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=1.844e^-1)
Null hypothesis is not rejected (p>0.05).
Interpretation: 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_K	0.000425

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_3R_K	17.1894	0.0002

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2880 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	19190980	3L_19190980_SNP [dm3] 3L_19197880_SNP [dm6]	C	T	2.385e^-8	0.025	INTRON fz2
3L	19190825	3L_19190825_SNP [dm3] 3L_19197725_SNP [dm6]	G	A	2.684e^-8	0.025	INTRON fz2	TF binding site mE1_TFBS_inv
3L	19190975	3L_19190975_SNP [dm3] 3L_19197875_SNP [dm6]	A	C	4.295e^-8	0.027	INTRON fz2
2L	1978904	2L_1978904_SNP [dm3] 2L_1978904_SNP [dm6]	C	T	6.397e^-7	0.227	NON_SYNONYMOUS_CODING CG15356	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	19199124	3L_19199124_SNP [dm3] 3L_19206024_SNP [dm6]	C	A	7.043e^-7	0.227	INTRON fz2
3L	19192537	3L_19192537_SNP [dm3] 3L_19199437_SNP [dm6]	C	T	7.266e^-7	0.227	INTRON fz2
3R	9973753	3R_9973753_SNP [dm3] 3R_14148031_SNP [dm6]	C	G	1.221e^-6	0.244	DOWNSTREAM CG14355 INTERGENIC
3L	19170261	3L_19170261_SNP [dm3] 3L_19177161_SNP [dm6]	C	T	1.238e^-6	0.244	INTRON fz2	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_ftz BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Kr
3L	19163884	3L_19163884_SNP [dm3] 3L_19170784_SNP [dm6]	A	C	1.257e^-6	0.244	UPSTREAM fz2 INTRON fz2	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_Dll mE1_TFBS_HSA mE1_TFBS_Trl
3R	10051720	3R_10051720_SNP [dm3] 3R_14225998_SNP [dm6]	T	C	1.302e^-6	0.244	NON_SYNONYMOUS_CODING CG9631	TF binding site mE1_TFBS_cad
3R	9999471	3R_9999471_SNP [dm3] 3R_14173749_SNP [dm6]	G	T	1.441e^-6	0.246	UTR_3_PRIME Dop1R1
2L	13699908	2L_13699908_SNP [dm3] 2L_13699908_SNP [dm6]	T	G	1.579e^-6	0.247	INTRON CG31814
2L	13097656	2L_13097656_SNP [dm3] 2L_13097656_SNP [dm6]	C	T	1.749e^-6	0.252	DOWNSTREAM CR45447 INTERGENIC
3R	9999606	3R_9999606_SNP [dm3] 3R_14173884_SNP [dm6]	G	A	2.056e^-6	0.275	UTR_3_PRIME Dop1R1
3R	6094480	3R_6094480_SNP [dm3] 3R_10268758_SNP [dm6]	G	C	2.260e^-6	0.275	INTRON CG43143	TF binding site mE1_TFBS_eve mE1_TFBS_HSA
3R	18602752	3R_18602752_SNP [dm3] 3R_22777030_SNP [dm6]	A	T	2.349e^-6	0.275	DOWNSTREAM Usp12-46 & 1 other INTRON CG7029
3R	9973767	3R_9973767_SNP [dm3] 3R_14148045_SNP [dm6]	T	C	2.819e^-6	0.311	DOWNSTREAM CG14355 INTERGENIC
3L	19190762	3L_19190762_SNP [dm3] 3L_19197662_SNP [dm6]	C	G	3.481e^-6	0.33	INTRON fz2	TF binding site mE1_TFBS_inv
3L	11017597	3L_11017597_SNP [dm3] 3L_11024497_SNP [dm6]	T	C	3.712e^-6	0.33	NON_SYNONYMOUS_CODING Fad2
3L	19378241	3L_19378241_INS [dm3] 3L_19385141_INS [dm6]	C	CATTTCCTAAAAAGTTA...	3.737e^-6	0.33	INTRON CG32206
3R	9986845	3R_9986845_DEL [dm3] 3R_14161123_DEL [dm6]	TTCTGGCCCT	T	3.767e^-6	0.33	UPSTREAM CG31327 INTERGENIC
3L	19192232	3L_19192232_SNP [dm3] 3L_19199132_SNP [dm6]	A	T	3.891e^-6	0.33	INTRON fz2
3R	13673639	3R_13673639_SNP [dm3] 3R_17847917_SNP [dm6]	G	A	4.200e^-6	0.33	INTRON tinc
3L	19200783	3L_19200783_SNP [dm3] 3L_19207683_SNP [dm6]	G	C	4.228e^-6	0.33	INTRON fz2	TF binding site mE1_TFBS_cad
3L	19197816	3L_19197816_SNP [dm3] 3L_19204716_SNP [dm6]	A	T	4.622e^-6	0.347	INTRON fz2
3L	19186522	3L_19186522_SNP [dm3] 3L_19193422_SNP [dm6]	C	A	5.154e^-6	0.356	INTRON fz2
2L	13712254	2L_13712254_SNP [dm3] 2L_13712254_SNP [dm6]	A	T	5.394e^-6	0.356	INTRON CG31814
3L	19546419	3L_19546419_SNP [dm3] 3L_19553319_SNP [dm6]	A	T	5.646e^-6	0.356	INTRON CG9300	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_sens
3L	19197381	3L_19197381_SNP [dm3] 3L_19204281_SNP [dm6]	G	C	5.841e^-6	0.356	INTRON fz2
3L	19199391	3L_19199391_SNP [dm3] 3L_19206291_SNP [dm6]	G	A	6.489e^-6	0.356	INTRON fz2
2L	6153986	2L_6153986_SNP [dm3] 2L_6153986_SNP [dm6]	A	T	6.670e^-6	0.356	UTR_3_PRIME CG31639 DOWNSTREAM Muc26B	TF binding site mE1_TFBS_HSA
3R	5276560	3R_5276560_SNP [dm3] 3R_9450838_SNP [dm6]	C	G	6.747e^-6	0.356	UTR_3_PRIME ps
2L	6153982	2L_6153982_SNP [dm3] 2L_6153982_SNP [dm6]	G	A	6.857e^-6	0.356	UTR_3_PRIME CG31639 DOWNSTREAM Muc26B	TF binding site mE1_TFBS_HSA
2L	6154000	2L_6154000_SNP [dm3] 2L_6154000_SNP [dm6]	C	T	6.857e^-6	0.356	UTR_3_PRIME CG31639 DOWNSTREAM Muc26B	TF binding site mE1_TFBS_HSA
3R	5278030	3R_5278030_DEL [dm3] 3R_9452308_DEL [dm6]	AAAAA	A	6.932e^-6	0.356	UTR_3_PRIME ps
2R	11239579	2R_11239579_INS [dm3] 2R_15352074_INS [dm6]	A	AACCA	6.959e^-6	0.356	INTRON unc-5	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_Dll mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_sens
3L	13900225	3L_13900225_SNP [dm3] 3L_13907125_SNP [dm6]	T	A	7.090e^-6	0.356	UTR_3_PRIME Rgl
3R	5276343	3R_5276343_SNP [dm3] 3R_9450621_SNP [dm6]	G	A	7.324e^-6	0.356	UTR_3_PRIME ps
2R	10631551	2R_10631551_SNP [dm3] 2R_14744046_SNP [dm6]	G	T	7.411e^-6	0.356	UTR_5_PRIME CG12858	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
X	2544334	X_2544334_SNP [dm3] X_2650301_SNP [dm6]	T	G	8.066e^-6	0.372	INTRON sgg
2L	10355033	2L_10355033_SNP [dm3] 2L_10355033_SNP [dm6]	A	C	8.140e^-6	0.372	INTRON CG5367
3L	19543144	3L_19543144_SNP [dm3] 3L_19550044_SNP [dm6]	T	G	8.507e^-6	0.373	NON_SYNONYMOUS_CODING l_3_76BDr
3L	19185491	3L_19185491_SNP [dm3] 3L_19192391_SNP [dm6]	T	C	9.023e^-6	0.373	INTRON fz2
3R	10051685	3R_10051685_SNP [dm3] 3R_14225963_SNP [dm6]	T	G	9.231e^-6	0.373	SYNONYMOUS_CODING CG9631	TF binding site mE1_TFBS_cad
3R	5275968	3R_5275968_SNP [dm3] 3R_9450246_SNP [dm6]	G	A	9.481e^-6	0.373	UTR_3_PRIME ps DOWNSTREAM ps
3L	19489863	3L_19489863_SNP [dm3] 3L_19496763_SNP [dm6]	G	A	9.746e^-6	0.373	START_GAINED CG9449 UTR_5_PRIME CG9449 UPSTREAM CG9449
3R	10187548	3R_10187548_SNP [dm3] 3R_14361826_SNP [dm6]	G	T	9.799e^-6	0.373	UPSTREAM CG31320 INTRON NK7.1	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2L	13490649	2L_13490649_SNP [dm3] 2L_13490649_SNP [dm6]	A	G	1.010e^-5	0.373	INTRON CG42784
3R	5276361	3R_5276361_SNP [dm3] 3R_9450639_SNP [dm6]	G	T	1.041e^-5	0.373	UTR_3_PRIME ps
3L	19194617	3L_19194617_SNP [dm3] 3L_19201517_SNP [dm6]	C	T	1.062e^-5	0.373	INTRON fz2
3L	19368784	3L_19368784_SNP [dm3] 3L_19375684_SNP [dm6]	A	G	1.064e^-5	0.373	INTRON CG32206
2L	6775324	2L_6775324_DEL [dm3] 2L_6775324_DEL [dm6]	CG	C	1.075e^-5	0.373	UPSTREAM CG17378 INTRON CG17378
3L	19192304	3L_19192304_SNP [dm3] 3L_19199204_SNP [dm6]	C	G	1.124e^-5	0.373	INTRON fz2
3R	26258254	3R_26258254_SNP [dm3] 3R_30432532_SNP [dm6]	C	T	1.171e^-5	0.373	SYNONYMOUS_CODING CG15534	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	19177520	3L_19177520_SNP [dm3] 3L_19184420_SNP [dm6]	G	A	1.173e^-5	0.373	INTRON fz2	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_kni BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens
2L	5432884	2L_5432884_SNP [dm3] 2L_5432884_SNP [dm6]	C	A	1.182e^-5	0.373	DOWNSTREAM CR43713 & 1 other EXON CR43714
3L	19189176	3L_19189176_DEL [dm3] 3L_19196076_DEL [dm6]	GA	C	1.211e^-5	0.373	INTRON fz2
3L	19172420	3L_19172420_SNP [dm3] 3L_19179320_SNP [dm6]	G	T	1.235e^-5	0.373	INTRON fz2	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	19179006	3L_19179006_SNP [dm3] 3L_19185906_SNP [dm6]	T	C	1.237e^-5	0.373	INTRON fz2
3R	2399129	3R_2399129_SNP [dm3] 3R_6573407_SNP [dm6]	G	T	1.246e^-5	0.373	INTRON dpr11
2L	280607	2L_280607_SNP [dm3] 2L_280607_SNP [dm6]	G	A	1.267e^-5	0.373	NON_SYNONYMOUS_CODING smo	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
3R	22916337	3R_22916337_SNP [dm3] 3R_27090615_SNP [dm6]	T	G	1.276e^-5	0.373	INTRON Cpr97Eb
3L	19547973	3L_19547973_DEL [dm3] 3L_19554873_DEL [dm6]	ATGGAATCCATATACGGCGA...	A	1.298e^-5	0.373	DOWNSTREAM CR44677 & 1 other INTERGENIC
3R	13673426	3R_13673426_INS [dm3] 3R_17847704_INS [dm6]	A	AT	1.313e^-5	0.373	INTRON tinc
3R	10608804	3R_10608804_SNP [dm3] 3R_14783082_SNP [dm6]	C	T	1.314e^-5	0.373	INTRON jvl
3R	4949587	3R_4949587_SNP [dm3] 3R_9123865_SNP [dm6]	C	T	1.334e^-5	0.373	INTRON pum
3L	21421813	3L_21421813_SNP [dm3] 3L_21428713_SNP [dm6]	T	A	1.342e^-5	0.373	INTRON barc & 1 other
3L	15225115	3L_15225115_SNP [dm3] 3L_15232015_SNP [dm6]	C	T	1.352e^-5	0.373	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	19185476	3L_19185476_SNP [dm3] 3L_19192376_SNP [dm6]	G	A	1.424e^-5	0.387	INTRON fz2
3R	10071085	3R_10071085_INS [dm3] 3R_14245363_INS [dm6]	T	TTC	1.502e^-5	0.402	UPSTREAM CG43291
3L	19163440	3L_19163440_SNP [dm3] 3L_19170340_SNP [dm6]	A	G	1.577e^-5	0.413	UTR_5_PRIME fz2 INTRON fz2	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_eve mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2R	6812410	2R_6812410_SNP [dm3] 2R_10924905_SNP [dm6]	C	T	1.613e^-5	0.413	INTERGENIC	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3L	19169460	3L_19169460_SNP [dm3] 3L_19176360_SNP [dm6]	G	T	1.636e^-5	0.413	INTRON fz2	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Kr
3R	9721734	3R_9721734_SNP [dm3] 3R_13896012_SNP [dm6]	A	C	1.645e^-5	0.413	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_sens
2R	17082320	2R_17082320_DEL [dm3] 2R_21194815_DEL [dm6]	GGGTGGTAATG...	G	1.660e^-5	0.413	INTRON Lapsyn	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
3L	19544740	3L_19544740_SNP [dm3] 3L_19551640_SNP [dm6]	T	A	1.757e^-5	0.413	NON_SYNONYMOUS_CODING l_3_76BDr UPSTREAM CG9300	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_sens
3R	3370557	3R_3370557_SNP [dm3] 3R_7544835_SNP [dm6]	G	A	1.771e^-5	0.413	SYNONYMOUS_CODING alpha-Est2 DOWNSTREAM alpha-Est1
3L	19167213	3L_19167213_SNP [dm3] 3L_19174113_SNP [dm6]	A	C	1.812e^-5	0.413	INTRON fz2	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
3R	9973416	3R_9973416_SNP [dm3] 3R_14147694_SNP [dm6]	A	T	1.822e^-5	0.413	DOWNSTREAM CG14355 INTERGENIC
2L	16379723	2L_16379723_SNP [dm3] 2L_16379723_SNP [dm6]	G	C	1.825e^-5	0.413	INTERGENIC
3L	19179367	3L_19179367_SNP [dm3] 3L_19186267_SNP [dm6]	T	A	1.838e^-5	0.413	INTRON fz2
3R	18974847	3R_18974847_SNP [dm3] 3R_23149125_SNP [dm6]	T	C	1.849e^-5	0.413	DOWNSTREAM unk INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	19377491	3L_19377491_SNP [dm3] 3L_19384391_SNP [dm6]	C	T	1.866e^-5	0.413	INTRON CG32206
3R	10035790	3R_10035790_SNP [dm3] 3R_14210068_SNP [dm6]	A	C	1.882e^-5	0.413	INTRON Dop1R1
3L	14481725	3L_14481725_SNP [dm3] 3L_14488625_SNP [dm6]	A	T	1.903e^-5	0.413	INTRON bbg	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
3R	9975155	3R_9975155_SNP [dm3] 3R_14149433_SNP [dm6]	A	T	1.915e^-5	0.413	SYNONYMOUS_CODING CG14355
3R	9974141	3R_9974141_SNP [dm3] 3R_14148419_SNP [dm6]	A	G	1.916e^-5	0.413	DOWNSTREAM CG14355 INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3R	4957594	3R_4957594_SNP [dm3] 3R_9131872_SNP [dm6]	A	G	2.005e^-5	0.422	INTRON pum	TF binding site mE1_TFBS_cad
2R	5715478	2R_5715478_SNP [dm3] 2R_9827973_SNP [dm6]	A	G	2.034e^-5	0.422	UPSTREAM dila DOWNSTREAM hebe INTERGENIC
3R	4958915	3R_4958915_SNP [dm3] 3R_9133193_SNP [dm6]	A	T	2.068e^-5	0.422	INTRON pum
3R	13429439	3R_13429439_SNP [dm3] 3R_17603717_SNP [dm6]	T	A	2.073e^-5	0.422	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	8131537	3R_8131537_SNP [dm3] 3R_12305815_SNP [dm6]	T	C	2.091e^-5	0.422	INTERGENIC
2L	3006337	2L_3006337_SNP [dm3] 2L_3006337_SNP [dm6]	G	A	2.113e^-5	0.422	INTRON CG17265	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	9975641	3R_9975641_SNP [dm3] 3R_14149919_SNP [dm6]	G	C	2.134e^-5	0.422	SYNONYMOUS_CODING CG14355
2L	2929884	2L_2929884_SNP [dm3] 2L_2929884_SNP [dm6]	T	C	2.135e^-5	0.422	INTRON lilli
3L	19155897	3L_19155897_SNP [dm3] 3L_19162797_SNP [dm6]	A	T	2.220e^-5	0.434	INTRON fz2	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_HSA mE1_TFBS_Trl
3R	10035925	3R_10035925_SNP [dm3] 3R_14210203_SNP [dm6]	C	T	2.299e^-5	0.435	INTRON Dop1R1
2L	2928746	2L_2928746_SNP [dm3] 2L_2928746_SNP [dm6]	A	T	2.309e^-5	0.435	INTRON lilli
3L	19543679	3L_19543679_SNP [dm3] 3L_19550579_SNP [dm6]	C	T	2.313e^-5	0.435	SYNONYMOUS_CODING l_3_76BDr	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	12596387	2L_12596387_SNP [dm3] 2L_12596387_SNP [dm6]	T	A	2.317e^-5	0.435	INTRON nub

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Missing results

By genomic position
Variant impact
Gene name

Cuticul_8_12_C28_2 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results