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=8.422e^-16)
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_K	0.0653

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_3R_K	7.4906	0.0236

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2787 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	4227332	2R_4227332_SNP [dm3] 2R_8339827_SNP [dm6]	C	G	3.153e^-7	0.402	INTRON pdm3	TF binding site mE1_TFBS_cad
2L	20563394	2L_20563394_SNP [dm3] 2L_20563394_SNP [dm6]	A	G	4.292e^-7	0.402	DOWNSTREAM mir-4973 INTRON CR45347
3L	5161961	3L_5161961_SNP [dm3] 3L_5168861_SNP [dm6]	C	T	1.125e^-6	0.433	INTRON shep	TF binding site mE1_TFBS_HSA mE1_TFBS_Kr
2L	3634285	2L_3634285_SNP [dm3] 2L_3634285_SNP [dm6]	C	T	1.216e^-6	0.433	SYNONYMOUS_CODING for	TF binding site BDTNP1_TFBS_dl mE1_TFBS_D mE1_TFBS_hkb mE1_TFBS_HSA
2L	20527572	2L_20527572_SNP [dm3] 2L_20527572_SNP [dm6]	T	G	1.372e^-6	0.433	INTERGENIC
3L	10402033	3L_10402033_INS [dm3] 3L_10408933_INS [dm6]	T	TT	1.386e^-6	0.433	INTERGENIC
2L	15466916	2L_15466916_DEL [dm3] 2L_15466916_DEL [dm6]	AA	A	1.969e^-6	0.468	INTERGENIC
2R	6246394	2R_6246394_SNP [dm3] 2R_10358889_SNP [dm6]	G	C	2.932e^-6	0.468	INTRON CG42732
2L	20560613	2L_20560613_SNP [dm3] 2L_20560613_SNP [dm6]	T	G	2.946e^-6	0.468	INTERGENIC
2R	4227403	2R_4227403_SNP [dm3] 2R_8339898_SNP [dm6]	C	A	2.998e^-6	0.468	INTRON pdm3	TF binding site mE1_TFBS_cad
2L	9966046	2L_9966046_SNP [dm3] 2L_9966046_SNP [dm6]	A	G	3.050e^-6	0.468	SYNONYMOUS_CODING Dref	TF binding site mE1_TFBS_sens
2R	18120062	2R_18120062_SNP [dm3] 2R_22232557_SNP [dm6]	T	G	3.226e^-6	0.468	INTERGENIC
2R	6239066	2R_6239066_SNP [dm3] 2R_10351561_SNP [dm6]	C	T	3.803e^-6	0.468	UTR_3_PRIME CG43172 & 1 other DOWNSTREAM CG43171 & 2 others INTRON CG42732
2L	15325079	2L_15325079_SNP [dm3] 2L_15325079_SNP [dm6]	A	G	3.825e^-6	0.468	INTERGENIC	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_shn BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Kr
2R	4235896	2R_4235896_SNP [dm3] 2R_8348391_SNP [dm6]	T	C	4.576e^-6	0.468	INTRON pdm3	TF binding site mE1_TFBS_cad
X	16824362	X_16824362_SNP [dm3] X_16930329_SNP [dm6]	C	T	4.785e^-6	0.468	INTRON CG4928
X	2224291	X_2224291_SNP [dm3] X_2330258_SNP [dm6]	T	A	4.876e^-6	0.468	INTRON phl EXON CR33218
3R	17740663	3R_17740663_SNP [dm3] 3R_21914941_SNP [dm6]	C	G	4.959e^-6	0.468	NON_SYNONYMOUS_CODING CG17843
2L	15465989	2L_15465989_SNP [dm3] 2L_15465989_SNP [dm6]	G	A	5.109e^-6	0.468	INTERGENIC
2L	20954736	2L_20954736_SNP [dm3] 2L_20954736_SNP [dm6]	C	A	5.195e^-6	0.468	INTERGENIC
2L	15467163	2L_15467163_SNP [dm3] 2L_15467163_SNP [dm6]	T	G	5.322e^-6	0.468	INTERGENIC	TF binding site BDTNP1_TFBS_dl
2L	20570414	2L_20570414_SNP [dm3] 2L_20570414_SNP [dm6]	T	C	5.792e^-6	0.468	INTRON CR45347
3L	4681184	3L_4681184_SNP [dm3] 3L_4681184_SNP [dm6]	A	T	6.025e^-6	0.468	INTRON axo
2L	3633813	2L_3633813_SNP [dm3] 2L_3633813_SNP [dm6]	A	T	6.618e^-6	0.468	INTRON for	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	7904834	2L_7904834_SNP [dm3] 2L_7904834_SNP [dm6]	T	C	6.900e^-6	0.468	INTRON Snoo	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2R	17159517	2R_17159517_SNP [dm3] 2R_21272012_SNP [dm6]	T	G	7.370e^-6	0.468	INTRON Rgk3
X	5892976	X_5892976_SNP [dm3] X_5998943_SNP [dm6]	T	G	7.408e^-6	0.468	SPLICE_SITE_REGION CG4766 INTRON CG4766	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	1433301	2L_1433301_SNP [dm3] 2L_1433301_SNP [dm6]	A	T	7.566e^-6	0.468	DOWNSTREAM snRNA:U3:22A INTERGENIC
2L	7916670	2L_7916670_SNP [dm3] 2L_7916670_SNP [dm6]	G	A	7.693e^-6	0.468	INTRON Snoo
2L	20566456	2L_20566456_SNP [dm3] 2L_20566456_SNP [dm6]	C	G	7.769e^-6	0.468	INTRON CR45347
2R	3907418	2R_3907418_DEL [dm3] 2R_8019913_DEL [dm6]	ACAA	T	7.912e^-6	0.468	EXON CR45267	TF binding site BDTNP1_TFBS_Med
2R	18972875	2R_18972875_SNP [dm3] 2R_23085352_SNP [dm6]	C	T	7.986e^-6	0.468	DOWNSTREAM CG9877 INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	9588212	3R_9588212_SNP [dm3] 3R_13762490_SNP [dm6]	G	T	8.522e^-6	0.477	DOWNSTREAM CG34383 INTRON CG34383
3L	4681182	3L_4681182_SNP [dm3] 3L_4681182_SNP [dm6]	A	T	8.898e^-6	0.477	INTRON axo
2L	20526081	2L_20526081_SNP [dm3] 2L_20526081_SNP [dm6]	A	G	8.940e^-6	0.477	INTERGENIC	TF binding site mE1_TFBS_inv
2R	16868203	2R_16868203_SNP [dm3] 2R_20980698_SNP [dm6]	A	C	9.148e^-6	0.477	INTRON CG9313
2L	20797822	2L_20797822_SNP [dm3] 2L_20797822_SNP [dm6]	G	A	9.477e^-6	0.48	UTR_5_PRIME CG9328 UPSTREAM vari	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_GATAe mE1_TFBS_HSA mE1_TFBS_jumu mE1_TFBS_Kr mE1_TFBS_run mE1_TFBS_Trl
3R	15575851	3R_15575851_SNP [dm3] 3R_19750129_SNP [dm6]	A	G	1.013e^-5	0.489	INTRON GluClalpha
3L	6668105	3L_6668105_SNP [dm3] 3L_6675005_SNP [dm6]	A	G	1.039e^-5	0.489	INTERGENIC
2L	20560484	2L_20560484_SNP [dm3] 2L_20560484_SNP [dm6]	T	A	1.047e^-5	0.489	INTERGENIC
3L	12125055	3L_12125055_SNP [dm3] 3L_12131955_SNP [dm6]	T	C	1.089e^-5	0.489	UPSTREAM CG11534 DOWNSTREAM Lsp2 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_sna mE1_TFBS_HSA
2R	18119910	2R_18119910_SNP [dm3] 2R_22232405_SNP [dm6]	C	G	1.095e^-5	0.489	INTERGENIC
3R	18851705	3R_18851705_SNP [dm3] 3R_23025983_SNP [dm6]	G	C	1.137e^-5	0.489	NON_SYNONYMOUS_CODING lmd	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	20954737	2L_20954737_SNP [dm3] 2L_20954737_SNP [dm6]	T	A	1.147e^-5	0.489	INTERGENIC
3L	2536146	3L_2536146_SNP [dm3] 3L_2536146_SNP [dm6]	G	A	1.240e^-5	0.495	SYNONYMOUS_CODING Spn	TF binding site mE1_TFBS_chinmo
2R	13805919	2R_13805919_SNP [dm3] 2R_17918414_SNP [dm6]	C	T	1.250e^-5	0.495	INTRON Elk
2R	3939954	2R_3939954_SNP [dm3] 2R_8052449_SNP [dm6]	G	A	1.280e^-5	0.495	UTR_3_PRIME CG12769	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_zfh1
X	16824361	X_16824361_SNP [dm3] X_16930328_SNP [dm6]	A	T	1.292e^-5	0.495	INTRON CG4928
2R	16377411	2R_16377411_SNP [dm3] 2R_20489906_SNP [dm6]	C	T	1.324e^-5	0.495	DOWNSTREAM CR44643 INTERGENIC
2L	4143034	2L_4143034_INS [dm3] 2L_4143034_INS [dm6]	A	AAA	1.359e^-5	0.495	INTERGENIC
X	19368586	X_19368586_SNP [dm3] X_19474553_SNP [dm6]	T	C	1.364e^-5	0.495	NON_SYNONYMOUS_CODING CG32533 UPSTREAM CG12200	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	12125048	3L_12125048_SNP [dm3] 3L_12131948_SNP [dm6]	T	A	1.442e^-5	0.495	UPSTREAM CG11534 DOWNSTREAM Lsp2 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_sna mE1_TFBS_HSA
3R	9637066	3R_9637066_SNP [dm3] 3R_13811344_SNP [dm6]	G	A	1.464e^-5	0.495	INTERGENIC	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_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	7819823	3R_7819823_SNP [dm3] 3R_11994101_SNP [dm6]	C	T	1.470e^-5	0.495	UPSTREAM mfas DOWNSTREAM Tk INTERGENIC	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
2R	14143171	2R_14143171_SNP [dm3] 2R_18255666_SNP [dm6]	G	C	1.486e^-5	0.495	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	1404473	2R_1404473_SNP [dm3] 2R_5516968_SNP [dm6]	T	C	1.511e^-5	0.495	INTRON CG30438	transposable element FlyBase
X	19368590	X_19368590_SNP [dm3] X_19474557_SNP [dm6]	G	C	1.554e^-5	0.495	SYNONYMOUS_CODING CG32533 UPSTREAM CG12200	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2R	4236095	2R_4236095_SNP [dm3] 2R_8348590_SNP [dm6]	C	A	1.622e^-5	0.495	INTRON pdm3
2R	15428222	2R_15428222_SNP [dm3] 2R_19540717_SNP [dm6]	G	C	1.622e^-5	0.495	INTRON sm
2L	16002975	2L_16002975_SNP [dm3] 2L_16002975_SNP [dm6]	G	C	1.633e^-5	0.495	DOWNSTREAM CG34167 & 2 others INTRON beat-Ic
2R	4079117	2R_4079117_SNP [dm3] 2R_8191612_SNP [dm6]	C	T	1.657e^-5	0.495	INTRON LRP1	TF binding site mE1_TFBS_GATAe mE1_TFBS_HSA
2R	18144372	2R_18144372_SNP [dm3] 2R_22256867_SNP [dm6]	T	C	1.663e^-5	0.495	INTRON dve	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
2R	18144373	2R_18144373_SNP [dm3] 2R_22256868_SNP [dm6]	G	A	1.663e^-5	0.495	INTRON dve	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
3R	2720642	3R_2720642_SNP [dm3] 3R_6894920_SNP [dm6]	T	C	1.702e^-5	0.499	DOWNSTREAM CR44932 INTERGENIC	regulatory region FlyBase REDfly_CRMs
3R	12509823	3R_12509823_SNP [dm3] 3R_16684101_SNP [dm6]	G	A	1.730e^-5	0.499	INTRON Ubx	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb
2L	15467115	2L_15467115_SNP [dm3] 2L_15467115_SNP [dm6]	G	A	1.760e^-5	0.5	INTERGENIC	TF binding site BDTNP1_TFBS_dl
X	19368793	X_19368793_SNP [dm3] X_19474760_SNP [dm6]	T	C	1.797e^-5	0.503	NON_SYNONYMOUS_CODING CG32533 UPSTREAM CG12200	TF binding site mE1_TFBS_cad
2L	6273091	2L_6273091_SNP [dm3] 2L_6273091_SNP [dm6]	T	G	2.031e^-5	0.526	NON_SYNONYMOUS_CODING Ddr
3L	13344573	3L_13344573_SNP [dm3] 3L_13351473_SNP [dm6]	G	A	2.037e^-5	0.526	SYNONYMOUS_CODING CG17687	TF binding site mE1_TFBS_HSA
3R	12648381	3R_12648381_SNP [dm3] 3R_16822659_SNP [dm6]	C	A	2.038e^-5	0.526	INTRON abd-A	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	12309809	3L_12309809_SNP [dm3] 3L_12316709_SNP [dm6]	T	C	2.045e^-5	0.526	INTERGENIC
3R	17239742	3R_17239742_SNP [dm3] 3R_21414020_SNP [dm6]	T	C	2.052e^-5	0.526	INTRON lbl	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	15181153	3L_15181153_SNP [dm3] 3L_15188053_SNP [dm6]	C	T	2.096e^-5	0.526	INTERGENIC	TF binding site mE1_TFBS_inv
2R	6240196	2R_6240196_SNP [dm3] 2R_10352691_SNP [dm6]	G	T	2.123e^-5	0.526	UTR_5_PRIME CG43178 UTR_3_PRIME CG43171 & 1 other UPSTREAM CG43172 & 2 others INTRON CG42732
2R	18774237	2R_18774237_SNP [dm3] 2R_22886714_SNP [dm6]	A	G	2.173e^-5	0.526	UPSTREAM CG3499 DOWNSTREAM Gmer INTRON asrij	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_tll mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Ubx
3R	14197225	3R_14197225_SNP [dm3] 3R_18371503_SNP [dm6]	G	A	2.196e^-5	0.526	INTRON gl	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
3R	15575841	3R_15575841_SNP [dm3] 3R_19750119_SNP [dm6]	G	C	2.254e^-5	0.526	INTRON GluClalpha
2R	4081526	2R_4081526_SNP [dm3] 2R_8194021_SNP [dm6]	A	G	2.275e^-5	0.526	INTRON LRP1
2L	20566535	2L_20566535_SNP [dm3] 2L_20566535_SNP [dm6]	C	A	2.287e^-5	0.526	INTRON CR45347
3L	16728893	3L_16728893_SNP [dm3] 3L_16735793_SNP [dm6]	G	A	2.333e^-5	0.526	INTRON CG9701
2L	16080943	2L_16080943_SNP [dm3] 2L_16080943_SNP [dm6]	T	A	2.336e^-5	0.526	UTR_3_PRIME beat-Ia	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
X	20142355	X_20142355_SNP [dm3] X_20271329_SNP [dm6]	T	C	2.396e^-5	0.526	INTERGENIC
2R	11119197	2R_11119197_SNP [dm3] 2R_15231692_SNP [dm6]	T	C	2.399e^-5	0.526	SPLICE_SITE_REGION CR44370 INTRON Fs EXON CR44370	TF binding site mE1_TFBS_cad mE1_TFBS_inv
3R	15576193	3R_15576193_SNP [dm3] 3R_19750471_SNP [dm6]	G	T	2.427e^-5	0.526	INTRON GluClalpha
2R	4816613	2R_4816613_SNP [dm3] 2R_8929108_SNP [dm6]	C	A	2.518e^-5	0.526	NON_SYNONYMOUS_CODING PAN2	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
X	11386909	X_11386909_SNP [dm3] X_11492876_SNP [dm6]	T	A	2.562e^-5	0.526	UPSTREAM Drak EXON CR44556	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	17069430	3L_17069430_SNP [dm3] 3L_17076330_SNP [dm6]	A	T	2.576e^-5	0.526	UTR_3_PRIME Rbp6 INTRON Rbp6
2R	8502880	2R_8502880_SNP [dm3] 2R_12615375_SNP [dm6]	G	A	2.589e^-5	0.526	UPSTREAM Galphaq INTRON Galphaq & 1 other	TF binding site mE1_TFBS_sens
X	15110214	X_15110214_SNP [dm3] X_15216181_SNP [dm6]	G	A	2.650e^-5	0.526	INTERGENIC	TF binding site BDTNP1_TFBS_twi
2R	15923502	2R_15923502_SNP [dm3] 2R_20035997_SNP [dm6]	G	A	2.669e^-5	0.526	INTERGENIC	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_sens
3R	5144317	3R_5144317_SNP [dm3] 3R_9318595_SNP [dm6]	C	G	2.694e^-5	0.526	INTRON CG8861
2R	9745439	2R_9745439_SNP [dm3] 2R_13857934_SNP [dm6]	G	A	2.778e^-5	0.526	SYNONYMOUS_CODING tum	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2R	18110805	2R_18110805_SNP [dm3] 2R_22223300_SNP [dm6]	C	G	2.847e^-5	0.526	DOWNSTREAM Oatp58Dc INTRON Oatp58Db	TF binding site mE1_TFBS_sens
3L	9208247	3L_9208247_SNP [dm3] 3L_9215147_SNP [dm6]	C	T	2.857e^-5	0.526	UTR_3_PRIME CG4476
2L	4143038	2L_4143038_SNP [dm3] 2L_4143038_SNP [dm6]	G	A	2.878e^-5	0.526	INTERGENIC
3L	16976348	3L_16976348_SNP [dm3] 3L_16983248_SNP [dm6]	A	T	2.924e^-5	0.526	SYNONYMOUS_CODING Exn	TF binding site mE1_TFBS_cad
2R	18121646	2R_18121646_SNP [dm3] 2R_22234141_SNP [dm6]	G	C	2.937e^-5	0.526	INTERGENIC
2L	20526439	2L_20526439_SNP [dm3] 2L_20526439_SNP [dm6]	T	C	2.977e^-5	0.526	INTERGENIC
3L	15181109	3L_15181109_SNP [dm3] 3L_15188009_SNP [dm6]	T	C	2.987e^-5	0.526	INTERGENIC	TF binding site mE1_TFBS_inv
2L	16073402	2L_16073402_SNP [dm3] 2L_16073402_SNP [dm6]	C	A	2.991e^-5	0.526	INTRON beat-Ia EXON CR44870

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By genomic position
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Variance phenotype

Phenotype distribution and association to known covariates

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GWAS results