE1_TFBS_cad
3L	18746854	3L_18746854_SNP [dm3] 3L_18753754_SNP [dm6]	A	T	1.151e^-5	0.243	INTRON ftz-f1
2R	9253357	2R_9253357_SNP [dm3] 2R_13365852_SNP [dm6]	C	A	1.190e^-5	0.248	INTERGENIC	TF binding site mE1_TFBS_cad
2R	10508075	2R_10508075_SNP [dm3] 2R_14620570_SNP [dm6]	A	T	1.243e^-5	0.256	DOWNSTREAM Sec61beta INTRON CG12863	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_inv
2L	17054078	2L_17054078_SNP [dm3] 2L_17054078_SNP [dm6]	T	G	1.282e^-5	0.261	INTERGENIC
2R	10160806	2R_10160806_SNP [dm3] 2R_14273301_SNP [dm6]	C	T	1.339e^-5	0.269	NON_SYNONYMOUS_CODING conv
2L	10809640	2L_10809640_SNP [dm3] 2L_10809640_SNP [dm6]	A	G	1.354e^-5	0.269	INTRON Nos
3R	5641701	3R_5641701_SNP [dm3] 3R_9815979_SNP [dm6]	G	T	1.364e^-5	0.269	UTR_3_PRIME CG16904 DOWNSTREAM eloF	TF binding site BDTNP1_TFBS_da
3R	20562591	3R_20562591_SNP [dm3] 3R_24736869_SNP [dm6]	T	A	1.392e^-5	0.272	INTRON tok
2R	3373740	2R_3373740_SNP [dm3] 2R_7486235_SNP [dm6]	G	A	1.456e^-5	0.282	UTR_5_PRIME wech INTRON wech	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Mad BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	10608631	2R_10608631_SNP [dm3] 2R_14721126_SNP [dm6]	G	A	1.482e^-5	0.284	INTERGENIC
2R	10700594	2R_10700594_SNP [dm3] 2R_14813089_SNP [dm6]	A	G	1.592e^-5	0.302	INTERGENIC
3L	13441776	3L_13441776_SNP [dm3] 3L_13448676_SNP [dm6]	A	T	1.614e^-5	0.302	SYNONYMOUS_CODING CG10732 DOWNSTREAM CG10133

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By genomic position
Variant impact
Gene name

Delta_Death.at.48h Experience 2 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results