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=3.705e^-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
wolba	0.08175
In_2L_t	0.02902
In_2R_NS	0.08410
In_3R_Mo	0.04730

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	6.6811	0.0354
In_3R_K	5.507	0.0637

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2240 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	15055734	3L_15055734_SNP [dm3] 3L_15062634_SNP [dm6]	T	C	3.712e^-7	0.536	UPSTREAM CG13460 & 1 other INTRON Sytbeta
3L	11142376	3L_11142376_SNP [dm3] 3L_11149276_SNP [dm6]	G	A	7.161e^-7	0.536	DOWNSTREAM CG6216 INTRON CG32082
3L	15881100	3L_15881100_SNP [dm3] 3L_15888000_SNP [dm6]	A	G	1.817e^-6	0.536	INTRON pHCl
3L	8675181	3L_8675181_SNP [dm3] 3L_8682081_SNP [dm6]	G	A	1.823e^-6	0.536	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_prd mE1_TFBS_HSA mE1_TFBS_sens
3L	15889722	3L_15889722_SNP [dm3] 3L_15896622_SNP [dm6]	A	G	1.867e^-6	0.536	INTRON pHCl
2R	9269114	2R_9269114_SNP [dm3] 2R_13381609_SNP [dm6]	T	G	1.970e^-6	0.536	INTERGENIC
3L	7330950	3L_7330950_SNP [dm3] 3L_7337850_SNP [dm6]	T	C	1.999e^-6	0.536	NON_SYNONYMOUS_CODING eco	TF binding site mE1_TFBS_cad mE1_TFBS_sens
3L	7331186	3L_7331186_SNP [dm3] 3L_7338086_SNP [dm6]	C	T	2.722e^-6	0.594	NON_SYNONYMOUS_CODING eco	TF binding site mE1_TFBS_cad mE1_TFBS_sens
3L	15886584	3L_15886584_SNP [dm3] 3L_15893484_SNP [dm6]	G	A	2.986e^-6	0.594	INTRON pHCl
2R	16921396	2R_16921396_SNP [dm3] 2R_21033891_SNP [dm6]	A	C	3.166e^-6	0.594	INTERGENIC	TF binding site BDTNP1_TFBS_twi
3R	17618570	3R_17618570_SNP [dm3] 3R_21792848_SNP [dm6]	A	G	4.356e^-6	0.694	INTRON CASK	TF binding site mE1_TFBS_cad
2L	11334482	2L_11334482_INS [dm3] 2L_11334482_INS [dm6]	G	GG	4.688e^-6	0.694	INTERGENIC
3R	17370221	3R_17370221_SNP [dm3] 3R_21544499_SNP [dm6]	C	A	4.886e^-6	0.694	INTERGENIC	TF binding site BDTNP1_TFBS_prd
3L	7799372	3L_7799372_SNP [dm3] 3L_7806272_SNP [dm6]	T	G	5.894e^-6	0.694	INTRON CG32369	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sbb mE1_TFBS_Trl
X	5449728	X_5449728_SNP [dm3] X_5555695_SNP [dm6]	C	A	5.900e^-6	0.694	INTRON Vsx2	TF binding site mE1_TFBS_cnc mE1_TFBS_Kr
2R	9269238	2R_9269238_SNP [dm3] 2R_13381733_SNP [dm6]	G	A	5.920e^-6	0.694	INTERGENIC
3R	24205174	3R_24205174_SNP [dm3] 3R_28379452_SNP [dm6]	A	G	7.008e^-6	0.709	INTERGENIC
3R	10249528	3R_10249528_SNP [dm3] 3R_14423806_SNP [dm6]	A	G	7.604e^-6	0.709	INTRON cv-c
3L	16235259	3L_16235259_SNP [dm3] 3L_16242159_SNP [dm6]	A	G	8.423e^-6	0.709	INTERGENIC
3L	4410601	3L_4410601_SNP [dm3] 3L_4410601_SNP [dm6]	T	C	9.057e^-6	0.709	INTRON DOR	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad
2R	9269202	2R_9269202_SNP [dm3] 2R_13381697_SNP [dm6]	G	A	9.198e^-6	0.709	INTERGENIC
X	2698884	X_2698884_SNP [dm3] X_2804851_SNP [dm6]	A	C	9.722e^-6	0.709	INTRON kirre	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	7799375	3L_7799375_SNP [dm3] 3L_7806275_SNP [dm6]	C	T	1.004e^-5	0.709	INTRON CG32369	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sbb mE1_TFBS_Trl
2R	6058050	2R_6058050_SNP [dm3] 2R_10170545_SNP [dm6]	C	T	1.026e^-5	0.709	INTRON KCNQ
2R	9269197	2R_9269197_SNP [dm3] 2R_13381692_SNP [dm6]	A	G	1.034e^-5	0.709	INTERGENIC
3L	4410596	3L_4410596_SNP [dm3] 3L_4410596_SNP [dm6]	T	A	1.042e^-5	0.709	INTRON DOR	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad
3L	4410589	3L_4410589_SNP [dm3] 3L_4410589_SNP [dm6]	T	G	1.048e^-5	0.709	INTRON DOR	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad
3L	15884162	3L_15884162_SNP [dm3] 3L_15891062_SNP [dm6]	A	G	1.082e^-5	0.709	INTRON pHCl
3L	8634391	3L_8634391_SNP [dm3] 3L_8641291_SNP [dm6]	T	A	1.122e^-5	0.709	INTRON Cpr66D
3L	14941736	3L_14941736_SNP [dm3] 3L_14948636_SNP [dm6]	G	A	1.199e^-5	0.709	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi
3L	15889772	3L_15889772_SNP [dm3] 3L_15896672_SNP [dm6]	G	A	1.232e^-5	0.709	INTRON pHCl
2R	10200612	2R_10200612_SNP [dm3] 2R_14313107_SNP [dm6]	G	A	1.378e^-5	0.709	INTRON Shroom	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	18651406	3R_18651406_SNP [dm3] 3R_22825684_SNP [dm6]	C	T	1.408e^-5	0.709	EXON CR44350
3R	21279810	3R_21279810_INS [dm3] 3R_25454088_INS [dm6]	G	GCACTTATAAGTGTAAG...	1.466e^-5	0.709	INTRON Fur1
3L	7799380	3L_7799380_SNP [dm3] 3L_7806280_SNP [dm6]	G	A	1.494e^-5	0.709	INTRON CG32369	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sbb mE1_TFBS_Trl
2R	10956731	2R_10956731_SNP [dm3] 2R_15069226_SNP [dm6]	C	T	1.511e^-5	0.709	INTERGENIC
3L	23033953	3L_23033953_SNP [dm3] 3L_23040853_SNP [dm6]	T	A	1.522e^-5	0.709	DOWNSTREAM nrm INTERGENIC
3L	4710364	3L_4710364_SNP [dm3] 3L_4710364_SNP [dm6]	T	A	1.538e^-5	0.709	UPSTREAM CG13712 INTRON RhoGEF64C	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	17365836	3R_17365836_SNP [dm3] 3R_21540114_SNP [dm6]	A	T	1.581e^-5	0.709	INTERGENIC
3L	7799352	3L_7799352_SNP [dm3] 3L_7806252_SNP [dm6]	C	T	1.614e^-5	0.709	INTRON CG32369	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sbb mE1_TFBS_Trl
3R	9738642	3R_9738642_SNP [dm3] 3R_13912920_SNP [dm6]	T	G	1.643e^-5	0.709	INTERGENIC	TF binding site mE1_TFBS_inv
2L	2671552	2L_2671552_SNP [dm3] 2L_2671552_SNP [dm6]	G	C	1.658e^-5	0.709	SYNONYMOUS_CODING Gr23a INTRON Gr23a	TF binding site mE1_TFBS_sens
2R	17767855	2R_17767855_SNP [dm3] 2R_21880350_SNP [dm6]	G	A	1.669e^-5	0.709	INTRON Fili	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	2318258	2L_2318258_SNP [dm3] 2L_2318258_SNP [dm6]	T	A	1.796e^-5	0.709	INTRON CG9967 & 1 other
3L	4710366	3L_4710366_SNP [dm3] 3L_4710366_SNP [dm6]	C	T	1.859e^-5	0.709	UPSTREAM CG13712 INTRON RhoGEF64C	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	995863	3L_995863_SNP [dm3] 3L_995863_SNP [dm6]	G	T	1.910e^-5	0.709	DOWNSTREAM trio & 1 other INTERGENIC
X	2540756	X_2540756_SNP [dm3] X_2646723_SNP [dm6]	C	G	1.940e^-5	0.709	UTR_5_PRIME sgg INTRON sgg	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
3L	4710349	3L_4710349_SNP [dm3] 3L_4710349_SNP [dm6]	A	G	1.941e^-5	0.709	UPSTREAM CG13712 INTRON RhoGEF64C	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	4710350	3L_4710350_DEL [dm3] 3L_4710350_DEL [dm6]	TAGAT	T	1.941e^-5	0.709	UPSTREAM CG13712 INTRON RhoGEF64C	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	4710363	3L_4710363_SNP [dm3] 3L_4710363_SNP [dm6]	G	A	1.941e^-5	0.709	UPSTREAM CG13712 INTRON RhoGEF64C	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	9882385	3R_9882385_DEL [dm3] 3R_14056663_DEL [dm6]	ATAG	T	1.974e^-5	0.709	UPSTREAM foxo INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
2R	9269137	2R_9269137_SNP [dm3] 2R_13381632_SNP [dm6]	T	A	2.118e^-5	0.709	INTERGENIC
2L	4523664	2L_4523664_SNP [dm3] 2L_4523664_SNP [dm6]	A	C	2.119e^-5	0.709	INTRON dp
3L	8607436	3L_8607436_SNP [dm3] 3L_8614336_SNP [dm6]	C	T	2.128e^-5	0.709	INTRON CG6282
2R	14762500	2R_14762500_SNP [dm3] 2R_18874995_SNP [dm6]	A	C	2.164e^-5	0.709	INTERGENIC
3L	4710377	3L_4710377_DEL [dm3] 3L_4710377_DEL [dm6]	AG	A	2.165e^-5	0.709	UPSTREAM CG13712 INTRON RhoGEF64C	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	3574190	2L_3574190_SNP [dm3] 2L_3574190_SNP [dm6]	C	T	2.191e^-5	0.709	INTERGENIC	silencer mE1_HDAC_PRE TF binding site mE1_TFBS_cad mE1_TFBS_Trl
2L	4523681	2L_4523681_SNP [dm3] 2L_4523681_SNP [dm6]	G	A	2.192e^-5	0.709	INTRON dp
2R	9269124	2R_9269124_DEL [dm3] 2R_13381619_DEL [dm6]	TG	T	2.242e^-5	0.713	INTERGENIC
2R	9269128	2R_9269128_SNP [dm3] 2R_13381623_SNP [dm6]	A	T	2.378e^-5	0.728	INTERGENIC
3L	7799586	3L_7799586_SNP [dm3] 3L_7806486_SNP [dm6]	G	C	2.409e^-5	0.728	INTRON CG32369	TF binding site mE1_TFBS_Trl
2R	9269117	2R_9269117_DEL [dm3] 2R_13381612_DEL [dm6]	AAAGA	TCT	2.420e^-5	0.728	INTERGENIC
3R	25919979	3R_25919979_SNP [dm3] 3R_30094257_SNP [dm6]	T	G	2.461e^-5	0.728	INTRON sima	TF binding site mE1_TFBS_inv
2R	17427710	2R_17427710_SNP [dm3] 2R_21540205_SNP [dm6]	G	A	2.486e^-5	0.728	UPSTREAM CG33226 INTRON Egfr & 1 other	TF binding site mE1_TFBS_D mE1_TFBS_HSA
2L	13539501	2L_13539501_SNP [dm3] 2L_13539501_SNP [dm6]	G	A	2.571e^-5	0.732	INTRON B4
3L	4709865	3L_4709865_SNP [dm3] 3L_4709865_SNP [dm6]	T	C	2.620e^-5	0.732	UTR_5_PRIME CG13712 INTRON RhoGEF64C	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	4709870	3L_4709870_SNP [dm3] 3L_4709870_SNP [dm6]	A	C	2.620e^-5	0.732	UTR_5_PRIME CG13712 INTRON RhoGEF64C	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	19703870	3R_19703870_SNP [dm3] 3R_23878148_SNP [dm6]	A	G	2.729e^-5	0.732	INTRON Pli
2L	3587900	2L_3587900_SNP [dm3] 2L_3587900_SNP [dm6]	G	A	2.837e^-5	0.732	DOWNSTREAM CR43823 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_sens
2L	7812417	2L_7812417_SNP [dm3] 2L_7812417_SNP [dm6]	C	A	2.867e^-5	0.732	INTRON LanB1	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi
3L	9819590	3L_9819590_SNP [dm3] 3L_9826490_SNP [dm6]	A	C	2.881e^-5	0.732	SYNONYMOUS_CODING CG43897 INTRON CG43897
3R	5366433	3R_5366433_SNP [dm3] 3R_9540711_SNP [dm6]	A	T	2.951e^-5	0.732	SYNONYMOUS_CODING mura	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3L	9819557	3L_9819557_SNP [dm3] 3L_9826457_SNP [dm6]	C	A	2.987e^-5	0.732	SYNONYMOUS_CODING CG43897 INTRON CG43897
3L	7799176	3L_7799176_SNP [dm3] 3L_7806076_SNP [dm6]	T	C	2.996e^-5	0.732	INTRON CG32369	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sbb mE1_TFBS_Trl
3L	5775282	3L_5775282_SNP [dm3] 3L_5782182_SNP [dm6]	A	C	3.029e^-5	0.732	NON_SYNONYMOUS_CODING PGRP-LD UTR_3_PRIME Pmi
3L	11444323	3L_11444323_SNP [dm3] 3L_11451223_SNP [dm6]	C	G	3.033e^-5	0.732	INTERGENIC
2R	11618430	2R_11618430_SNP [dm3] 2R_15730925_SNP [dm6]	T	G	3.113e^-5	0.732	INTRON CG30089	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	11618438	2R_11618438_SNP [dm3] 2R_15730933_SNP [dm6]	T	A	3.113e^-5	0.732	INTRON CG30089	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	7813951	2L_7813951_SNP [dm3] 2L_7813951_SNP [dm6]	T	C	3.152e^-5	0.732	UPSTREAM LanB1 INTRON LanB1
2L	2671684	2L_2671684_SNP [dm3] 2L_2671684_SNP [dm6]	C	T	3.180e^-5	0.732	SYNONYMOUS_CODING Gr23a INTRON Gr23a
3L	22641876	3L_22641876_SNP [dm3] 3L_22648776_SNP [dm6]	G	A	3.181e^-5	0.732	UPSTREAM CG33771 DOWNSTREAM CG33769 INTRON CG33770
3L	16887438	3L_16887438_SNP [dm3] 3L_16894338_SNP [dm6]	A	G	3.279e^-5	0.732	INTRON Lmpt
3L	18364980	3L_18364980_SNP [dm3] 3L_18371880_SNP [dm6]	C	T	3.308e^-5	0.732	INTERGENIC
2R	17092769	2R_17092769_SNP [dm3] 2R_21205264_SNP [dm6]	T	C	3.318e^-5	0.732	SYNONYMOUS_CODING Glycogenin INTRON CG44245
3L	12853276	3L_12853276_SNP [dm3] 3L_12860176_SNP [dm6]	G	A	3.384e^-5	0.732	SYNONYMOUS_CODING CG32107	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	18651445	3R_18651445_SNP [dm3] 3R_22825723_SNP [dm6]	G	A	3.396e^-5	0.732	EXON CR44350
X	14247752	X_14247752_SNP [dm3] X_14353719_SNP [dm6]	C	T	3.495e^-5	0.732	INTRON dpr8
3L	9252399	3L_9252399_SNP [dm3] 3L_9259299_SNP [dm6]	T	A	3.552e^-5	0.732	INTRON GluRIB	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3L	12519071	3L_12519071_SNP [dm3] 3L_12525971_SNP [dm6]	A	T	3.646e^-5	0.732	DOWNSTREAM ver INTRON eIF-2beta	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	9252371	3L_9252371_SNP [dm3] 3L_9259271_SNP [dm6]	T	A	3.653e^-5	0.732	INTRON GluRIB	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2R	19601518	2R_19601518_SNP [dm3] 2R_23713995_SNP [dm6]	C	T	3.714e^-5	0.732	UTR_5_PRIME Sesn	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
X	5449785	X_5449785_SNP [dm3] X_5555752_SNP [dm6]	G	A	3.714e^-5	0.732	INTRON Vsx2	TF binding site mE1_TFBS_Kr
3L	9627046	3L_9627046_SNP [dm3] 3L_9633946_SNP [dm6]	G	A	3.716e^-5	0.732	INTRON fry	TF binding site mE1_TFBS_cad
2R	7719578	2R_7719578_SNP [dm3] 2R_11832073_SNP [dm6]	A	G	3.752e^-5	0.732	INTRON Sobp	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	4749581	2L_4749581_SNP [dm3] 2L_4749581_SNP [dm6]	C	A	3.791e^-5	0.732	INTRON CG15630
2L	4023666	2L_4023666_SNP [dm3] 2L_4023666_SNP [dm6]	G	A	3.823e^-5	0.732	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	996409	3L_996409_SNP [dm3] 3L_996409_SNP [dm6]	T	C	3.853e^-5	0.732	UTR_3_PRIME trio DOWNSTREAM CG12038 & 1 other
3R	18651398	3R_18651398_SNP [dm3] 3R_22825676_SNP [dm6]	C	T	3.857e^-5	0.732	EXON CR44350
3R	17618547	3R_17618547_SNP [dm3] 3R_21792825_SNP [dm6]	C	A	3.894e^-5	0.732	INTRON CASK	TF binding site mE1_TFBS_cad
2R	14383138	2R_14383138_SNP [dm3] 2R_18495633_SNP [dm6]	T	A	3.996e^-5	0.732	INTRON CG30116

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By genomic position
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idx_Surv_10MeHg phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results