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=2.765e^-2)
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	0.01449

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_3R_P	2.8847	0.0894

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1635 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
X	8477222	X_8477222_SNP [dm3] X_8583189_SNP [dm6]	G	A	1.802e^-6	0.815	INTRON CG12065
3L	11208027	3L_11208027_SNP [dm3] 3L_11214927_SNP [dm6]	A	G	2.703e^-6	0.815	UPSTREAM CG42671 DOWNSTREAM CG7600 INTRON CG42671	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_Dll mE1_TFBS_Kr mE1_TFBS_Trl
3L	11208193	3L_11208193_SNP [dm3] 3L_11215093_SNP [dm6]	C	G	2.960e^-6	0.815	UPSTREAM CG42671 DOWNSTREAM CG7600 INTRON CG42671	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_Dll mE1_TFBS_Kr mE1_TFBS_Trl
2L	9132306	2L_9132306_SNP [dm3] 2L_9132306_SNP [dm6]	A	T	3.026e^-6	0.815	INTRON CG32982
3L	11208724	3L_11208724_SNP [dm3] 3L_11215624_SNP [dm6]	A	T	3.345e^-6	0.815	UPSTREAM CG42671 INTRON CG42671	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_hkb mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_Trl
2L	5895016	2L_5895016_SNP [dm3] 2L_5895016_SNP [dm6]	G	A	3.418e^-6	0.815	INTERGENIC
2R	20201980	2R_20201980_SNP [dm3] 2R_24314457_SNP [dm6]	T	A	4.066e^-6	0.815	INTERGENIC
2R	5904225	2R_5904225_SNP [dm3] 2R_10016720_SNP [dm6]	T	C	4.295e^-6	0.815	INTRON Pka-R2
2L	17682283	2L_17682283_SNP [dm3] 2L_17682283_SNP [dm6]	T	G	4.772e^-6	0.815	INTRON CadN
3L	12035373	3L_12035373_SNP [dm3] 3L_12042273_SNP [dm6]	T	A	5.118e^-6	0.815	UPSTREAM CG6793 INTRON rols	TF binding site mE1_TFBS_chinmo
2L	6886174	2L_6886174_SNP [dm3] 2L_6886174_SNP [dm6]	T	C	5.856e^-6	0.815	INTRON Nlg2
2L	5895011	2L_5895011_SNP [dm3] 2L_5895011_SNP [dm6]	G	A	6.319e^-6	0.815	INTERGENIC
X	12388124	X_12388124_SNP [dm3] X_12494091_SNP [dm6]	C	G	6.698e^-6	0.815	DOWNSTREAM Mks1 INTERGENIC
X	12388126	X_12388126_SNP [dm3] X_12494093_SNP [dm6]	A	T	6.698e^-6	0.815	DOWNSTREAM Mks1 INTERGENIC
3L	12035409	3L_12035409_SNP [dm3] 3L_12042309_SNP [dm6]	C	A	7.106e^-6	0.815	UPSTREAM CG6793 INTRON rols	TF binding site mE1_TFBS_chinmo
X	12387047	X_12387047_SNP [dm3] X_12493014_SNP [dm6]	A	C	7.291e^-6	0.815	DOWNSTREAM Lsp1alpha INTERGENIC
2R	6141472	2R_6141472_SNP [dm3] 2R_10253967_SNP [dm6]	C	T	8.297e^-6	0.815	SYNONYMOUS_CODING CG12913	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_inv
2R	5283898	2R_5283898_SNP [dm3] 2R_9396393_SNP [dm6]	C	A	8.663e^-6	0.815	UTR_3_PRIME CG8801 UPSTREAM CG8800	TF binding site mE1_TFBS_cad
X	12388723	X_12388723_SNP [dm3] X_12494690_SNP [dm6]	A	G	9.550e^-6	0.815	SYNONYMOUS_CODING Mks1
3L	8840699	3L_8840699_SNP [dm3] 3L_8847599_SNP [dm6]	T	A	9.794e^-6	0.815	INTRON dally
2R	5285409	2R_5285409_SNP [dm3] 2R_9397904_SNP [dm6]	G	A	9.930e^-6	0.815	SYNONYMOUS_CODING CG8801	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3L	11208298	3L_11208298_SNP [dm3] 3L_11215198_SNP [dm6]	C	A	1.120e^-5	0.815	UPSTREAM CG42671 INTRON CG42671	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_Dll mE1_TFBS_Kr mE1_TFBS_Trl
3L	2335729	3L_2335729_SNP [dm3] 3L_2335729_SNP [dm6]	T	G	1.167e^-5	0.815	INTRON MsR1
3R	5201224	3R_5201224_SNP [dm3] 3R_9375502_SNP [dm6]	C	T	1.172e^-5	0.815	UPSTREAM FER INTRON FER	regulatory region REDfly_CRMs
3L	17902944	3L_17902944_SNP [dm3] 3L_17909844_SNP [dm6]	A	G	1.412e^-5	0.815	NON_SYNONYMOUS_CODING CG5290 DOWNSTREAM CG14353
3L	8840684	3L_8840684_SNP [dm3] 3L_8847584_SNP [dm6]	C	G	1.539e^-5	0.815	INTRON dally
2R	7634908	2R_7634908_SNP [dm3] 2R_11747403_SNP [dm6]	T	C	1.568e^-5	0.815	INTERGENIC
3L	11715659	3L_11715659_SNP [dm3] 3L_11722559_SNP [dm6]	G	A	1.583e^-5	0.815	INTRON Bmcp	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
X	12387044	X_12387044_SNP [dm3] X_12493011_SNP [dm6]	G	T	1.645e^-5	0.815	DOWNSTREAM Lsp1alpha INTERGENIC
X	12387064	X_12387064_SNP [dm3] X_12493031_SNP [dm6]	G	T	1.645e^-5	0.815	DOWNSTREAM Lsp1alpha INTERGENIC
X	12387065	X_12387065_SNP [dm3] X_12493032_SNP [dm6]	C	T	1.645e^-5	0.815	DOWNSTREAM Lsp1alpha INTERGENIC
X	12387069	X_12387069_SNP [dm3] X_12493036_SNP [dm6]	T	G	1.645e^-5	0.815	DOWNSTREAM Lsp1alpha INTERGENIC
X	12387073	X_12387073_SNP [dm3] X_12493040_SNP [dm6]	A	T	1.645e^-5	0.815	DOWNSTREAM Lsp1alpha INTERGENIC
2L	5867149	2L_5867149_SNP [dm3] 2L_5867149_SNP [dm6]	C	T	1.700e^-5	0.815	INTRON rau	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_sens
2R	2895304	2R_2895304_SNP [dm3] 2R_7007799_SNP [dm6]	G	A	1.704e^-5	0.815	NON_SYNONYMOUS_CODING Tsp42Ec	TF binding site mE1_TFBS_cad mE1_TFBS_sens
X	11896397	X_11896397_INS [dm3] X_12002364_INS [dm6]	T	TT	1.753e^-5	0.815	UTR_5_PRIME fw UPSTREAM fw
3R	11566531	3R_11566531_SNP [dm3] 3R_15740809_SNP [dm6]	G	T	1.777e^-5	0.815	INTERGENIC
3R	11566547	3R_11566547_SNP [dm3] 3R_15740825_SNP [dm6]	A	G	1.777e^-5	0.815	INTERGENIC
2R	7634940	2R_7634940_SNP [dm3] 2R_11747435_SNP [dm6]	T	A	1.792e^-5	0.815	INTERGENIC
2L	2629899	2L_2629899_SNP [dm3] 2L_2629899_SNP [dm6]	G	A	1.813e^-5	0.815	INTERGENIC
3L	2559825	3L_2559825_SNP [dm3] 3L_2559825_SNP [dm6]	T	A	1.887e^-5	0.815	INTRON msn
X	12388447	X_12388447_DEL [dm3] X_12494414_DEL [dm6]	TA	T	1.919e^-5	0.815	UTR_3_PRIME Mks1
3L	7440662	3L_7440662_SNP [dm3] 3L_7447562_SNP [dm6]	G	A	2.023e^-5	0.815	INTRON CG42458
3L	7440731	3L_7440731_SNP [dm3] 3L_7447631_SNP [dm6]	A	G	2.023e^-5	0.815	INTRON CG42458
3L	12035406	3L_12035406_SNP [dm3] 3L_12042306_SNP [dm6]	T	C	2.064e^-5	0.815	UPSTREAM CG6793 INTRON rols	TF binding site mE1_TFBS_chinmo
3L	12035410	3L_12035410_SNP [dm3] 3L_12042310_SNP [dm6]	C	G	2.064e^-5	0.815	UPSTREAM CG6793 INTRON rols	TF binding site mE1_TFBS_chinmo
3L	12560215	3L_12560215_SNP [dm3] 3L_12567115_SNP [dm6]	T	A	2.116e^-5	0.818	INTRON sowah	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	11715678	3L_11715678_SNP [dm3] 3L_11722578_SNP [dm6]	T	C	2.331e^-5	0.882	INTRON Bmcp	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3L	7440700	3L_7440700_SNP [dm3] 3L_7447600_SNP [dm6]	T	C	2.407e^-5	0.892	INTRON CG42458
3R	18440769	3R_18440769_SNP [dm3] 3R_22615047_SNP [dm6]	A	T	2.463e^-5	0.895	SYNONYMOUS_CODING EF-G2
3L	7440778	3L_7440778_SNP [dm3] 3L_7447678_SNP [dm6]	G	T	2.552e^-5	0.908	INTRON CG42458	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3L	12282492	3L_12282492_SNP [dm3] 3L_12289392_SNP [dm6]	C	G	2.650e^-5	0.908	EXON CR45658
3L	12282496	3L_12282496_SNP [dm3] 3L_12289396_SNP [dm6]	C	T	2.650e^-5	0.908	EXON CR45658
3L	1974594	3L_1974594_SNP [dm3] 3L_1974594_SNP [dm6]	A	G	2.920e^-5	0.965	DOWNSTREAM CG1139 INTERGENIC
3R	11566583	3R_11566583_SNP [dm3] 3R_15740861_SNP [dm6]	T	C	2.969e^-5	0.965	INTERGENIC
X	14759210	X_14759210_SNP [dm3] X_14865177_SNP [dm6]	T	G	3.159e^-5	0.965	SYNONYMOUS_CODING CG9518 INTRON Flo2	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3L	17904485	3L_17904485_SNP [dm3] 3L_17911385_SNP [dm6]	T	G	3.197e^-5	0.965	SYNONYMOUS_CODING CG5290	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	2629920	2L_2629920_SNP [dm3] 2L_2629920_SNP [dm6]	T	C	3.240e^-5	0.965	INTERGENIC
3L	12035289	3L_12035289_SNP [dm3] 3L_12042189_SNP [dm6]	T	C	3.374e^-5	0.965	UPSTREAM CG6793 INTRON rols
X	12387048	X_12387048_SNP [dm3] X_12493015_SNP [dm6]	A	T	3.491e^-5	0.965	DOWNSTREAM Lsp1alpha INTERGENIC
2R	6355870	2R_6355870_SNP [dm3] 2R_10468365_SNP [dm6]	C	A	3.581e^-5	0.965	SYNONYMOUS_CODING Caf1-105 UPSTREAM CG11777	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	121672	2L_121672_DEL [dm3] 2L_121672_DEL [dm6]	TT	T	3.638e^-5	0.965	UTR_5_PRIME CG4822 UPSTREAM CG4822 DOWNSTREAM CG3164 INTRON CG11455
3L	13336050	3L_13336050_SNP [dm3] 3L_13342950_SNP [dm6]	T	G	3.665e^-5	0.965	DOWNSTREAM CR44559 INTERGENIC
2R	16839043	2R_16839043_DEL [dm3] 2R_20951538_DEL [dm6]	AAAGAGCATGA...	A	3.903e^-5	0.965	DOWNSTREAM CG33704 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	17783203	3R_17783203_SNP [dm3] 3R_21957481_SNP [dm6]	G	A	4.221e^-5	0.965	INTRON Eip93F
2R	15398133	2R_15398133_SNP [dm3] 2R_19510628_SNP [dm6]	T	C	4.423e^-5	0.965	SYNONYMOUS_CODING Ir56c DOWNSTREAM Ir56b
3L	22021397	3L_22021397_SNP [dm3] 3L_22028297_SNP [dm6]	A	C	4.425e^-5	0.965	UTR_5_PRIME CG7140
3R	20298039	3R_20298039_SNP [dm3] 3R_24472317_SNP [dm6]	A	C	4.454e^-5	0.965	INTERGENIC
3R	20106625	3R_20106625_DEL [dm3] 3R_24280903_DEL [dm6]	ACGG	T	4.530e^-5	0.965		TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	10844907	2L_10844907_SNP [dm3] 2L_10844907_SNP [dm6]	G	C	4.615e^-5	0.965	SYNONYMOUS_CODING CG17139 START_GAINED CG17140 UTR_5_PRIME CG17140 UPSTREAM CG17140 DOWNSTREAM Porin2
2R	6961523	2R_6961523_INS [dm3] 2R_11074018_INS [dm6]	A	AA	4.674e^-5	0.965	INTRON luna
3R	13970456	3R_13970456_SNP [dm3] 3R_18144734_SNP [dm6]	G	A	4.742e^-5	0.965	INTERGENIC
3R	19544875	3R_19544875_SNP [dm3] 3R_23719153_SNP [dm6]	A	G	4.855e^-5	0.965	UPSTREAM nau DOWNSTREAM CG10232 INTERGENIC
3L	486876	3L_486876_SNP [dm3] 3L_486876_SNP [dm6]	C	A	5.092e^-5	0.965	INTRON klar	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	6252747	3R_6252747_SNP [dm3] 3R_10427025_SNP [dm6]	C	T	5.159e^-5	0.965	INTERGENIC
2R	14087413	2R_14087413_SNP [dm3] 2R_18199908_SNP [dm6]	G	A	5.227e^-5	0.965	INTERGENIC
2R	14087421	2R_14087421_SNP [dm3] 2R_18199916_SNP [dm6]	A	G	5.227e^-5	0.965	INTERGENIC
3R	26394899	3R_26394899_SNP [dm3] 3R_30569177_SNP [dm6]	G	C	5.306e^-5	0.965	INTRON tmod	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	26394906	3R_26394906_SNP [dm3] 3R_30569184_SNP [dm6]	T	C	5.306e^-5	0.965	INTRON tmod	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
X	18274472	X_18274472_SNP [dm3] X_18380439_SNP [dm6]	A	G	5.370e^-5	0.965	SYNONYMOUS_CODING CG6179 UPSTREAM por	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	15182240	2L_15182240_SNP [dm3] 2L_15182240_SNP [dm6]	C	A	5.390e^-5	0.965	INTRON CG4168	TF binding site mE1_TFBS_cad
X	10613143	X_10613143_DEL [dm3] X_10719110_DEL [dm6]	TAGCATAAAGTG...	T	5.488e^-5	0.965	INTRON CG32676
X	10613157	X_10613157_SNP [dm3] X_10719124_SNP [dm6]	G	A	5.488e^-5	0.965	INTRON CG32676
X	10613158	X_10613158_SNP [dm3] X_10719125_SNP [dm6]	T	G	5.488e^-5	0.965	INTRON CG32676
2R	15742241	2R_15742241_SNP [dm3] 2R_19854736_SNP [dm6]	G	A	5.541e^-5	0.965	INTERGENIC	TF binding site BDTNP1_TFBS_da
3L	7440697	3L_7440697_SNP [dm3] 3L_7447597_SNP [dm6]	A	G	5.633e^-5	0.965	INTRON CG42458
3L	17903214	3L_17903214_SNP [dm3] 3L_17910114_SNP [dm6]	A	G	5.929e^-5	0.965	SYNONYMOUS_CODING CG5290 DOWNSTREAM CG14353	TF binding site mE1_TFBS_chinmo
3L	3238210	3L_3238210_SNP [dm3] 3L_3238210_SNP [dm6]	C	G	6.061e^-5	0.965	INTRON CG17746	TF binding site BDTNP1_TFBS_twi
2R	6738795	2R_6738795_INS [dm3] 2R_10851290_INS [dm6]	A	AAA	6.069e^-5	0.965	INTRON CG30015
2L	8396603	2L_8396603_SNP [dm3] 2L_8396603_SNP [dm6]	C	A	6.125e^-5	0.965	UPSTREAM CG13385 & 1 other INTERGENIC	TF binding site mE1_TFBS_cad
3R	26602045	3R_26602045_SNP [dm3] 3R_30776323_SNP [dm6]	G	A	6.252e^-5	0.965	INTRON zfh1	TF binding site BDTNP1_TFBS_dl
3R	22030425	3R_22030425_SNP [dm3] 3R_26204703_SNP [dm6]	G	C	6.485e^-5	0.965	INTRON CR44320
2L	15371920	2L_15371920_SNP [dm3] 2L_15371920_SNP [dm6]	A	C	6.506e^-5	0.965	INTERGENIC
2R	15742229	2R_15742229_SNP [dm3] 2R_19854724_SNP [dm6]	G	A	6.704e^-5	0.965	INTERGENIC	TF binding site BDTNP1_TFBS_da
2R	20201815	2R_20201815_SNP [dm3] 2R_24314292_SNP [dm6]	G	C	6.794e^-5	0.965	INTERGENIC
2R	20201954	2R_20201954_SNP [dm3] 2R_24314431_SNP [dm6]	G	A	6.794e^-5	0.965	INTERGENIC
3L	12282638	3L_12282638_SNP [dm3] 3L_12289538_SNP [dm6]	A	T	6.861e^-5	0.965	EXON CR45658
3L	12282646	3L_12282646_SNP [dm3] 3L_12289546_SNP [dm6]	G	T	6.861e^-5	0.965	EXON CR45658
3L	12282655	3L_12282655_SNP [dm3] 3L_12289555_SNP [dm6]	G	T	6.861e^-5	0.965	EXON CR45658
3L	4313089	3L_4313089_SNP [dm3] 3L_4313089_SNP [dm6]	G	C	6.887e^-5	0.965	UPSTREAM Claspin INTERGENIC

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Missing results

By genomic position
Variant impact
Gene name

pc_FL_PElem_SC phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results