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=8.481e^-9)
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
No significant result.

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	4.6905	0.0958
In_3R_Mo	5.0204	0.0813

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

3035 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	16516810	3R_16516810_SNP [dm3] 3R_20691088_SNP [dm6]	A	C	1.292e^-10	2.384e^-4	SYNONYMOUS_CODING Oamb	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3R	14486560	3R_14486560_SNP [dm3] 3R_18660838_SNP [dm6]	C	T	9.137e^-8	0.067	SYNONYMOUS_CODING CstF-64 DOWNSTREAM Cpsf73	TF binding site BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo
2L	10631641	2L_10631641_SNP [dm3] 2L_10631641_SNP [dm6]	G	A	1.446e^-7	0.067	UPSTREAM CG7329 INTRON CG7329
2R	18292971	2R_18292971_SNP [dm3] 2R_22405466_SNP [dm6]	T	G	1.450e^-7	0.067	INTRON CG6044
3R	16020451	3R_16020451_DEL [dm3] 3R_20194729_DEL [dm6]	AA	C	3.171e^-7	0.117	INTERGENIC
2R	18292924	2R_18292924_SNP [dm3] 2R_22405419_SNP [dm6]	A	G	4.955e^-7	0.117	INTRON CG6044
3L	13549841	3L_13549841_SNP [dm3] 3L_13556741_SNP [dm6]	A	G	6.005e^-7	0.117	INTRON bru-3
2L	20121375	2L_20121375_SNP [dm3] 2L_20121375_SNP [dm6]	G	C	6.430e^-7	0.117	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_ttk mE1_TFBS_zfh1
3R	16017336	3R_16017336_DEL [dm3] 3R_20191614_DEL [dm6]	TTA	T	6.769e^-7	0.117	INTERGENIC
3R	23685303	3R_23685303_SNP [dm3] 3R_27859581_SNP [dm6]	T	A	8.012e^-7	0.117	INTRON CG34353
3R	19906908	3R_19906908_SNP [dm3] 3R_24081186_SNP [dm6]	A	G	8.464e^-7	0.117	INTRON 4EHP
X	16881674	X_16881674_SNP [dm3] X_16987641_SNP [dm6]	T	A	8.529e^-7	0.117	UPSTREAM CG45002 INTRON CG45002
3R	23684476	3R_23684476_SNP [dm3] 3R_27858754_SNP [dm6]	C	A	1.027e^-6	0.117	INTRON CG34353
3R	23684661	3R_23684661_SNP [dm3] 3R_27858939_SNP [dm6]	G	C	1.027e^-6	0.117	INTRON CG34353
3R	16642119	3R_16642119_SNP [dm3] 3R_20816397_SNP [dm6]	C	T	1.080e^-6	0.117	UPSTREAM Fancd2 DOWNSTREAM CG17270 INTERGENIC
3R	16642159	3R_16642159_SNP [dm3] 3R_20816437_SNP [dm6]	C	T	1.080e^-6	0.117	UPSTREAM Fancd2 DOWNSTREAM CG17270 INTERGENIC
3R	16642166	3R_16642166_SNP [dm3] 3R_20816444_SNP [dm6]	C	T	1.080e^-6	0.117	UPSTREAM Fancd2 DOWNSTREAM CG17270 INTERGENIC
2L	20098873	2L_20098873_SNP [dm3] 2L_20098873_SNP [dm6]	A	T	1.146e^-6	0.117	INTRON Kua	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	16642160	3R_16642160_SNP [dm3] 3R_20816438_SNP [dm6]	C	T	1.535e^-6	0.142	UPSTREAM Fancd2 DOWNSTREAM CG17270 INTERGENIC
3R	23681568	3R_23681568_SNP [dm3] 3R_27855846_SNP [dm6]	C	A	1.612e^-6	0.142	INTRON CG34353
3R	23685460	3R_23685460_SNP [dm3] 3R_27859738_SNP [dm6]	G	T	1.616e^-6	0.142	INTRON CG34353
X	5440279	X_5440279_SNP [dm3] X_5546246_SNP [dm6]	C	T	1.985e^-6	0.153	INTRON Vsx2	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_slp1 mE1_TFBS_HSA
3R	16017410	3R_16017410_SNP [dm3] 3R_20191688_SNP [dm6]	G	A	2.038e^-6	0.153	INTERGENIC
3R	23685739	3R_23685739_SNP [dm3] 3R_27860017_SNP [dm6]	C	T	2.253e^-6	0.153	INTRON CG34353
3R	23686464	3R_23686464_SNP [dm3] 3R_27860742_SNP [dm6]	C	T	2.253e^-6	0.153	INTRON CG34353
3R	23686627	3R_23686627_SNP [dm3] 3R_27860905_SNP [dm6]	A	G	2.253e^-6	0.153	INTRON CG34353
3L	564841	3L_564841_DEL [dm3] 3L_564841_DEL [dm6]	TCCT	T	2.429e^-6	0.153	INTRON hipk	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	23688461	3R_23688461_SNP [dm3] 3R_27862739_SNP [dm6]	A	C	2.477e^-6	0.153	INTRON CG34353
3R	23685688	3R_23685688_DEL [dm3] 3R_27859966_DEL [dm6]	TTT	T	2.552e^-6	0.153	INTRON CG34353
X	7717072	X_7717072_SNP [dm3] X_7823039_SNP [dm6]	T	G	2.567e^-6	0.153	INTERGENIC
3R	24109942	3R_24109942_SNP [dm3] 3R_28284220_SNP [dm6]	C	T	2.574e^-6	0.153	NON_SYNONYMOUS_CODING CG34437 DOWNSTREAM CG34436
3R	16017524	3R_16017524_SNP [dm3] 3R_20191802_SNP [dm6]	C	T	3.202e^-6	0.176	INTERGENIC
3R	23684214	3R_23684214_SNP [dm3] 3R_27858492_SNP [dm6]	G	A	3.316e^-6	0.176	INTRON CG34353
3R	23969846	3R_23969846_SNP [dm3] 3R_28144124_SNP [dm6]	A	C	3.426e^-6	0.176	INTERGENIC
3R	25029970	3R_25029970_SNP [dm3] 3R_29204248_SNP [dm6]	A	G	3.583e^-6	0.176	UPSTREAM CG14508 INTERGENIC
3R	24888686	3R_24888686_SNP [dm3] 3R_29062964_SNP [dm6]	G	A	3.632e^-6	0.176	UTR_5_PRIME Cul5 UPSTREAM CG11873	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_sens
3R	24888705	3R_24888705_SNP [dm3] 3R_29062983_SNP [dm6]	T	C	3.632e^-6	0.176	UPSTREAM CG11873 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_h mE1_TFBS_HSA
3R	24889111	3R_24889111_SNP [dm3] 3R_29063389_SNP [dm6]	A	T	3.632e^-6	0.176	UPSTREAM CG11873 & 1 other INTRON CG11873	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_HSA
3L	1326284	3L_1326284_SNP [dm3] 3L_1326284_SNP [dm6]	A	G	4.028e^-6	0.182	SYNONYMOUS_CODING Myo61F	TF binding site BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3R	23969845	3R_23969845_SNP [dm3] 3R_28144123_SNP [dm6]	A	T	4.184e^-6	0.182	INTERGENIC
3R	26170393	3R_26170393_SNP [dm3] 3R_30344671_SNP [dm6]	A	C	4.448e^-6	0.182	INTRON hdc	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
3R	11493089	3R_11493089_SNP [dm3] 3R_15667367_SNP [dm6]	T	C	4.547e^-6	0.182	UPSTREAM CR43849 INTRON pxb	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_sens
3R	24900397	3R_24900397_SNP [dm3] 3R_29074675_SNP [dm6]	G	A	4.986e^-6	0.182	INTRON CG11873	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_kni BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3R	23919197	3R_23919197_SNP [dm3] 3R_28093475_SNP [dm6]	A	G	5.037e^-6	0.182	INTERGENIC
X	5900006	X_5900006_SNP [dm3] X_6005973_SNP [dm6]	C	T	5.050e^-6	0.182	DOWNSTREAM CR44498 INTERGENIC
3R	22633766	3R_22633766_SNP [dm3] 3R_26808044_SNP [dm6]	G	A	5.101e^-6	0.182	INTRON Tl
3R	23687976	3R_23687976_SNP [dm3] 3R_27862254_SNP [dm6]	C	G	5.334e^-6	0.182	INTRON CG34353
3R	14118819	3R_14118819_SNP [dm3] 3R_18293097_SNP [dm6]	A	G	5.362e^-6	0.182	UPSTREAM l_3_05822 INTRON l_3_05822	TF binding site BDTNP1_TFBS_twi
3L	15616897	3L_15616897_SNP [dm3] 3L_15623797_SNP [dm6]	G	A	5.425e^-6	0.182	UTR_3_PRIME CG7372 INTRON comm3
3R	20309921	3R_20309921_SNP [dm3] 3R_24484199_SNP [dm6]	G	A	5.480e^-6	0.182	INTERGENIC
3R	19906839	3R_19906839_SNP [dm3] 3R_24081117_SNP [dm6]	C	G	5.486e^-6	0.182	INTRON 4EHP
X	7931558	X_7931558_SNP [dm3] X_8037525_SNP [dm6]	T	G	5.487e^-6	0.182	UPSTREAM CG2233 DOWNSTREAM fs_1_h INTERGENIC
2L	3954087	2L_3954087_DEL [dm3] 2L_3954087_DEL [dm6]	AGTCTTAAAATCA...	A	5.544e^-6	0.182	INTRON fred
3R	12199421	3R_12199421_SNP [dm3] 3R_16373699_SNP [dm6]	T	A	5.569e^-6	0.182	UPSTREAM CR45193 DOWNSTREAM ss INTERGENIC	TF binding site mE1_TFBS_sens
2L	15523538	2L_15523538_SNP [dm3] 2L_15523538_SNP [dm6]	C	T	5.626e^-6	0.182	EXON CR43761
3R	22289463	3R_22289463_SNP [dm3] 3R_26463741_SNP [dm6]	T	C	5.626e^-6	0.182	INTRON CG5455
2L	3954117	2L_3954117_SNP [dm3] 2L_3954117_SNP [dm6]	C	T	5.651e^-6	0.182	INTRON fred
3R	23681424	3R_23681424_INS [dm3] 3R_27855702_INS [dm6]	T	TT	5.709e^-6	0.182	INTRON CG34353
2L	19949447	2L_19949447_SNP [dm3] 2L_19949447_SNP [dm6]	A	G	6.096e^-6	0.191	INTRON sick	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	19223386	3R_19223386_SNP [dm3] 3R_23397664_SNP [dm6]	T	G	6.412e^-6	0.194	INTERGENIC
3L	565424	3L_565424_SNP [dm3] 3L_565424_SNP [dm6]	G	A	6.545e^-6	0.194	INTRON hipk
3R	26669699	3R_26669699_SNP [dm3] 3R_30843977_SNP [dm6]	C	T	6.618e^-6	0.194	INTERGENIC
3L	510646	3L_510646_SNP [dm3] 3L_510646_SNP [dm6]	G	T	6.826e^-6	0.194	INTRON klar
3L	510684	3L_510684_SNP [dm3] 3L_510684_SNP [dm6]	G	T	6.826e^-6	0.194	INTRON klar
3R	6281600	3R_6281600_SNP [dm3] 3R_10455878_SNP [dm6]	G	A	6.833e^-6	0.194	INTERGENIC
3L	15286989	3L_15286989_SNP [dm3] 3L_15293889_SNP [dm6]	A	G	7.409e^-6	0.205	INTERGENIC
3L	8974527	3L_8974527_SNP [dm3] 3L_8981427_SNP [dm6]	G	T	7.452e^-6	0.205	UPSTREAM CG13314 DOWNSTREAM Galk INTERGENIC
X	5899924	X_5899924_SNP [dm3] X_6005891_SNP [dm6]	C	A	7.658e^-6	0.205	DOWNSTREAM CR44498 INTERGENIC
3R	14391963	3R_14391963_SNP [dm3] 3R_18566241_SNP [dm6]	T	A	7.670e^-6	0.205	INTERGENIC
3L	6321710	3L_6321710_SNP [dm3] 3L_6328610_SNP [dm6]	T	A	8.187e^-6	0.21	SYNONYMOUS_CODING Or65c DOWNSTREAM CG13300
3L	18483926	3L_18483926_SNP [dm3] 3L_18490826_SNP [dm6]	A	C	8.332e^-6	0.21	INTRON AstC-R2
X	395147	X_395147_SNP [dm3] X_501114_SNP [dm6]	T	G	8.359e^-6	0.21	INTRON svr
3R	11493077	3R_11493077_SNP [dm3] 3R_15667355_SNP [dm6]	T	C	8.370e^-6	0.21	UPSTREAM CR43849 INTRON pxb	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_sens
2L	3954103	2L_3954103_SNP [dm3] 2L_3954103_SNP [dm6]	C	A	8.573e^-6	0.21	INTRON fred
3R	22269922	3R_22269922_SNP [dm3] 3R_26444200_SNP [dm6]	A	G	8.616e^-6	0.21	INTRON tx
3L	8772489	3L_8772489_SNP [dm3] 3L_8779389_SNP [dm6]	C	T	8.631e^-6	0.21	INTRON Fhos	TF binding site mE1_TFBS_cad
2L	1105262	2L_1105262_SNP [dm3] 2L_1105262_SNP [dm6]	T	A	9.017e^-6	0.216	NON_SYNONYMOUS_CODING mtRNApol	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3R	23886152	3R_23886152_SNP [dm3] 3R_28060430_SNP [dm6]	C	G	9.424e^-6	0.22	INTRON CG34362
2R	10149931	2R_10149931_SNP [dm3] 2R_14262426_SNP [dm6]	T	C	9.435e^-6	0.22	INTRON CG8547	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3R	9542639	3R_9542639_SNP [dm3] 3R_13716917_SNP [dm6]	C	G	9.786e^-6	0.22	DOWNSTREAM CG9602 INTRON CG34383	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb mE1_TFBS_cad
2L	14861417	2L_14861417_SNP [dm3] 2L_14861417_SNP [dm6]	G	T	1.007e^-5	0.22	INTERGENIC
3L	13816903	3L_13816903_SNP [dm3] 3L_13823803_SNP [dm6]	T	A	1.007e^-5	0.22	INTERGENIC
3R	17907829	3R_17907829_SNP [dm3] 3R_22082107_SNP [dm6]	A	T	1.021e^-5	0.22	INTRON CG13408
3R	15216297	3R_15216297_DEL [dm3] 3R_19390575_DEL [dm6]	CATT	C	1.025e^-5	0.22	DOWNSTREAM CG3734 INTRON Ino80 & 1 other
2L	5582346	2L_5582346_SNP [dm3] 2L_5582346_SNP [dm6]	T	A	1.031e^-5	0.22	INTERGENIC
2L	5582370	2L_5582370_SNP [dm3] 2L_5582370_SNP [dm6]	C	T	1.031e^-5	0.22	INTERGENIC
2L	3974305	2L_3974305_SNP [dm3] 2L_3974305_SNP [dm6]	A	C	1.039e^-5	0.22	INTRON fred	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	23277000	3R_23277000_SNP [dm3] 3R_27451278_SNP [dm6]	C	A	1.122e^-5	0.235	INTERGENIC
3R	16017625	3R_16017625_SNP [dm3] 3R_20191903_SNP [dm6]	A	G	1.162e^-5	0.241	INTERGENIC
3R	6281497	3R_6281497_SNP [dm3] 3R_10455775_SNP [dm6]	G	A	1.241e^-5	0.254	INTERGENIC
3R	11191092	3R_11191092_SNP [dm3] 3R_15365370_SNP [dm6]	G	A	1.328e^-5	0.262	INTRON CG34404	TF binding site mE1_TFBS_chinmo
2R	19393610	2R_19393610_SNP [dm3] 2R_23506087_SNP [dm6]	G	A	1.339e^-5	0.262	DOWNSTREAM CR43794 INTERGENIC
3R	23687957	3R_23687957_DEL [dm3] 3R_27862235_DEL [dm6]	AAA	A	1.347e^-5	0.262	INTRON CG34353
2L	20100105	2L_20100105_SNP [dm3] 2L_20100105_SNP [dm6]	A	T	1.356e^-5	0.262	INTRON Kua
2L	13901794	2L_13901794_SNP [dm3] 2L_13901794_SNP [dm6]	C	A	1.361e^-5	0.262	SYNONYMOUS_CODING Smg5
3R	22269947	3R_22269947_DEL [dm3] 3R_26444225_DEL [dm6]	CTTC	C	1.389e^-5	0.262	INTRON tx
3R	22269951	3R_22269951_INS [dm3] 3R_26444229_INS [dm6]	A	AGAAAGTATATACTGCAAAA...	1.389e^-5	0.262	INTRON tx
3R	24021514	3R_24021514_SNP [dm3] 3R_28195792_SNP [dm6]	C	A	1.394e^-5	0.262	INTRON CG34354
X	395162	X_395162_SNP [dm3] X_501129_SNP [dm6]	C	T	1.418e^-5	0.262	INTRON svr
X	395217	X_395217_SNP [dm3] X_501184_SNP [dm6]	T	C	1.418e^-5	0.262	INTRON svr

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By genomic position
Variant impact
Gene name

pc_MB_Beta_Fusion phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results