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=7.621e^-18)
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	0.09457

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1910 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	11967139	3L_11967139_SNP [dm3] 3L_11974039_SNP [dm6]	A	T	1.301e^-7	0.094	UPSTREAM CG42397 & 1 other INTERGENIC
3L	11016619	3L_11016619_SNP [dm3] 3L_11023519_SNP [dm6]	T	A	1.437e^-7	0.094	UPSTREAM Fad2 INTERGENIC	TF binding site BDTNP1_TFBS_twi
3L	11967156	3L_11967156_SNP [dm3] 3L_11974056_SNP [dm6]	T	C	1.506e^-7	0.094	UPSTREAM CG42397 & 1 other INTERGENIC
3L	5988869	3L_5988869_INS [dm3] 3L_5995769_INS [dm6]	G	GCAGG	1.692e^-6	0.493	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi
3R	23969845	3R_23969845_SNP [dm3] 3R_28144123_SNP [dm6]	A	T	2.496e^-6	0.493	INTERGENIC
3R	25387833	3R_25387833_SNP [dm3] 3R_29562111_SNP [dm6]	T	G	2.553e^-6	0.493	INTRON Dr
3R	25919032	3R_25919032_SNP [dm3] 3R_30093310_SNP [dm6]	C	T	2.766e^-6	0.493	INTRON sima
3L	9102730	3L_9102730_SNP [dm3] 3L_9109630_SNP [dm6]	A	C	2.905e^-6	0.493	INTRON bol
3R	19590175	3R_19590175_SNP [dm3] 3R_23764453_SNP [dm6]	G	T	3.072e^-6	0.493	SYNONYMOUS_CODING Lsd-1 START_GAINED Lsd-1 UTR_5_PRIME Lsd-1	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	25372305	3R_25372305_SNP [dm3] 3R_29546583_SNP [dm6]	A	T	3.127e^-6	0.493	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
X	8530718	X_8530718_SNP [dm3] X_8636685_SNP [dm6]	C	A	3.694e^-6	0.493	INTRON oc	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Kr
3R	25919311	3R_25919311_SNP [dm3] 3R_30093589_SNP [dm6]	G	A	3.740e^-6	0.493	INTRON sima
3L	13466794	3L_13466794_SNP [dm3] 3L_13473694_SNP [dm6]	G	C	3.765e^-6	0.493	INTRON CG10089
3L	11172885	3L_11172885_SNP [dm3] 3L_11179785_SNP [dm6]	G	A	3.848e^-6	0.493	INTRON GlcAT-P
3R	25934000	3R_25934000_SNP [dm3] 3R_30108278_SNP [dm6]	C	G	4.104e^-6	0.493	INTRON sima	TF binding site mE1_TFBS_inv
2L	12489325	2L_12489325_SNP [dm3] 2L_12489325_SNP [dm6]	G	C	4.423e^-6	0.493	INTRON bun	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	23969846	3R_23969846_SNP [dm3] 3R_28144124_SNP [dm6]	A	C	4.494e^-6	0.493	INTERGENIC
3R	13714710	3R_13714710_SNP [dm3] 3R_17888988_SNP [dm6]	C	T	4.728e^-6	0.493	INTRON Rim
3R	27166882	3R_27166882_INS [dm3] 3R_31341160_INS [dm6]	C	CGC	5.570e^-6	0.55	INTRON CG34347
3R	25372307	3R_25372307_SNP [dm3] 3R_29546585_SNP [dm6]	G	T	6.320e^-6	0.589	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3L	11017014	3L_11017014_SNP [dm3] 3L_11023914_SNP [dm6]	C	A	6.593e^-6	0.589	SYNONYMOUS_CODING Fad2	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3R	13714805	3R_13714805_SNP [dm3] 3R_17889083_SNP [dm6]	T	G	8.365e^-6	0.69	INTRON Rim
2R	20106169	2R_20106169_SNP [dm3] 2R_24218646_SNP [dm6]	A	G	8.462e^-6	0.69	INTRON CG30419
3L	11017013	3L_11017013_SNP [dm3] 3L_11023913_SNP [dm6]	C	A	8.846e^-6	0.691	SYNONYMOUS_CODING Fad2	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3L	4846164	3L_4846164_SNP [dm3] 3L_4846164_SNP [dm6]	A	C	9.294e^-6	0.697	INTERGENIC
3L	4846156	3L_4846156_SNP [dm3] 3L_4846156_SNP [dm6]	A	C	1.027e^-5	0.701	INTERGENIC
3L	11223576	3L_11223576_DEL [dm3] 3L_11230476_DEL [dm6]	ACAAA	A	1.038e^-5	0.701	UTR_3_PRIME CG42671 DOWNSTREAM CG42671 & 1 other
2L	13819846	2L_13819846_SNP [dm3] 2L_13819846_SNP [dm6]	A	G	1.097e^-5	0.701	DOWNSTREAM Sos INTERGENIC	TF binding site BDTNP1_TFBS_prd mE1_TFBS_HSA
3R	25933477	3R_25933477_SNP [dm3] 3R_30107755_SNP [dm6]	C	T	1.179e^-5	0.701	INTRON sima
2L	12403814	2L_12403814_SNP [dm3] 2L_12403814_SNP [dm6]	G	C	1.215e^-5	0.701	NON_SYNONYMOUS_CODING vir-1	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	25917094	3R_25917094_SNP [dm3] 3R_30091372_SNP [dm6]	A	T	1.222e^-5	0.701	INTRON sima	TF binding site mE1_TFBS_Trl
3L	5988949	3L_5988949_SNP [dm3] 3L_5995849_SNP [dm6]	C	T	1.269e^-5	0.701	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi
3R	25915748	3R_25915748_SNP [dm3] 3R_30090026_SNP [dm6]	T	A	1.270e^-5	0.701	INTRON sima	TF binding site mE1_TFBS_Trl
3R	18510949	3R_18510949_SNP [dm3] 3R_22685227_SNP [dm6]	G	A	1.270e^-5	0.701	UTR_3_PRIME Gclm DOWNSTREAM Gclm
3R	25394321	3R_25394321_SNP [dm3] 3R_29568599_SNP [dm6]	T	G	1.459e^-5	0.718	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	11967835	3L_11967835_SNP [dm3] 3L_11974735_SNP [dm6]	T	G	1.466e^-5	0.718	UPSTREAM CG42397 & 1 other INTERGENIC
3L	11967796	3L_11967796_SNP [dm3] 3L_11974696_SNP [dm6]	A	T	1.467e^-5	0.718	UPSTREAM CG42397 & 1 other INTERGENIC
3R	12625669	3R_12625669_DEL [dm3] 3R_16799947_DEL [dm6]	AAGT	A	1.580e^-5	0.718	UPSTREAM CR45750 INTERGENIC
3R	12625674	3R_12625674_SNP [dm3] 3R_16799952_SNP [dm6]	G	T	1.580e^-5	0.718	UPSTREAM CR45750 INTERGENIC
3L	13464630	3L_13464630_SNP [dm3] 3L_13471530_SNP [dm6]	G	A	1.589e^-5	0.718	INTRON CG10089
3L	11172923	3L_11172923_SNP [dm3] 3L_11179823_SNP [dm6]	A	G	1.603e^-5	0.718	INTRON GlcAT-P
3L	1065801	3L_1065801_SNP [dm3] 3L_1065801_SNP [dm6]	G	C	1.624e^-5	0.718	INTRON bab1
3L	11020960	3L_11020960_SNP [dm3] 3L_11027860_SNP [dm6]	G	A	1.647e^-5	0.718	NON_SYNONYMOUS_CODING CG32081 DOWNSTREAM CG32079
3R	21279908	3R_21279908_SNP [dm3] 3R_25454186_SNP [dm6]	T	C	1.700e^-5	0.719	INTRON Fur1
2L	3021662	2L_3021662_SNP [dm3] 2L_3021662_SNP [dm6]	C	T	1.769e^-5	0.719	UTR_3_PRIME alpha4GT1 DOWNSTREAM CG17264
2R	5262516	2R_5262516_SNP [dm3] 2R_9375011_SNP [dm6]	T	C	1.788e^-5	0.719	INTRON CG13954	TF binding site mE1_TFBS_cad
3L	10737919	3L_10737919_SNP [dm3] 3L_10744819_SNP [dm6]	A	C	1.806e^-5	0.719	INTERGENIC
3R	19130852	3R_19130852_SNP [dm3] 3R_23305130_SNP [dm6]	A	C	1.921e^-5	0.719	INTRON pnt
3R	12625675	3R_12625675_DEL [dm3] 3R_16799953_DEL [dm6]	AAAGACAAAGCCCGC...	A	2.046e^-5	0.719	UPSTREAM CR45750 INTERGENIC
3R	12625691	3R_12625691_MNP [dm3] 3R_16799969_MNP [dm6]	GAG	TGT	2.046e^-5	0.719	UPSTREAM CR45750 INTERGENIC
3R	26392635	3R_26392635_DEL [dm3] 3R_30566913_DEL [dm6]	GG	G	2.123e^-5	0.719	INTRON tmod	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	18808589	2L_18808589_SNP [dm3] 2L_18808589_SNP [dm6]	C	T	2.236e^-5	0.719	DOWNSTREAM CG42502 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_inv
3R	25927798	3R_25927798_SNP [dm3] 3R_30102076_SNP [dm6]	A	C	2.238e^-5	0.719	INTRON sima
2L	12195422	2L_12195422_SNP [dm3] 2L_12195422_SNP [dm6]	A	G	2.239e^-5	0.719	INTRON aret
2R	16019985	2R_16019985_SNP [dm3] 2R_20132480_SNP [dm6]	C	G	2.264e^-5	0.719	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
3L	20554424	3L_20554424_SNP [dm3] 3L_20561324_SNP [dm6]	A	C	2.269e^-5	0.719	INTERGENIC
2R	12214457	2R_12214457_SNP [dm3] 2R_16326952_SNP [dm6]	A	G	2.279e^-5	0.719	INTRON Vha44
2L	12403835	2L_12403835_SNP [dm3] 2L_12403835_SNP [dm6]	C	T	2.285e^-5	0.719	NON_SYNONYMOUS_CODING vir-1	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	10766070	2L_10766070_DEL [dm3] 2L_10766070_DEL [dm6]	GTTG	G	2.302e^-5	0.719	UTR_3_PRIME UbcD2
2L	12925293	2L_12925293_SNP [dm3] 2L_12925293_SNP [dm6]	T	A	2.319e^-5	0.719	UTR_3_PRIME ACXA UPSTREAM ACXE
3L	5988886	3L_5988886_SNP [dm3] 3L_5995786_SNP [dm6]	C	G	2.375e^-5	0.719	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi
3R	13714693	3R_13714693_SNP [dm3] 3R_17888971_SNP [dm6]	A	G	2.378e^-5	0.719	INTRON Rim
2R	9736966	2R_9736966_SNP [dm3] 2R_13849461_SNP [dm6]	A	G	2.437e^-5	0.725	SPLICE_SITE_REGION CG30484 UPSTREAM CG30485 INTRON CG30484
3R	19126526	3R_19126526_SNP [dm3] 3R_23300804_SNP [dm6]	A	G	2.529e^-5	0.731	INTRON pnt	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	11017325	3L_11017325_SNP [dm3] 3L_11024225_SNP [dm6]	C	G	2.585e^-5	0.731	SYNONYMOUS_CODING Fad2	TF binding site BDTNP1_TFBS_twi mE1_TFBS_sens
X	19890700	X_19890700_SNP [dm3] X_19996667_SNP [dm6]	C	G	2.672e^-5	0.731	INTERGENIC
X	10798932	X_10798932_MNP [dm3] X_10904899_MNP [dm6]	ATCAG	GGGTA	2.695e^-5	0.731	UPSTREAM CG43901 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
X	10798939	X_10798939_DEL [dm3] X_10904906_DEL [dm6]	TTTATGTTC	T	2.695e^-5	0.731	UPSTREAM CG43901 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	11297944	3L_11297944_SNP [dm3] 3L_11304844_SNP [dm6]	T	G	2.739e^-5	0.731	INTERGENIC
X	11069407	X_11069407_SNP [dm3] X_11175374_SNP [dm6]	T	C	2.753e^-5	0.731	INTERGENIC
2L	10275074	2L_10275074_SNP [dm3] 2L_10275074_SNP [dm6]	A	T	2.785e^-5	0.731	SPLICE_SITE_REGION Utx INTRON Utx
3L	8199668	3L_8199668_SNP [dm3] 3L_8206568_SNP [dm6]	T	A	2.807e^-5	0.731	INTERGENIC
X	2924894	X_2924894_SNP [dm3] X_3030861_SNP [dm6]	A	G	2.855e^-5	0.733	INTRON kirre
X	12951187	X_12951187_SNP [dm3] X_13057154_SNP [dm6]	A	G	2.953e^-5	0.741	INTRON rad
2L	12925608	2L_12925608_SNP [dm3] 2L_12925608_SNP [dm6]	G	T	2.988e^-5	0.741	UPSTREAM ACXE DOWNSTREAM ACXA INTERGENIC
3L	11017597	3L_11017597_SNP [dm3] 3L_11024497_SNP [dm6]	T	C	3.003e^-5	0.741	NON_SYNONYMOUS_CODING Fad2
2L	18159458	2L_18159458_SNP [dm3] 2L_18159458_SNP [dm6]	C	G	3.040e^-5	0.741	UPSTREAM CG7200 DOWNSTREAM CG42750 INTERGENIC	TF binding site mE1_TFBS_cad transposable element FlyBase
X	19890698	X_19890698_SNP [dm3] X_19996665_SNP [dm6]	C	G	3.101e^-5	0.746	INTERGENIC
3L	11967127	3L_11967127_SNP [dm3] 3L_11974027_SNP [dm6]	G	A	3.208e^-5	0.762	UPSTREAM CG42397 & 1 other INTERGENIC
3L	13464113	3L_13464113_SNP [dm3] 3L_13471013_SNP [dm6]	C	T	3.252e^-5	0.762	INTRON CG10089	TF binding site mE1_TFBS_cad
X	8290127	X_8290127_SNP [dm3] X_8396094_SNP [dm6]	G	A	3.317e^-5	0.765	INTERGENIC
3R	19130829	3R_19130829_SNP [dm3] 3R_23305107_SNP [dm6]	A	G	3.345e^-5	0.765	INTRON pnt
3R	19146694	3R_19146694_SNP [dm3] 3R_23320972_SNP [dm6]	G	A	3.423e^-5	0.774	INTRON pnt	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	9198748	2R_9198748_SNP [dm3] 2R_13311243_SNP [dm6]	C	T	3.476e^-5	0.776	INTERGENIC
3R	9296977	3R_9296977_SNP [dm3] 3R_13471255_SNP [dm6]	C	G	3.573e^-5	0.781	INTERGENIC
3R	16674156	3R_16674156_SNP [dm3] 3R_20848434_SNP [dm6]	T	C	3.691e^-5	0.781	DOWNSTREAM CG15696 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	9731067	2L_9731067_SNP [dm3] 2L_9731067_SNP [dm6]	T	C	3.692e^-5	0.781	DOWNSTREAM CG13116 INTRON Nckx30C	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_bab1
3R	16674011	3R_16674011_SNP [dm3] 3R_20848289_SNP [dm6]	G	A	3.845e^-5	0.781	DOWNSTREAM CG15696 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
2L	18349623	2L_18349623_SNP [dm3] 2L_18349623_SNP [dm6]	C	T	3.923e^-5	0.781	INTRON Fas3	TF binding site mE1_TFBS_inv
3L	14848518	3L_14848518_DEL [dm3] 3L_14855418_DEL [dm6]	AA	A	3.940e^-5	0.781	INTRON CG17839
2L	1630051	2L_1630051_SNP [dm3] 2L_1630051_SNP [dm6]	C	G	3.980e^-5	0.781	INTERGENIC
2L	12509860	2L_12509860_SNP [dm3] 2L_12509860_SNP [dm6]	C	T	4.018e^-5	0.781	INTRON bun
3R	25915769	3R_25915769_SNP [dm3] 3R_30090047_SNP [dm6]	T	A	4.021e^-5	0.781	INTRON sima	TF binding site mE1_TFBS_Trl
3L	5124281	3L_5124281_SNP [dm3] 3L_5131181_SNP [dm6]	C	G	4.083e^-5	0.781	UPSTREAM CG15212 DOWNSTREAM CG4597 INTERGENIC
X	3915222	X_3915222_SNP [dm3] X_4021189_SNP [dm6]	C	T	4.166e^-5	0.781	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi
X	2924827	X_2924827_SNP [dm3] X_3030794_SNP [dm6]	G	C	4.202e^-5	0.781	INTRON kirre
2L	10860898	2L_10860898_SNP [dm3] 2L_10860898_SNP [dm6]	G	A	4.208e^-5	0.781	NON_SYNONYMOUS_CODING Stam	TF binding site mE1_TFBS_cad
3L	7547964	3L_7547964_SNP [dm3] 3L_7554864_SNP [dm6]	G	A	4.358e^-5	0.781	DOWNSTREAM CG14837 INTERGENIC
3R	3413144	3R_3413144_SNP [dm3] 3R_7587422_SNP [dm6]	T	C	4.431e^-5	0.781	INTRON CG34127	TF binding site mE1_TFBS_inv
X	9075338	X_9075338_SNP [dm3] X_9181305_SNP [dm6]	A	C	4.563e^-5	0.781	UTR_3_PRIME mei-P26

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Missing results

By genomic position
Variant impact
Gene name

Cuticul_NI_20 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results