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=2.089e^-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_Mo	0.02214

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1268 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
3R	13758101	3R_13758101_SNP [dm3] 3R_17932379_SNP [dm6]	T	C	1.360e^-6	0.98	UTR_5_PRIME cpo INTRON cpo
2R	10199786	2R_10199786_SNP [dm3] 2R_14312281_SNP [dm6]	A	C	3.376e^-6	0.98	INTRON Shroom	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	10199785	2R_10199785_SNP [dm3] 2R_14312280_SNP [dm6]	A	T	4.435e^-6	0.98	INTRON Shroom	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	9740613	3R_9740613_SNP [dm3] 3R_13914891_SNP [dm6]	A	G	4.835e^-6	0.98	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	1998443	2L_1998443_SNP [dm3] 2L_1998443_SNP [dm6]	T	C	4.941e^-6	0.98	SYNONYMOUS_CODING CG33543
2L	7657831	2L_7657831_SNP [dm3] 2L_7657831_SNP [dm6]	T	C	5.024e^-6	0.98	INTRON Slob
2L	7657841	2L_7657841_SNP [dm3] 2L_7657841_SNP [dm6]	A	G	6.741e^-6	0.98	INTRON Slob
X	3994156	X_3994156_SNP [dm3] X_4100123_SNP [dm6]	G	A	8.016e^-6	0.98	SYNONYMOUS_CODING CG6379	TF binding site mE1_TFBS_sens
X	3994558	X_3994558_SNP [dm3] X_4100525_SNP [dm6]	C	T	8.016e^-6	0.98	SYNONYMOUS_CODING CG6379 UPSTREAM CG15375	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
X	3994561	X_3994561_SNP [dm3] X_4100528_SNP [dm6]	G	A	8.016e^-6	0.98	SYNONYMOUS_CODING CG6379 UPSTREAM CG15375	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
3R	10887069	3R_10887069_DEL [dm3] 3R_15061347_DEL [dm6]	TT	T	8.337e^-6	0.98	INTRON dpr9
3R	8133574	3R_8133574_SNP [dm3] 3R_12307852_SNP [dm6]	T	G	8.680e^-6	0.98	INTERGENIC
3L	21867568	3L_21867568_SNP [dm3] 3L_21874468_SNP [dm6]	A	C	9.110e^-6	0.98	INTRON mub
2R	20102229	2R_20102229_SNP [dm3] 2R_24214706_SNP [dm6]	C	T	9.926e^-6	0.98	UTR_3_PRIME CG30419
2L	10132387	2L_10132387_SNP [dm3] 2L_10132387_SNP [dm6]	C	A	9.945e^-6	0.98	INTRON CG44153
3R	14755658	3R_14755658_SNP [dm3] 3R_18929936_SNP [dm6]	T	C	1.128e^-5	0.98	INTRON CG42613	TF binding site BDTNP1_TFBS_dl
3R	9740640	3R_9740640_SNP [dm3] 3R_13914918_SNP [dm6]	G	C	1.204e^-5	0.98	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
X	1035433	X_1035433_SNP [dm3] X_1141400_SNP [dm6]	T	C	1.365e^-5	0.98	INTERGENIC
3R	9740645	3R_9740645_SNP [dm3] 3R_13914923_SNP [dm6]	T	G	1.366e^-5	0.98	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
X	9181144	X_9181144_SNP [dm3] X_9287111_SNP [dm6]	T	C	1.392e^-5	0.98	INTRON lz
2L	14265739	2L_14265739_SNP [dm3] 2L_14265739_SNP [dm6]	G	A	1.567e^-5	0.98	INTRON wb	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Kr
3L	3390317	3L_3390317_SNP [dm3] 3L_3390317_SNP [dm6]	A	G	1.585e^-5	0.98	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	9087612	3R_9087612_SNP [dm3] 3R_13261890_SNP [dm6]	T	C	1.776e^-5	0.98	DOWNSTREAM Ravus INTRON CG11686
2R	5131633	2R_5131633_SNP [dm3] 2R_9244128_SNP [dm6]	A	G	1.955e^-5	0.98	INTRON hig & 1 other
2R	5131647	2R_5131647_SNP [dm3] 2R_9244142_SNP [dm6]	A	G	1.955e^-5	0.98	INTRON hig & 1 other
2R	5131651	2R_5131651_SNP [dm3] 2R_9244146_SNP [dm6]	G	T	1.955e^-5	0.98	INTRON hig & 1 other
2R	5131668	2R_5131668_SNP [dm3] 2R_9244163_SNP [dm6]	C	T	1.955e^-5	0.98	INTRON hig & 1 other
2R	5131670	2R_5131670_SNP [dm3] 2R_9244165_SNP [dm6]	T	A	1.955e^-5	0.98	INTRON hig & 1 other
2L	14265675	2L_14265675_SNP [dm3] 2L_14265675_SNP [dm6]	A	G	2.065e^-5	0.98	INTRON wb	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Kr
3R	4759694	3R_4759694_SNP [dm3] 3R_8933972_SNP [dm6]	T	G	2.073e^-5	0.98	DOWNSTREAM CR44020 INTERGENIC	TF binding site BDTNP1_TFBS_da
3L	12634826	3L_12634826_SNP [dm3] 3L_12641726_SNP [dm6]	T	C	2.076e^-5	0.98	INTRON CR32111	TF binding site BDTNP1_TFBS_twi
3R	9095758	3R_9095758_SNP [dm3] 3R_13270036_SNP [dm6]	C	A	2.127e^-5	0.98	UTR_3_PRIME Su_var_3-7 DOWNSTREAM Su_var_3-7 INTRON CG8449
2R	18640254	2R_18640254_SNP [dm3] 2R_22752749_SNP [dm6]	A	G	2.135e^-5	0.98	INTRON CG42260
2R	18818784	2R_18818784_SNP [dm3] 2R_22931261_SNP [dm6]	C	G	2.213e^-5	0.98	SYNONYMOUS_CODING CG42678 DOWNSTREAM CG3788 INTRON CG42678
2R	18819000	2R_18819000_SNP [dm3] 2R_22931477_SNP [dm6]	T	G	2.213e^-5	0.98	DOWNSTREAM CG3788 INTRON CG42678
2R	16339026	2R_16339026_SNP [dm3] 2R_20451521_SNP [dm6]	G	C	2.238e^-5	0.98	INTRON CG12484
3R	10887155	3R_10887155_SNP [dm3] 3R_15061433_SNP [dm6]	G	T	2.278e^-5	0.98	INTRON dpr9
3L	3390456	3L_3390456_SNP [dm3] 3L_3390456_SNP [dm6]	C	G	2.428e^-5	0.98	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3L	3390458	3L_3390458_SNP [dm3] 3L_3390458_SNP [dm6]	A	T	2.428e^-5	0.98	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3L	3390512	3L_3390512_INS [dm3] 3L_3390512_INS [dm6]	C	TAAG	2.428e^-5	0.98	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3L	3390516	3L_3390516_DEL [dm3] 3L_3390516_DEL [dm6]	CT	C	2.428e^-5	0.98	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
2L	14265716	2L_14265716_SNP [dm3] 2L_14265716_SNP [dm6]	G	A	2.580e^-5	0.98	INTRON wb	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Kr
3L	750430	3L_750430_SNP [dm3] 3L_750430_SNP [dm6]	A	G	2.583e^-5	0.98	INTRON hng3 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_disco
2L	10132385	2L_10132385_SNP [dm3] 2L_10132385_SNP [dm6]	G	A	2.583e^-5	0.98	INTRON CG44153
3R	9740632	3R_9740632_SNP [dm3] 3R_13914910_SNP [dm6]	G	A	2.664e^-5	0.98	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	21496715	3R_21496715_SNP [dm3] 3R_25670993_SNP [dm6]	G	T	2.803e^-5	0.98	INTRON Lgr3
3R	14754796	3R_14754796_SNP [dm3] 3R_18929074_SNP [dm6]	C	T	2.897e^-5	0.98	UPSTREAM CG42613 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
3R	10886791	3R_10886791_SNP [dm3] 3R_15061069_SNP [dm6]	T	A	2.914e^-5	0.98	INTRON dpr9
3R	10886794	3R_10886794_SNP [dm3] 3R_15061072_SNP [dm6]	T	C	2.914e^-5	0.98	INTRON dpr9
3R	10886807	3R_10886807_SNP [dm3] 3R_15061085_SNP [dm6]	A	T	2.914e^-5	0.98	INTRON dpr9
3R	10915767	3R_10915767_DEL [dm3] 3R_15090045_DEL [dm6]	ATAGATTCAATTCTACA...	A	2.915e^-5	0.98	INTRON CG6966	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
3L	6756837	3L_6756837_SNP [dm3] 3L_6763737_SNP [dm6]	T	C	2.994e^-5	0.98	UPSTREAM CG32392 INTERGENIC	TF binding site mE1_TFBS_bab1
3R	7873493	3R_7873493_SNP [dm3] 3R_12047771_SNP [dm6]	C	G	3.114e^-5	0.98	DOWNSTREAM CG14739 INTERGENIC
3L	6756838	3L_6756838_SNP [dm3] 3L_6763738_SNP [dm6]	G	A	3.134e^-5	0.98	UPSTREAM CG32392 INTERGENIC	TF binding site mE1_TFBS_bab1
3L	6756840	3L_6756840_SNP [dm3] 3L_6763740_SNP [dm6]	A	G	3.134e^-5	0.98	UPSTREAM CG32392 INTERGENIC	TF binding site mE1_TFBS_bab1
3L	1828364	3L_1828364_SNP [dm3] 3L_1828364_SNP [dm6]	A	G	3.272e^-5	0.98	INTRON Cpr62Ba
3R	14754839	3R_14754839_SNP [dm3] 3R_18929117_SNP [dm6]	A	T	3.403e^-5	0.98	UPSTREAM CG42613 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
3L	6756868	3L_6756868_SNP [dm3] 3L_6763768_SNP [dm6]	G	A	3.673e^-5	0.98	UPSTREAM CG32392 INTERGENIC	TF binding site mE1_TFBS_bab1
3L	6756881	3L_6756881_SNP [dm3] 3L_6763781_SNP [dm6]	A	T	3.673e^-5	0.98	UPSTREAM CG32392 INTERGENIC	TF binding site mE1_TFBS_bab1
3L	5814998	3L_5814998_SNP [dm3] 3L_5821898_SNP [dm6]	C	T	3.682e^-5	0.98	INTRON vn
3R	9530012	3R_9530012_SNP [dm3] 3R_13704290_SNP [dm6]	G	C	3.817e^-5	0.98	INTRON Adgf-D	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	15058527	2L_15058527_SNP [dm3] 2L_15058527_SNP [dm6]	A	C	3.820e^-5	0.98	SYNONYMOUS_CODING CG33679 UPSTREAM ck DOWNSTREAM TfIIS	TF binding site BDTNP1_TFBS_dl
3R	10910192	3R_10910192_SNP [dm3] 3R_15084470_SNP [dm6]	G	T	3.913e^-5	0.98	INTRON CG6966
2L	14265677	2L_14265677_SNP [dm3] 2L_14265677_SNP [dm6]	A	G	4.078e^-5	0.98	INTRON wb	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Kr
2L	10630882	2L_10630882_SNP [dm3] 2L_10630882_SNP [dm6]	A	G	4.103e^-5	0.98	SYNONYMOUS_CODING CG7329
2L	10630900	2L_10630900_SNP [dm3] 2L_10630900_SNP [dm6]	T	C	4.103e^-5	0.98	SYNONYMOUS_CODING CG7329
3L	8401421	3L_8401421_SNP [dm3] 3L_8408321_SNP [dm6]	T	A	4.553e^-5	0.98	SYNONYMOUS_CODING Oseg1 DOWNSTREAM CG13667
3R	10915578	3R_10915578_SNP [dm3] 3R_15089856_SNP [dm6]	G	A	4.778e^-5	0.98	INTRON CG6966	TF binding site mE1_TFBS_Trl
2R	18818906	2R_18818906_SNP [dm3] 2R_22931383_SNP [dm6]	C	T	4.794e^-5	0.98	DOWNSTREAM CG3788 INTRON CG42678
2R	17614570	2R_17614570_SNP [dm3] 2R_21727065_SNP [dm6]	T	C	5.075e^-5	0.98	DOWNSTREAM CR44750 INTERGENIC
3L	5815167	3L_5815167_SNP [dm3] 3L_5822067_SNP [dm6]	C	G	5.093e^-5	0.98	INTRON vn
3L	5815175	3L_5815175_SNP [dm3] 3L_5822075_SNP [dm6]	T	G	5.093e^-5	0.98	INTRON vn
3R	14754808	3R_14754808_SNP [dm3] 3R_18929086_SNP [dm6]	G	A	5.151e^-5	0.98	UPSTREAM CG42613 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
3L	5815094	3L_5815094_SNP [dm3] 3L_5821994_SNP [dm6]	G	A	5.529e^-5	0.98	INTRON vn
3L	7590825	3L_7590825_SNP [dm3] 3L_7597725_SNP [dm6]	T	C	5.724e^-5	0.98	INTRON CG33275
2R	18819015	2R_18819015_SNP [dm3] 2R_22931492_SNP [dm6]	T	A	5.796e^-5	0.98	DOWNSTREAM CG3788 INTRON CG42678
3L	22017686	3L_22017686_SNP [dm3] 3L_22024586_SNP [dm6]	C	T	5.852e^-5	0.98	INTERGENIC
2L	4753753	2L_4753753_SNP [dm3] 2L_4753753_SNP [dm6]	A	T	6.115e^-5	0.98	INTRON CG15630
3R	25850660	3R_25850660_SNP [dm3] 3R_30024938_SNP [dm6]	T	G	6.565e^-5	0.98	INTRON Axn
3R	7869981	3R_7869981_SNP [dm3] 3R_12044259_SNP [dm6]	T	C	6.601e^-5	0.98	DOWNSTREAM CG14736 INTERGENIC
2L	14265526	2L_14265526_SNP [dm3] 2L_14265526_SNP [dm6]	A	C	6.617e^-5	0.98	INTRON wb	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Kr
3L	7123609	3L_7123609_SNP [dm3] 3L_7130509_SNP [dm6]	A	T	6.645e^-5	0.98	UPSTREAM CG8628 DOWNSTREAM CG15829 INTERGENIC	TF binding site mE1_TFBS_cnc
3L	21889842	3L_21889842_SNP [dm3] 3L_21896742_SNP [dm6]	T	A	7.120e^-5	0.98	INTRON mub
3R	20734950	3R_20734950_SNP [dm3] 3R_24909228_SNP [dm6]	T	C	7.183e^-5	0.98	INTERGENIC
3R	10915855	3R_10915855_SNP [dm3] 3R_15090133_SNP [dm6]	G	C	7.199e^-5	0.98	INTRON CG6966	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
3R	8152800	3R_8152800_SNP [dm3] 3R_12327078_SNP [dm6]	C	A	7.229e^-5	0.98	UPSTREAM CR45584 INTERGENIC
3R	8152807	3R_8152807_SNP [dm3] 3R_12327085_SNP [dm6]	C	A	7.229e^-5	0.98	UPSTREAM CR45584 INTERGENIC
3R	8152809	3R_8152809_DEL [dm3] 3R_12327087_DEL [dm6]	GG	C	7.229e^-5	0.98	UPSTREAM CR45584 INTERGENIC
3R	8218856	3R_8218856_SNP [dm3] 3R_12393134_SNP [dm6]	G	A	7.304e^-5	0.98	UTR_5_PRIME CG10096 UTR_3_PRIME CG10097 UPSTREAM CG10096 DOWNSTREAM CG10097 INTRON CG34402	TF binding site mE1_TFBS_cad
2R	18643231	2R_18643231_SNP [dm3] 2R_22755726_SNP [dm6]	T	C	7.376e^-5	0.98	SYNONYMOUS_CODING CG13526 UPSTREAM CR30267 INTRON CG42260	TF binding site BDTNP1_TFBS_da
2R	17614573	2R_17614573_SNP [dm3] 2R_21727068_SNP [dm6]	G	A	7.560e^-5	0.98	DOWNSTREAM CR44750 INTERGENIC
3L	5398609	3L_5398609_SNP [dm3] 3L_5405509_SNP [dm6]	T	C	7.845e^-5	0.98	INTERGENIC
2R	8273165	2R_8273165_SNP [dm3] 2R_12385660_SNP [dm6]	G	A	7.895e^-5	0.98	INTERGENIC
3L	8216698	3L_8216698_SNP [dm3] 3L_8223598_SNP [dm6]	C	A	7.940e^-5	0.98	DOWNSTREAM CG13678 INTERGENIC	TF binding site mE1_TFBS_cad
3L	22030669	3L_22030669_SNP [dm3] 3L_22037569_SNP [dm6]	G	A	7.996e^-5	0.98	INTRON Oct-TyrR
3L	750429	3L_750429_SNP [dm3] 3L_750429_SNP [dm6]	T	A	8.209e^-5	0.98	INTRON hng3 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_disco
3L	750435	3L_750435_SNP [dm3] 3L_750435_SNP [dm6]	T	G	8.209e^-5	0.98	INTRON hng3 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_disco
3L	750450	3L_750450_MNP [dm3] 3L_750450_MNP [dm6]	CGA	ACC	8.209e^-5	0.98	INTRON hng3 & 1 other	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_disco
3L	750457	3L_750457_SNP [dm3] 3L_750457_SNP [dm6]	C	A	8.209e^-5	0.98	INTRON hng3 & 1 other	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_disco
3L	750458	3L_750458_SNP [dm3] 3L_750458_SNP [dm6]	G	C	8.209e^-5	0.98	INTRON hng3 & 1 other	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_disco

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By genomic position
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Temperature phenotype

Phenotype distribution and association to known covariates

QQplot

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GWAS results