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=4.594e^-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
wolba	0.05917

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2021 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
X	5208441	X_5208441_SNP [dm3] X_5314408_SNP [dm6]	G	C	6.876e^-7	0.76	NON_SYNONYMOUS_CODING CG4198 DOWNSTREAM CG15930	TF binding site BDTNP1_TFBS_ftz BDTNP1_TFBS_sna mE1_TFBS_chinmo mE1_TFBS_HSA
3R	16520981	3R_16520981_SNP [dm3] 3R_20695259_SNP [dm6]	C	T	8.105e^-7	0.76	INTRON Oamb
3R	14675777	3R_14675777_SNP [dm3] 3R_18850055_SNP [dm6]	T	A	1.817e^-6	0.888	UPSTREAM CG18208 DOWNSTREAM CR45633 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3L	12392251	3L_12392251_SNP [dm3] 3L_12399151_SNP [dm6]	A	G	3.731e^-6	0.888	SYNONYMOUS_CODING CG32104 DOWNSTREAM Smyd4	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
3R	20919249	3R_20919249_SNP [dm3] 3R_25093527_SNP [dm6]	G	A	3.822e^-6	0.888	INTERGENIC
2R	10264871	2R_10264871_SNP [dm3] 2R_14377366_SNP [dm6]	G	A	4.168e^-6	0.888	UPSTREAM Dh44-R1 DOWNSTREAM CG30075 INTERGENIC
3L	1325184	3L_1325184_SNP [dm3] 3L_1325184_SNP [dm6]	G	A	4.620e^-6	0.888	UTR_5_PRIME Myo61F UPSTREAM CR45166 INTRON Myo61F	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
3L	12411617	3L_12411617_SNP [dm3] 3L_12418517_SNP [dm6]	A	G	5.095e^-6	0.888	UPSTREAM ArfGAP1 INTERGENIC	TF binding site mE1_TFBS_cnc
X	5208428	X_5208428_SNP [dm3] X_5314395_SNP [dm6]	T	C	5.179e^-6	0.888	SYNONYMOUS_CODING CG4198 DOWNSTREAM CG15930	TF binding site BDTNP1_TFBS_ftz BDTNP1_TFBS_sna mE1_TFBS_chinmo mE1_TFBS_HSA
3L	12431406	3L_12431406_SNP [dm3] 3L_12438306_SNP [dm6]	C	A	5.209e^-6	0.888	INTERGENIC	TF binding site mE1_TFBS_HSA
3L	897184	3L_897184_SNP [dm3] 3L_897184_SNP [dm6]	A	G	5.685e^-6	0.888	NON_SYNONYMOUS_CODING CG34056 UPSTREAM CG34057
3L	12411612	3L_12411612_SNP [dm3] 3L_12418512_SNP [dm6]	A	T	6.276e^-6	0.888	UPSTREAM ArfGAP1 INTERGENIC	TF binding site mE1_TFBS_cnc
3L	4630672	3L_4630672_SNP [dm3] 3L_4630672_SNP [dm6]	C	G	6.565e^-6	0.888	INTRON axo
2R	19905970	2R_19905970_SNP [dm3] 2R_24018447_SNP [dm6]	A	G	7.055e^-6	0.888	SYNONYMOUS_CODING CG3121	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3R	25328692	3R_25328692_SNP [dm3] 3R_29502970_SNP [dm6]	T	C	7.632e^-6	0.888	SYNONYMOUS_CODING Trc8	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_sens
X	3546984	X_3546984_INS [dm3] X_3652951_INS [dm6]	T	TC	9.398e^-6	0.888	INTRON AstA-R1
3R	18797737	3R_18797737_SNP [dm3] 3R_22972015_SNP [dm6]	G	T	9.845e^-6	0.888	INTERGENIC
3R	19870845	3R_19870845_SNP [dm3] 3R_24045123_SNP [dm6]	A	G	1.018e^-5	0.888	SYNONYMOUS_CODING Rox8	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	6542226	3L_6542226_SNP [dm3] 3L_6549126_SNP [dm6]	A	T	1.059e^-5	0.888	UTR_3_PRIME sfl
3L	13725500	3L_13725500_DEL [dm3] 3L_13732400_DEL [dm6]	ACTGACAGA	A	1.180e^-5	0.888	INTRON bru-3
3L	13727086	3L_13727086_DEL [dm3] 3L_13733986_DEL [dm6]	CAGTCCGTGAACCCAGAGTC...	C	1.315e^-5	0.888	INTRON bru-3
3L	13724770	3L_13724770_SNP [dm3] 3L_13731670_SNP [dm6]	A	C	1.424e^-5	0.888	INTRON bru-3
3R	19995838	3R_19995838_SNP [dm3] 3R_24170116_SNP [dm6]	G	T	1.428e^-5	0.888	UPSTREAM CG5510 INTERGENIC
2L	20412981	2L_20412981_SNP [dm3] 2L_20412981_SNP [dm6]	C	G	1.527e^-5	0.888	INTRON CG10947
3R	10764650	3R_10764650_SNP [dm3] 3R_14938928_SNP [dm6]	A	G	1.537e^-5	0.888	INTERGENIC
3L	18928910	3L_18928910_SNP [dm3] 3L_18935810_SNP [dm6]	C	A	1.651e^-5	0.888	INTRON CG32204
3L	1368309	3L_1368309_SNP [dm3] 3L_1368309_SNP [dm6]	G	A	1.732e^-5	0.888	INTRON Ptp61F	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi
3R	18797071	3R_18797071_SNP [dm3] 3R_22971349_SNP [dm6]	C	A	1.775e^-5	0.888	INTERGENIC	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3L	7852125	3L_7852125_SNP [dm3] 3L_7859025_SNP [dm6]	T	C	1.801e^-5	0.888	INTRON Pdp1
3L	9751229	3L_9751229_SNP [dm3] 3L_9758129_SNP [dm6]	T	G	1.825e^-5	0.888	INTRON CG42268
3R	15670105	3R_15670105_SNP [dm3] 3R_19844383_SNP [dm6]	C	A	1.901e^-5	0.888	INTERGENIC
3L	1263078	3L_1263078_SNP [dm3] 3L_1263078_SNP [dm6]	G	C	2.087e^-5	0.888	INTRON CG9134
3R	16505584	3R_16505584_SNP [dm3] 3R_20679862_SNP [dm6]	C	T	2.097e^-5	0.888	DOWNSTREAM CR43452 INTERGENIC
3L	6068385	3L_6068385_SNP [dm3] 3L_6075285_SNP [dm6]	G	C	2.103e^-5	0.888	UPSTREAM CG6610 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_GATAe mE1_TFBS_HSA mE1_TFBS_sens
2R	12260774	2R_12260774_SNP [dm3] 2R_16373269_SNP [dm6]	G	T	2.173e^-5	0.888	INTERGENIC
3R	18792563	3R_18792563_SNP [dm3] 3R_22966841_SNP [dm6]	C	T	2.308e^-5	0.888	SYNONYMOUS_CODING Tpl94D	TF binding site mE1_TFBS_cad
3L	7852205	3L_7852205_SNP [dm3] 3L_7859105_SNP [dm6]	T	A	2.401e^-5	0.888	INTRON Pdp1
3R	14676991	3R_14676991_DEL [dm3] 3R_18851269_DEL [dm6]	CG	T	2.451e^-5	0.888	UPSTREAM CR45633 DOWNSTREAM CG31226 INTERGENIC
3L	16991961	3L_16991961_SNP [dm3] 3L_16998861_SNP [dm6]	A	G	2.459e^-5	0.888	SYNONYMOUS_CODING CG3764 UPSTREAM mir-2500	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3L	7199551	3L_7199551_SNP [dm3] 3L_7206451_SNP [dm6]	C	T	2.540e^-5	0.888	INTERGENIC
3L	18645916	3L_18645916_SNP [dm3] 3L_18652816_SNP [dm6]	T	A	2.596e^-5	0.888	INTRON MYPT-75D
3L	16731035	3L_16731035_SNP [dm3] 3L_16737935_SNP [dm6]	G	A	2.613e^-5	0.888	SYNONYMOUS_CODING CG9701	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	7286655	2R_7286655_SNP [dm3] 2R_11399150_SNP [dm6]	T	C	2.739e^-5	0.888	DOWNSTREAM tRNA:CR30506 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_kni BDTNP1_TFBS_Med BDTNP1_TFBS_shn BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2L	7133482	2L_7133482_SNP [dm3] 2L_7133482_SNP [dm6]	A	C	2.815e^-5	0.888	START_GAINED Pvf3 UTR_5_PRIME Pvf3 INTRON Pvf3	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	16519233	3R_16519233_SNP [dm3] 3R_20693511_SNP [dm6]	A	G	2.847e^-5	0.888	SYNONYMOUS_CODING Oamb INTRON Oamb	TF binding site mE1_TFBS_cad
3L	1136992	3L_1136992_SNP [dm3] 3L_1136992_SNP [dm6]	T	A	2.868e^-5	0.888	INTERGENIC
2R	10265506	2R_10265506_SNP [dm3] 2R_14378001_SNP [dm6]	A	T	2.972e^-5	0.888	UPSTREAM Dh44-R1 INTERGENIC
3R	10420289	3R_10420289_SNP [dm3] 3R_14594567_SNP [dm6]	A	T	2.997e^-5	0.888	INTRON stumps	regulatory region REDfly_CRMs
3L	897188	3L_897188_SNP [dm3] 3L_897188_SNP [dm6]	T	C	3.040e^-5	0.888	SYNONYMOUS_CODING CG34056 UPSTREAM CG34057
2R	12851813	2R_12851813_SNP [dm3] 2R_16964308_SNP [dm6]	C	G	3.044e^-5	0.888	EXON CR44376
3L	1334406	3L_1334406_SNP [dm3] 3L_1334406_SNP [dm6]	C	G	3.061e^-5	0.888	SYNONYMOUS_CODING CG2211 UPSTREAM l_3_02640	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_sens
3R	15673811	3R_15673811_SNP [dm3] 3R_19848089_SNP [dm6]	A	G	3.172e^-5	0.888	INTRON CG4662	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad
3R	14676984	3R_14676984_SNP [dm3] 3R_18851262_SNP [dm6]	C	T	3.297e^-5	0.888	UPSTREAM CR45633 DOWNSTREAM CG31226 INTERGENIC
3L	7852135	3L_7852135_SNP [dm3] 3L_7859035_SNP [dm6]	G	C	3.355e^-5	0.888	INTRON Pdp1
3R	18797809	3R_18797809_SNP [dm3] 3R_22972087_SNP [dm6]	C	T	3.414e^-5	0.888	INTERGENIC
2R	10265199	2R_10265199_SNP [dm3] 2R_14377694_SNP [dm6]	A	C	3.481e^-5	0.888	UPSTREAM Dh44-R1 INTERGENIC
3L	3099166	3L_3099166_SNP [dm3] 3L_3099166_SNP [dm6]	C	T	3.491e^-5	0.888	INTRON Cht7
2R	19905679	2R_19905679_SNP [dm3] 2R_24018156_SNP [dm6]	C	A	3.524e^-5	0.888	SYNONYMOUS_CODING CG3121 UPSTREAM CG4324	TF binding site BDTNP1_TFBS_twi mE1_TFBS_sens
2R	7887972	2R_7887972_SNP [dm3] 2R_12000467_SNP [dm6]	A	C	3.612e^-5	0.888	INTERGENIC
3L	3098955	3L_3098955_SNP [dm3] 3L_3098955_SNP [dm6]	G	A	3.628e^-5	0.888	INTRON Cht7
3L	2495965	3L_2495965_SNP [dm3] 3L_2495965_SNP [dm6]	G	T	3.689e^-5	0.888	SPLICE_SITE_REGION CG45186 INTRON CG45186	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2R	8133130	2R_8133130_SNP [dm3] 2R_12245625_SNP [dm6]	G	C	3.692e^-5	0.888	UPSTREAM CG43244 INTERGENIC
3L	18645967	3L_18645967_SNP [dm3] 3L_18652867_SNP [dm6]	A	C	3.785e^-5	0.888	INTRON MYPT-75D
3L	17683770	3L_17683770_SNP [dm3] 3L_17690670_SNP [dm6]	A	G	3.832e^-5	0.888	INTRON Ccn
3R	10420212	3R_10420212_SNP [dm3] 3R_14594490_SNP [dm6]	A	T	3.975e^-5	0.888	INTRON stumps	regulatory region REDfly_CRMs
X	3548545	X_3548545_SNP [dm3] X_3654512_SNP [dm6]	C	A	3.996e^-5	0.888	INTRON AstA-R1
2R	3633470	2R_3633470_SNP [dm3] 2R_7745965_SNP [dm6]	G	A	4.035e^-5	0.888	UPSTREAM CG30497 & 1 other INTRON CG30497 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
X	18352906	X_18352906_SNP [dm3] X_18458873_SNP [dm6]	G	A	4.114e^-5	0.888	SYNONYMOUS_CODING CG32547 DOWNSTREAM CG43843
3R	14307711	3R_14307711_SNP [dm3] 3R_18481989_SNP [dm6]	G	A	4.186e^-5	0.888	INTRON fru
2R	7244367	2R_7244367_SNP [dm3] 2R_11356862_SNP [dm6]	C	A	4.224e^-5	0.888	SYNONYMOUS_CODING iotaTry UPSTREAM CG13202 DOWNSTREAM deltaTry & 1 other	TF binding site mE1_TFBS_sens
X	16886317	X_16886317_SNP [dm3] X_16992284_SNP [dm6]	A	T	4.280e^-5	0.888	INTRON CG45002
2R	10265477	2R_10265477_SNP [dm3] 2R_14377972_SNP [dm6]	G	T	4.310e^-5	0.888	UPSTREAM Dh44-R1 INTERGENIC
2R	10265479	2R_10265479_INS [dm3] 2R_14377974_INS [dm6]	C	CC	4.310e^-5	0.888	UPSTREAM Dh44-R1 INTERGENIC
3L	1136985	3L_1136985_MNP [dm3] 3L_1136985_MNP [dm6]	TTT	CAC	4.321e^-5	0.888	INTERGENIC
3R	13571163	3R_13571163_SNP [dm3] 3R_17745441_SNP [dm6]	A	G	4.341e^-5	0.888	NON_SYNONYMOUS_CODING TyrRII	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	7851272	3L_7851272_SNP [dm3] 3L_7858172_SNP [dm6]	A	C	4.358e^-5	0.888	INTRON Pdp1	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
X	15666530	X_15666530_SNP [dm3] X_15772497_SNP [dm6]	C	T	4.373e^-5	0.888	SYNONYMOUS_CODING CG33172 UPSTREAM CG43672
3L	16553341	3L_16553341_SNP [dm3] 3L_16560241_SNP [dm6]	G	T	4.385e^-5	0.888	INTERGENIC
3L	2430863	3L_2430863_SNP [dm3] 3L_2430863_SNP [dm6]	A	G	4.482e^-5	0.888	INTRON CG45186
3R	17110690	3R_17110690_SNP [dm3] 3R_21284968_SNP [dm6]	A	G	4.604e^-5	0.888	DOWNSTREAM CG17298 INTRON SIFaR
2R	14490438	2R_14490438_SNP [dm3] 2R_18602933_SNP [dm6]	T	C	4.606e^-5	0.888	INTRON GEFmeso
2R	8133171	2R_8133171_SNP [dm3] 2R_12245666_SNP [dm6]	C	T	4.703e^-5	0.888	UPSTREAM CG43244 INTERGENIC
3R	11165246	3R_11165246_SNP [dm3] 3R_15339524_SNP [dm6]	T	C	4.747e^-5	0.888	NON_SYNONYMOUS_CODING CG6218
3L	13724740	3L_13724740_DEL [dm3] 3L_13731640_DEL [dm6]	GCCACAT	G	4.865e^-5	0.888	INTRON bru-3
2R	19719313	2R_19719313_SNP [dm3] 2R_23831790_SNP [dm6]	G	A	4.949e^-5	0.888	INTRON CG5549
X	3546939	X_3546939_SNP [dm3] X_3652906_SNP [dm6]	C	T	4.985e^-5	0.888	INTRON AstA-R1
3L	14729839	3L_14729839_SNP [dm3] 3L_14736739_SNP [dm6]	G	C	5.015e^-5	0.888	INTRON ome
2R	10265507	2R_10265507_SNP [dm3] 2R_14378002_SNP [dm6]	T	A	5.133e^-5	0.888	UPSTREAM Dh44-R1 INTERGENIC
3L	18645898	3L_18645898_SNP [dm3] 3L_18652798_SNP [dm6]	A	G	5.145e^-5	0.888	INTRON MYPT-75D
2R	10265406	2R_10265406_SNP [dm3] 2R_14377901_SNP [dm6]	G	C	5.187e^-5	0.888	UPSTREAM Dh44-R1 INTERGENIC
X	5447460	X_5447460_SNP [dm3] X_5553427_SNP [dm6]	T	G	5.189e^-5	0.888	INTRON Vsx2	TF binding site BDTNP1_TFBS_dl
2R	8586240	2R_8586240_SNP [dm3] 2R_12698735_SNP [dm6]	T	C	5.252e^-5	0.888	INTERGENIC
2L	20064873	2L_20064873_SNP [dm3] 2L_20064873_SNP [dm6]	G	C	5.561e^-5	0.888	SYNONYMOUS_CODING vls DOWNSTREAM lok	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	7133460	2L_7133460_SNP [dm3] 2L_7133460_SNP [dm6]	C	T	5.577e^-5	0.888	UTR_5_PRIME Pvf3 INTRON Pvf3	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi
2L	7133456	2L_7133456_SNP [dm3] 2L_7133456_SNP [dm6]	G	T	5.654e^-5	0.888	UTR_5_PRIME Pvf3 INTRON Pvf3	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi
2R	19482135	2R_19482135_SNP [dm3] 2R_23594612_SNP [dm6]	G	C	5.756e^-5	0.888	INTRON apt	TF binding site mE1_TFBS_sens
3R	18642020	3R_18642020_SNP [dm3] 3R_22816298_SNP [dm6]	T	G	5.764e^-5	0.888	UPSTREAM CG13840 INTERGENIC
3R	10420226	3R_10420226_SNP [dm3] 3R_14594504_SNP [dm6]	T	C	5.806e^-5	0.888	INTRON stumps	regulatory region REDfly_CRMs
3L	2510391	3L_2510391_SNP [dm3] 3L_2510391_SNP [dm6]	G	T	5.818e^-5	0.888	SYNONYMOUS_CODING Spn INTRON Spn	TF binding site mE1_TFBS_chinmo
3L	7111439	3L_7111439_SNP [dm3] 3L_7118339_SNP [dm6]	C	T	5.881e^-5	0.888	SYNONYMOUS_CODING form3	TF binding site mE1_TFBS_chinmo

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Missing results

By genomic position
Variant impact
Gene name

Shared_TEs phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results