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=9.953e^-14)
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_2L_t	0.02639
In_3R_P	0.01057

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2257 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
3L	11505068	3L_11505068_SNP [dm3] 3L_11511968_SNP [dm6]	G	C	5.104e^-7	0.612	UPSTREAM Sgs3 INTERGENIC	regulatory region REDfly_CRMs transposable element FlyBase
2R	20515299	2R_20515299_SNP [dm3] 2R_24627776_SNP [dm6]	T	C	1.032e^-6	0.612	DOWNSTREAM snoRNA:Me18S-G393 INTRON CG13594
X	21910670	X_21910670_SNP [dm3] X_22508834_SNP [dm6]	G	A	2.493e^-6	0.612	DOWNSTREAM l_1_G0196 INTERGENIC	TF binding site BDTNP1_TFBS_dl
2L	8371319	2L_8371319_INS [dm3] 2L_8371319_INS [dm6]	A	ATCTA	2.805e^-6	0.612	UPSTREAM CR45341 INTRON CG17292
3L	896058	3L_896058_SNP [dm3] 3L_896058_SNP [dm6]	G	T	2.984e^-6	0.612	UTR_5_PRIME CG34056 DOWNSTREAM CG32479
2R	5085833	2R_5085833_SNP [dm3] 2R_9198328_SNP [dm6]	A	C	4.214e^-6	0.612	INTRON unpg	transposable element FlyBase
2L	8224856	2L_8224856_SNP [dm3] 2L_8224856_SNP [dm6]	C	G	4.682e^-6	0.612	NON_SYNONYMOUS_CODING Pvr
3L	442004	3L_442004_SNP [dm3] 3L_442004_SNP [dm6]	G	A	5.754e^-6	0.612	UPSTREAM klar DOWNSTREAM klar INTRON klar	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_hkb mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_run mE1_TFBS_Trl
3R	2276781	3R_2276781_SNP [dm3] 3R_6451059_SNP [dm6]	G	A	5.817e^-6	0.612	UTR_3_PRIME CG9727 DOWNSTREAM CG9727	TF binding site mE1_TFBS_cad
3R	26071350	3R_26071350_SNP [dm3] 3R_30245628_SNP [dm6]	T	G	7.501e^-6	0.612	SYNONYMOUS_CODING CG9733
X	21931684	X_21931684_SNP [dm3] X_22529848_SNP [dm6]	T	G	7.601e^-6	0.612	UPSTREAM S6kII INTRON CG17600	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb mE1_TFBS_HSA
X	5224774	X_5224774_SNP [dm3] X_5330741_SNP [dm6]	G	A	8.187e^-6	0.612	SYNONYMOUS_CODING XRCC1	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
X	5224782	X_5224782_SNP [dm3] X_5330749_SNP [dm6]	C	T	8.187e^-6	0.612	NON_SYNONYMOUS_CODING XRCC1	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3R	2264922	3R_2264922_SNP [dm3] 3R_6439200_SNP [dm6]	C	T	9.539e^-6	0.612	INTRON gpp
3R	2273966	3R_2273966_SNP [dm3] 3R_6448244_SNP [dm6]	A	T	9.539e^-6	0.612	UTR_3_PRIME gpp DOWNSTREAM gpp	TF binding site mE1_TFBS_zfh1
3R	2282737	3R_2282737_SNP [dm3] 3R_6457015_SNP [dm6]	G	T	9.539e^-6	0.612	UPSTREAM Zif & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 mE1_TFBS_HSA
3R	2288776	3R_2288776_SNP [dm3] 3R_6463054_SNP [dm6]	C	A	9.539e^-6	0.612	INTERGENIC
2L	20336420	2L_20336420_SNP [dm3] 2L_20336420_SNP [dm6]	G	A	1.073e^-5	0.612	INTRON spir
2R	20518354	2R_20518354_SNP [dm3] 2R_24630831_SNP [dm6]	G	T	1.163e^-5	0.612	UPSTREAM Cyp9c1 DOWNSTREAM CR43787 INTRON CG13594
3L	3650964	3L_3650964_SNP [dm3] 3L_3650964_SNP [dm6]	A	C	1.185e^-5	0.612	INTRON dar1
2L	4568543	2L_4568543_SNP [dm3] 2L_4568543_SNP [dm6]	G	T	1.202e^-5	0.612	INTRON dp	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
3R	26070670	3R_26070670_SNP [dm3] 3R_30244948_SNP [dm6]	T	A	1.202e^-5	0.612	INTRON CG9733
2L	8224852	2L_8224852_SNP [dm3] 2L_8224852_SNP [dm6]	T	G	1.207e^-5	0.612	SYNONYMOUS_CODING Pvr
3L	6111784	3L_6111784_SNP [dm3] 3L_6118684_SNP [dm6]	A	G	1.222e^-5	0.612	INTRON Ets65A
3R	26045641	3R_26045641_SNP [dm3] 3R_30219919_SNP [dm6]	A	T	1.276e^-5	0.612	INTERGENIC
3R	26045647	3R_26045647_SNP [dm3] 3R_30219925_SNP [dm6]	C	T	1.276e^-5	0.612	INTERGENIC
3R	26045651	3R_26045651_SNP [dm3] 3R_30219929_SNP [dm6]	G	A	1.276e^-5	0.612	INTERGENIC
3R	24990570	3R_24990570_SNP [dm3] 3R_29164848_SNP [dm6]	A	T	1.377e^-5	0.612	UTR_3_PRIME CG11897 UPSTREAM CG11898
2R	20514412	2R_20514412_SNP [dm3] 2R_24626889_SNP [dm6]	A	C	1.395e^-5	0.612	INTRON CG13594	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
2L	4073253	2L_4073253_SNP [dm3] 2L_4073253_SNP [dm6]	C	G	1.440e^-5	0.612	INTRON ed
3L	22855146	3L_22855146_SNP [dm3] 3L_22862046_SNP [dm6]	A	G	1.451e^-5	0.612	DOWNSTREAM CG13239 INTERGENIC	TF binding site BDTNP1_TFBS_sna
3L	22855291	3L_22855291_SNP [dm3] 3L_22862191_SNP [dm6]	G	C	1.451e^-5	0.612	DOWNSTREAM CG13239 INTERGENIC	TF binding site BDTNP1_TFBS_sna
3R	1917898	3R_1917898_SNP [dm3] 3R_6092176_SNP [dm6]	G	T	1.454e^-5	0.612	DOWNSTREAM Gasp INTRON Gasp
2L	3238057	2L_3238057_SNP [dm3] 2L_3238057_SNP [dm6]	C	T	1.500e^-5	0.612	INTERGENIC
3R	26045650	3R_26045650_SNP [dm3] 3R_30219928_SNP [dm6]	A	G	1.562e^-5	0.612	INTERGENIC
3L	11504300	3L_11504300_SNP [dm3] 3L_11511200_SNP [dm6]	T	C	1.585e^-5	0.612	UPSTREAM CG33272 DOWNSTREAM Sgs7 INTERGENIC	TF binding site mE1_TFBS_bab1
3R	26045653	3R_26045653_SNP [dm3] 3R_30219931_SNP [dm6]	A	T	1.605e^-5	0.612	INTERGENIC
3L	22855081	3L_22855081_SNP [dm3] 3L_22861981_SNP [dm6]	G	T	1.642e^-5	0.612	DOWNSTREAM CG13239 INTERGENIC	TF binding site BDTNP1_TFBS_sna
3R	2195865	3R_2195865_SNP [dm3] 3R_6370143_SNP [dm6]	C	T	1.644e^-5	0.612	NON_SYNONYMOUS_CODING CG10286 DOWNSTREAM CG1041	TF binding site mE1_TFBS_cad mE1_TFBS_sens
3R	2210505	3R_2210505_SNP [dm3] 3R_6384783_SNP [dm6]	C	T	1.644e^-5	0.612	INTRON godzilla
3R	2238897	3R_2238897_SNP [dm3] 3R_6413175_SNP [dm6]	G	A	1.644e^-5	0.612	INTRON gpp
3R	2174189	3R_2174189_SNP [dm3] 3R_6348467_SNP [dm6]	A	G	1.717e^-5	0.612	UPSTREAM Hr83 DOWNSTREAM CG18048 INTERGENIC
3R	2248059	3R_2248059_SNP [dm3] 3R_6422337_SNP [dm6]	G	A	1.717e^-5	0.612	INTRON gpp	TF binding site BDTNP1_TFBS_dl
3R	26070971	3R_26070971_DEL [dm3] 3R_30245249_DEL [dm6]	AGAGATT	G	1.734e^-5	0.612	INTRON CG9733
X	6331536	X_6331536_SNP [dm3] X_6437503_SNP [dm6]	A	G	1.756e^-5	0.612	INTRON CG42340
2L	13314061	2L_13314061_SNP [dm3] 2L_13314061_SNP [dm6]	C	T	1.810e^-5	0.612	INTRON CG43778
3R	2234513	3R_2234513_SNP [dm3] 3R_6408791_SNP [dm6]	C	T	1.836e^-5	0.612	DOWNSTREAM CR44017 INTRON gpp	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_Trl
3L	105174	3L_105174_SNP [dm3] 3L_105174_SNP [dm6]	C	T	1.847e^-5	0.612	INTERGENIC
3R	2184082	3R_2184082_SNP [dm3] 3R_6358360_SNP [dm6]	G	A	1.898e^-5	0.612	NON_SYNONYMOUS_CODING Pak	TF binding site mE1_TFBS_cad
3L	5847440	3L_5847440_SNP [dm3] 3L_5854340_SNP [dm6]	C	T	1.905e^-5	0.612	INTERGENIC	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	26281962	3R_26281962_SNP [dm3] 3R_30456240_SNP [dm6]	T	G	1.961e^-5	0.612	UPSTREAM aralar1 DOWNSTREAM CG2224 INTERGENIC
3R	3685944	3R_3685944_SNP [dm3] 3R_7860222_SNP [dm6]	A	G	1.961e^-5	0.612	INTRON CG17816
X	15247660	X_15247660_SNP [dm3] X_15353627_SNP [dm6]	A	T	2.021e^-5	0.612	INTRON acj6	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_HSA
3L	3650942	3L_3650942_SNP [dm3] 3L_3650942_SNP [dm6]	C	G	2.057e^-5	0.612	INTRON dar1
3R	23491102	3R_23491102_SNP [dm3] 3R_27665380_SNP [dm6]	G	T	2.124e^-5	0.612	SPLICE_SITE_REGION unc80 INTRON unc80	TF binding site mE1_TFBS_cad
X	21910588	X_21910588_SNP [dm3] X_22508752_SNP [dm6]	T	C	2.137e^-5	0.612	DOWNSTREAM l_1_G0196 INTERGENIC	TF binding site BDTNP1_TFBS_dl
2L	20331596	2L_20331596_SNP [dm3] 2L_20331596_SNP [dm6]	G	C	2.185e^-5	0.612	INTRON spir
X	21942729	X_21942729_SNP [dm3] X_22540893_SNP [dm6]	T	C	2.197e^-5	0.612	SPLICE_SITE_REGION CG17600 UPSTREAM CG17598 INTRON CG17600	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
X	21910669	X_21910669_SNP [dm3] X_22508833_SNP [dm6]	A	G	2.202e^-5	0.612	DOWNSTREAM l_1_G0196 INTERGENIC	TF binding site BDTNP1_TFBS_dl
3L	22861312	3L_22861312_SNP [dm3] 3L_22868212_SNP [dm6]	T	C	2.213e^-5	0.612	UTR_5_PRIME CG11137 DOWNSTREAM Arf79F & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
3R	2161052	3R_2161052_SNP [dm3] 3R_6335330_SNP [dm6]	G	A	2.243e^-5	0.612	UPSTREAM Osi19 INTERGENIC
3R	19447315	3R_19447315_SNP [dm3] 3R_23621593_SNP [dm6]	T	A	2.263e^-5	0.612	INTRON CG31145
3L	7221082	3L_7221082_SNP [dm3] 3L_7227982_SNP [dm6]	T	A	2.263e^-5	0.612	INTERGENIC
3L	4881815	3L_4881815_SNP [dm3] 3L_4881815_SNP [dm6]	T	G	2.274e^-5	0.612	INTRON CG17150
3L	11633769	3L_11633769_SNP [dm3] 3L_11640669_SNP [dm6]	C	T	2.281e^-5	0.612	SYNONYMOUS_CODING CG32091
3R	2240193	3R_2240193_SNP [dm3] 3R_6414471_SNP [dm6]	A	T	2.353e^-5	0.612	INTRON gpp	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
2R	7442907	2R_7442907_SNP [dm3] 2R_11555402_SNP [dm6]	T	C	2.363e^-5	0.612	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	15790682	3L_15790682_DEL [dm3] 3L_15797582_DEL [dm6]	TA	T	2.388e^-5	0.612	INTERGENIC
3R	24976270	3R_24976270_SNP [dm3] 3R_29150548_SNP [dm6]	C	A	2.396e^-5	0.612	NON_SYNONYMOUS_CODING ligatin DOWNSTREAM Pglym78	TF binding site mE1_TFBS_chinmo mE1_TFBS_sens
2L	8433919	2L_8433919_DEL [dm3] 2L_8433919_DEL [dm6]	AGCGATTAT	A	2.419e^-5	0.612	UPSTREAM grk DOWNSTREAM D12 INTERGENIC	insulator Insulator_Class_II.mE01 TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
2L	17797674	2L_17797674_SNP [dm3] 2L_17797674_SNP [dm6]	T	G	2.558e^-5	0.612	SYNONYMOUS_CODING CadN2
2L	20331580	2L_20331580_SNP [dm3] 2L_20331580_SNP [dm6]	T	G	2.563e^-5	0.612	INTRON spir
3L	7290467	3L_7290467_SNP [dm3] 3L_7297367_SNP [dm6]	A	G	2.590e^-5	0.612	INTRON unc-13-4A
2R	3883625	2R_3883625_SNP [dm3] 2R_7996120_SNP [dm6]	A	C	2.630e^-5	0.612	SYNONYMOUS_CODING Hey	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3R	2154506	3R_2154506_SNP [dm3] 3R_6328784_SNP [dm6]	C	T	2.658e^-5	0.612	INTERGENIC
3R	2154581	3R_2154581_SNP [dm3] 3R_6328859_SNP [dm6]	G	A	2.669e^-5	0.612	INTERGENIC
3L	12858903	3L_12858903_SNP [dm3] 3L_12865803_SNP [dm6]	A	C	2.732e^-5	0.612	INTERGENIC
3L	12734395	3L_12734395_SNP [dm3] 3L_12741295_SNP [dm6]	A	G	2.812e^-5	0.612	UTR_3_PRIME Ptp69D UPSTREAM CG32112
3R	2222238	3R_2222238_SNP [dm3] 3R_6396516_SNP [dm6]	A	T	2.847e^-5	0.612	INTRON Dmtn
2R	20080559	2R_20080559_SNP [dm3] 2R_24193036_SNP [dm6]	G	A	2.895e^-5	0.612	SYNONYMOUS_CODING ocm
2R	19138965	2R_19138965_SNP [dm3] 2R_23251442_SNP [dm6]	G	T	2.910e^-5	0.612	INTERGENIC
3L	4881780	3L_4881780_SNP [dm3] 3L_4881780_SNP [dm6]	C	T	2.969e^-5	0.612	INTRON CG17150
3L	4881790	3L_4881790_SNP [dm3] 3L_4881790_SNP [dm6]	T	C	2.969e^-5	0.612	INTRON CG17150
3L	4881799	3L_4881799_SNP [dm3] 3L_4881799_SNP [dm6]	G	A	2.969e^-5	0.612	INTRON CG17150
X	11096273	X_11096273_SNP [dm3] X_11202240_SNP [dm6]	A	G	3.012e^-5	0.612	UPSTREAM CG11106 INTERGENIC
3R	11107909	3R_11107909_SNP [dm3] 3R_15282187_SNP [dm6]	T	C	3.080e^-5	0.612	INTRON Tm1	TF binding site mE1_TFBS_Trl
3R	26070926	3R_26070926_SNP [dm3] 3R_30245204_SNP [dm6]	T	G	3.100e^-5	0.612	INTRON CG9733
3R	26070928	3R_26070928_DEL [dm3] 3R_30245206_DEL [dm6]	TTA	T	3.100e^-5	0.612	INTRON CG9733
3R	5055986	3R_5055986_SNP [dm3] 3R_9230264_SNP [dm6]	C	A	3.158e^-5	0.612	INTRON pum EXON CR45196	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_Trl
X	21910584	X_21910584_INS [dm3] X_22508748_INS [dm6]	T	TT	3.159e^-5	0.612	DOWNSTREAM l_1_G0196 INTERGENIC	TF binding site BDTNP1_TFBS_dl
3L	4357029	3L_4357029_SNP [dm3] 3L_4357029_SNP [dm6]	C	G	3.210e^-5	0.612	INTRON Cip4
2R	10547226	2R_10547226_SNP [dm3] 2R_14659721_SNP [dm6]	A	T	3.335e^-5	0.612	UPSTREAM Adgf-E INTERGENIC	TF binding site mE1_TFBS_cad
3L	5854619	3L_5854619_SNP [dm3] 3L_5861519_SNP [dm6]	A	G	3.341e^-5	0.612	INTERGENIC	TF binding site mE1_TFBS_HSA
3L	5854714	3L_5854714_SNP [dm3] 3L_5861614_SNP [dm6]	T	G	3.341e^-5	0.612	INTERGENIC
3L	5854779	3L_5854779_DEL [dm3] 3L_5861679_DEL [dm6]	TG	T	3.341e^-5	0.612	INTERGENIC
3L	5854794	3L_5854794_SNP [dm3] 3L_5861694_SNP [dm6]	A	G	3.341e^-5	0.612	INTERGENIC
3L	5859607	3L_5859607_SNP [dm3] 3L_5866507_SNP [dm6]	G	C	3.341e^-5	0.612	INTERGENIC	TF binding site mE1_TFBS_cad
2R	5073573	2R_5073573_SNP [dm3] 2R_9186068_SNP [dm6]	G	A	3.377e^-5	0.612	UTR_5_PRIME ltd DOWNSTREAM CG8026 & 1 other INTRON ltd	regulatory region REDfly_CRMs
3L	3650931	3L_3650931_INS [dm3] 3L_3650931_INS [dm6]	T	TAT	3.385e^-5	0.612	INTRON dar1
2R	20586267	2R_20586267_SNP [dm3] 2R_24698744_SNP [dm6]	A	T	3.437e^-5	0.612	UTR_3_PRIME Mid1 DOWNSTREAM Mid1

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By genomic position
Variant impact
Gene name

pc_Other phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results