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=3.269e^-13)
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	<2e-16

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
wolba	124.3935	6.909e-29
In_2L_t	8.2081	0.0165

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2234 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	13746320	2R_13746320_SNP [dm3] 2R_17858815_SNP [dm6]	C	T	1.012e^-6	0.83	INTRON olf186-F
2R	9201997	2R_9201997_SNP [dm3] 2R_13314492_SNP [dm6]	C	T	1.220e^-6	0.83	INTERGENIC
X	14962284	X_14962284_SNP [dm3] X_15068251_SNP [dm6]	G	C	2.163e^-6	0.83	NON_SYNONYMOUS_CODING dob DOWNSTREAM Lsd-2
3L	9728221	3L_9728221_SNP [dm3] 3L_9735121_SNP [dm6]	A	G	2.186e^-6	0.83	SYNONYMOUS_CODING CG42268 UTR_3_PRIME CG42268
3L	10066407	3L_10066407_DEL [dm3] 3L_10073307_DEL [dm6]	TAC	A	3.090e^-6	0.83	INTRON dpr6
2R	12364551	2R_12364551_SNP [dm3] 2R_16477046_SNP [dm6]	A	C	3.466e^-6	0.83	INTERGENIC
2L	13163495	2L_13163495_SNP [dm3] 2L_13163495_SNP [dm6]	T	C	4.049e^-6	0.83	NON_SYNONYMOUS_CODING DnaJ-H UTR_3_PRIME DnaJ-H DOWNSTREAM CG5204	TF binding site mE1_TFBS_cad
2R	13745797	2R_13745797_SNP [dm3] 2R_17858292_SNP [dm6]	A	G	4.206e^-6	0.83	INTRON olf186-F
3L	15884504	3L_15884504_SNP [dm3] 3L_15891404_SNP [dm6]	T	C	5.195e^-6	0.83	INTRON pHCl
X	6476394	X_6476394_SNP [dm3] X_6582361_SNP [dm6]	G	C	5.742e^-6	0.83	SYNONYMOUS_CODING CG34417 INTRON CG34417
3L	15884625	3L_15884625_SNP [dm3] 3L_15891525_SNP [dm6]	A	G	5.880e^-6	0.83	INTRON pHCl
3R	6923260	3R_6923260_SNP [dm3] 3R_11097538_SNP [dm6]	G	A	5.990e^-6	0.83	INTERGENIC
3L	15883094	3L_15883094_SNP [dm3] 3L_15889994_SNP [dm6]	C	T	6.203e^-6	0.83	INTRON pHCl
3L	5966628	3L_5966628_SNP [dm3] 3L_5973528_SNP [dm6]	T	C	6.297e^-6	0.83	INTRON CG10479	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi
2L	16804548	2L_16804548_SNP [dm3] 2L_16804548_SNP [dm6]	T	A	7.122e^-6	0.83	UPSTREAM CG13272 & 1 other INTRON CG13280
2L	16162246	2L_16162246_SNP [dm3] 2L_16162246_SNP [dm6]	C	T	7.658e^-6	0.83	INTERGENIC
3L	5966535	3L_5966535_SNP [dm3] 3L_5973435_SNP [dm6]	A	T	8.165e^-6	0.83	INTRON CG10479	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi
3L	6757397	3L_6757397_INS [dm3] 3L_6764297_INS [dm6]	T	TGCAG	8.342e^-6	0.83	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_D mE1_TFBS_HSA
3L	5056818	3L_5056818_SNP [dm3] 3L_5056818_SNP [dm6]	C	G	9.393e^-6	0.83	INTRON Con
3L	14341635	3L_14341635_SNP [dm3] 3L_14348535_SNP [dm6]	G	C	9.784e^-6	0.83	INTRON fz	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	23019195	3R_23019195_SNP [dm3] 3R_27193473_SNP [dm6]	C	T	9.892e^-6	0.83	INTRON Ser	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_sbb mE1_TFBS_Trl
3L	5056820	3L_5056820_SNP [dm3] 3L_5056820_SNP [dm6]	T	G	9.957e^-6	0.83	INTRON Con
2R	9203115	2R_9203115_SNP [dm3] 2R_13315610_SNP [dm6]	G	A	1.064e^-5	0.83	INTERGENIC
3L	6757339	3L_6757339_SNP [dm3] 3L_6764239_SNP [dm6]	A	G	1.080e^-5	0.83	UPSTREAM CG32392 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_D mE1_TFBS_HSA
3L	6757340	3L_6757340_SNP [dm3] 3L_6764240_SNP [dm6]	A	C	1.169e^-5	0.83	UPSTREAM CG32392 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_D mE1_TFBS_HSA
3L	1403624	3L_1403624_SNP [dm3] 3L_1403624_SNP [dm6]	A	G	1.180e^-5	0.83	INTRON Ptp61F	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med
3R	18128446	3R_18128446_SNP [dm3] 3R_22302724_SNP [dm6]	T	G	1.261e^-5	0.83	INTRON CG7084	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2R	9203420	2R_9203420_SNP [dm3] 2R_13315915_SNP [dm6]	T	C	1.366e^-5	0.83	INTERGENIC
2R	8895851	2R_8895851_SNP [dm3] 2R_13008346_SNP [dm6]	G	A	1.369e^-5	0.83	DOWNSTREAM Su_z_2 INTERGENIC	silencer mE1_HDAC_PRE TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	6757387	3L_6757387_SNP [dm3] 3L_6764287_SNP [dm6]	T	A	1.467e^-5	0.83	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_D mE1_TFBS_HSA
3R	14840851	3R_14840851_SNP [dm3] 3R_19015129_SNP [dm6]	C	T	1.499e^-5	0.83	INTRON gukh	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
3L	18753910	3L_18753910_INS [dm3] 3L_18760810_INS [dm6]	C	CTCTCCC	1.653e^-5	0.83	INTRON ftz-f1	TF binding site mE1_TFBS_Trl
3L	6757470	3L_6757470_SNP [dm3] 3L_6764370_SNP [dm6]	T	C	1.663e^-5	0.83	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_D mE1_TFBS_HSA
3L	10536562	3L_10536562_SNP [dm3] 3L_10543462_SNP [dm6]	T	G	1.690e^-5	0.83	INTRON A2bp1
2L	4778958	2L_4778958_SNP [dm3] 2L_4778958_SNP [dm6]	C	A	1.698e^-5	0.83	INTRON CG15630
2L	15819726	2L_15819726_SNP [dm3] 2L_15819726_SNP [dm6]	C	A	1.745e^-5	0.83	INTERGENIC	TF binding site mE1_TFBS_run
2R	13745804	2R_13745804_SNP [dm3] 2R_17858299_SNP [dm6]	C	T	1.759e^-5	0.83	INTRON olf186-F
3L	5483287	3L_5483287_SNP [dm3] 3L_5490187_SNP [dm6]	T	G	1.852e^-5	0.83	INTERGENIC
2L	17782654	2L_17782654_INS [dm3] 2L_17782654_INS [dm6]	C	CTGTTTAAGTCACAGC...	1.870e^-5	0.83	INTERGENIC
2R	16251297	2R_16251297_SNP [dm3] 2R_20363792_SNP [dm6]	A	T	1.929e^-5	0.83	INTERGENIC
3L	6757468	3L_6757468_SNP [dm3] 3L_6764368_SNP [dm6]	T	C	1.980e^-5	0.83	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_D mE1_TFBS_HSA
2R	7612650	2R_7612650_SNP [dm3] 2R_11725145_SNP [dm6]	T	C	1.989e^-5	0.83	SYNONYMOUS_CODING pyr	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_sna mE1_TFBS_chinmo mE1_TFBS_HSA
3R	20331319	3R_20331319_SNP [dm3] 3R_24505597_SNP [dm6]	G	A	2.042e^-5	0.83	INTERGENIC
X	5946894	X_5946894_DEL [dm3] X_6052861_DEL [dm6]	CGGCTCAGCTC...	C	2.046e^-5	0.83	INTRON CG5921
2R	8895935	2R_8895935_SNP [dm3] 2R_13008430_SNP [dm6]	C	A	2.093e^-5	0.83	DOWNSTREAM Su_z_2 INTERGENIC	silencer mE1_HDAC_PRE TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	15886310	3L_15886310_SNP [dm3] 3L_15893210_SNP [dm6]	C	T	2.108e^-5	0.83	INTRON pHCl
3R	13893851	3R_13893851_INS [dm3] 3R_18068129_INS [dm6]	A	AA	2.168e^-5	0.83	INTERGENIC
3L	7002669	3L_7002669_SNP [dm3] 3L_7009569_SNP [dm6]	T	C	2.297e^-5	0.83	INTRON Mp
3L	10066439	3L_10066439_SNP [dm3] 3L_10073339_SNP [dm6]	A	C	2.298e^-5	0.83	INTRON dpr6
3L	6757343	3L_6757343_SNP [dm3] 3L_6764243_SNP [dm6]	C	A	2.319e^-5	0.83	UPSTREAM CG32392 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_D mE1_TFBS_HSA
3L	18753899	3L_18753899_SNP [dm3] 3L_18760799_SNP [dm6]	C	A	2.326e^-5	0.83	INTRON ftz-f1	TF binding site mE1_TFBS_Trl
X	2463412	X_2463412_SNP [dm3] X_2569379_SNP [dm6]	A	G	2.504e^-5	0.83	INTRON Pdfr
2R	14170768	2R_14170768_SNP [dm3] 2R_18283263_SNP [dm6]	A	T	2.585e^-5	0.83	INTRON sbb	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2R	7612542	2R_7612542_SNP [dm3] 2R_11725037_SNP [dm6]	T	C	2.757e^-5	0.83	SYNONYMOUS_CODING pyr	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_sna mE1_TFBS_chinmo mE1_TFBS_HSA
3R	25557404	3R_25557404_SNP [dm3] 3R_29731682_SNP [dm6]	A	G	2.784e^-5	0.83	SYNONYMOUS_CODING Kul UTR_3_PRIME Kul	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	9203495	2R_9203495_SNP [dm3] 2R_13315990_SNP [dm6]	G	A	2.809e^-5	0.83	INTERGENIC
2L	1093771	2L_1093771_SNP [dm3] 2L_1093771_SNP [dm6]	G	C	2.809e^-5	0.83	INTRON CG4629
X	14962447	X_14962447_SNP [dm3] X_15068414_SNP [dm6]	G	A	2.814e^-5	0.83	NON_SYNONYMOUS_CODING dob DOWNSTREAM Lsd-2	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
X	18249326	X_18249326_SNP [dm3] X_18355293_SNP [dm6]	G	A	2.822e^-5	0.83	INTRON CG6123
3R	13965223	3R_13965223_SNP [dm3] 3R_18139501_SNP [dm6]	A	G	2.851e^-5	0.83	INTERGENIC
3L	11571893	3L_11571893_SNP [dm3] 3L_11578793_SNP [dm6]	G	C	2.920e^-5	0.83	UPSTREAM CG33270 DOWNSTREAM CG43390 INTERGENIC
2L	3514424	2L_3514424_SNP [dm3] 2L_3514424_SNP [dm6]	C	T	3.055e^-5	0.83	UPSTREAM CG17593 INTRON CG33123	TF binding site mE1_TFBS_cad
2L	17789691	2L_17789691_SNP [dm3] 2L_17789691_SNP [dm6]	A	C	3.107e^-5	0.83	INTRON CadN2
X	13683486	X_13683486_SNP [dm3] X_13789453_SNP [dm6]	T	C	3.215e^-5	0.83	DOWNSTREAM CG10993 INTRON inaE
2R	10292473	2R_10292473_SNP [dm3] 2R_14404968_SNP [dm6]	A	G	3.221e^-5	0.83	INTERGENIC
3R	17238782	3R_17238782_SNP [dm3] 3R_21413060_SNP [dm6]	G	T	3.249e^-5	0.83	INTRON lbl	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	17238781	3R_17238781_SNP [dm3] 3R_21413059_SNP [dm6]	A	G	3.269e^-5	0.83	INTRON lbl	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	11000178	2R_11000178_SNP [dm3] 2R_15112673_SNP [dm6]	C	A	3.373e^-5	0.83	INTERGENIC
2R	9203456	2R_9203456_INS [dm3] 2R_13315951_INS [dm6]	C	CC	3.398e^-5	0.83	INTERGENIC
2L	9112662	2L_9112662_SNP [dm3] 2L_9112662_SNP [dm6]	G	T	3.435e^-5	0.83	INTRON Or30a
3L	18685820	3L_18685820_SNP [dm3] 3L_18692720_SNP [dm6]	C	A	3.502e^-5	0.83	DOWNSTREAM CR43987 INTERGENIC
2L	9112660	2L_9112660_SNP [dm3] 2L_9112660_SNP [dm6]	T	G	3.549e^-5	0.83	INTRON Or30a
3R	16533989	3R_16533989_SNP [dm3] 3R_20708267_SNP [dm6]	C	A	3.572e^-5	0.83	INTRON Oamb
2L	12182857	2L_12182857_SNP [dm3] 2L_12182857_SNP [dm6]	G	A	3.588e^-5	0.83	INTRON aret
3R	13893806	3R_13893806_DEL [dm3] 3R_18068084_DEL [dm6]	TG	A	3.655e^-5	0.83	INTERGENIC
X	10411688	X_10411688_SNP [dm3] X_10517655_SNP [dm6]	A	T	3.705e^-5	0.83	INTRON spri	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	6407920	2L_6407920_SNP [dm3] 2L_6407920_SNP [dm6]	T	A	3.777e^-5	0.83	INTRON CG42368
3L	6757409	3L_6757409_SNP [dm3] 3L_6764309_SNP [dm6]	C	T	3.788e^-5	0.83	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_D mE1_TFBS_HSA
3L	7851788	3L_7851788_SNP [dm3] 3L_7858688_SNP [dm6]	A	G	3.854e^-5	0.83	INTRON Pdp1	TF binding site mE1_TFBS_HSA
2R	6851414	2R_6851414_SNP [dm3] 2R_10963909_SNP [dm6]	A	T	3.903e^-5	0.83	INTERGENIC
2R	9249016	2R_9249016_SNP [dm3] 2R_13361511_SNP [dm6]	A	T	3.957e^-5	0.83	DOWNSTREAM CR45312 INTERGENIC
3L	2091195	3L_2091195_SNP [dm3] 3L_2091195_SNP [dm6]	G	A	3.962e^-5	0.83	INTRON sls	TF binding site mE1_TFBS_HSA
2L	17782672	2L_17782672_SNP [dm3] 2L_17782672_SNP [dm6]	T	A	4.030e^-5	0.83	INTERGENIC
3R	19253522	3R_19253522_SNP [dm3] 3R_23427800_SNP [dm6]	T	G	4.053e^-5	0.83	INTRON CG4374	TF binding site BDTNP1_TFBS_prd
3R	26879026	3R_26879026_SNP [dm3] 3R_31053304_SNP [dm6]	C	T	4.068e^-5	0.83	NON_SYNONYMOUS_CODING l_3_03670 DOWNSTREAM Aph-4 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_sens
2R	9261718	2R_9261718_SNP [dm3] 2R_13374213_SNP [dm6]	T	C	4.237e^-5	0.83	INTERGENIC
2L	19100397	2L_19100397_SNP [dm3] 2L_19100397_SNP [dm6]	C	T	4.310e^-5	0.83	INTRON Lim3
3R	9951655	3R_9951655_SNP [dm3] 3R_14125933_SNP [dm6]	A	G	4.362e^-5	0.83	START_GAINED RpII140 UTR_5_PRIME RpII140 UPSTREAM 140up	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	5966665	3L_5966665_SNP [dm3] 3L_5973565_SNP [dm6]	T	G	4.509e^-5	0.83	INTRON CG10479	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi
3R	9683940	3R_9683940_SNP [dm3] 3R_13858218_SNP [dm6]	T	G	4.522e^-5	0.83	INTERGENIC
2L	17782894	2L_17782894_INS [dm3] 2L_17782894_INS [dm6]	T	TCC	4.535e^-5	0.83	INTERGENIC
2L	12479186	2L_12479186_SNP [dm3] 2L_12479186_SNP [dm6]	C	T	4.569e^-5	0.83	INTRON bun	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	2462011	3L_2462011_SNP [dm3] 3L_2462011_SNP [dm6]	T	C	4.649e^-5	0.83	UPSTREAM CG45186 INTRON CG45186
3R	9950932	3R_9950932_SNP [dm3] 3R_14125210_SNP [dm6]	G	A	4.691e^-5	0.83	SYNONYMOUS_CODING 140up UPSTREAM RpII140 DOWNSTREAM twf
2L	3464695	2L_3464695_SNP [dm3] 2L_3464695_SNP [dm6]	G	A	4.737e^-5	0.83	SYNONYMOUS_CODING msl-2	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_sens
2L	12582825	2L_12582825_SNP [dm3] 2L_12582825_SNP [dm6]	A	T	4.856e^-5	0.83	EXON CR44595 & 1 other
3L	8797613	3L_8797613_SNP [dm3] 3L_8804513_SNP [dm6]	C	T	4.890e^-5	0.83	UPSTREAM CG34427 & 1 other DOWNSTREAM CG34426 INTERGENIC
3L	14121021	3L_14121021_SNP [dm3] 3L_14127921_SNP [dm6]	T	C	4.930e^-5	0.83	INTRON Sox21b
3R	14840861	3R_14840861_SNP [dm3] 3R_19015139_SNP [dm6]	C	T	4.993e^-5	0.83	INTRON gukh	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
3L	6757150	3L_6757150_SNP [dm3] 3L_6764050_SNP [dm6]	C	A	5.005e^-5	0.83	UPSTREAM CG32392 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_prd mE1_TFBS_bab1 mE1_TFBS_HSA

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By genomic position
Variant impact
Gene name

Wolbachia_Map_Reads phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results