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=5.163e^-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_Mo	0.09434

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_3R_Mo	4.6339	0.0986

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2242 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
2R	4225845	2R_4225845_SNP [dm3] 2R_8338340_SNP [dm6]	G	C	1.943e^-6	0.733	INTRON pdm3
3L	506052	3L_506052_SNP [dm3] 3L_506052_SNP [dm6]	A	G	3.550e^-6	0.733	SPLICE_SITE_REGION klar INTRON klar	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_jumu mE1_TFBS_kn mE1_TFBS_ttk mE1_TFBS_zfh1
2L	16810806	2L_16810806_SNP [dm3] 2L_16810806_SNP [dm6]	C	T	3.643e^-6	0.733	INTRON CG13280 & 1 other
X	20707576	X_20707576_SNP [dm3] X_20836549_SNP [dm6]	T	G	4.046e^-6	0.733	INTRON shakB
2R	7617805	2R_7617805_DEL [dm3] 2R_11730300_DEL [dm6]	CCCCTACCTATC...	TTTATTA	4.660e^-6	0.733	INTERGENIC
3L	3446266	3L_3446266_SNP [dm3] 3L_3446266_SNP [dm6]	C	T	5.176e^-6	0.733	INTRON eIF5B
2L	2455526	2L_2455526_SNP [dm3] 2L_2455526_SNP [dm6]	C	T	5.826e^-6	0.733	SYNONYMOUS_CODING dpp	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3R	6418761	3R_6418761_SNP [dm3] 3R_10593039_SNP [dm6]	G	T	5.857e^-6	0.733	INTRON hth	TF binding site mE1_TFBS_cad
3L	506082	3L_506082_SNP [dm3] 3L_506082_SNP [dm6]	T	G	6.133e^-6	0.733	INTRON klar	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_jumu mE1_TFBS_kn mE1_TFBS_ttk mE1_TFBS_zfh1
3L	506064	3L_506064_SNP [dm3] 3L_506064_SNP [dm6]	G	A	6.268e^-6	0.733	INTRON klar	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_jumu mE1_TFBS_kn mE1_TFBS_ttk mE1_TFBS_zfh1
3R	14889966	3R_14889966_SNP [dm3] 3R_19064244_SNP [dm6]	C	T	6.479e^-6	0.733	INTRON cdi	TF binding site BDTNP1_TFBS_twi
3L	15002978	3L_15002978_SNP [dm3] 3L_15009878_SNP [dm6]	T	G	6.639e^-6	0.733	INTRON Reck
3R	17557665	3R_17557665_SNP [dm3] 3R_21731943_SNP [dm6]	C	A	7.286e^-6	0.733	INTERGENIC
X	20707550	X_20707550_SNP [dm3] X_20836523_SNP [dm6]	T	C	7.495e^-6	0.733	INTRON shakB
2R	19890320	2R_19890320_SNP [dm3] 2R_24002797_SNP [dm6]	G	C	7.799e^-6	0.733	SYNONYMOUS_CODING Unc-89	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	4660158	3L_4660158_SNP [dm3] 3L_4660158_SNP [dm6]	C	A	7.903e^-6	0.733	SYNONYMOUS_CODING axo
X	15357177	X_15357177_SNP [dm3] X_15463144_SNP [dm6]	G	A	8.407e^-6	0.733	NON_SYNONYMOUS_CODING CG6294 UTR_5_PRIME CG6299 UPSTREAM shtd	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_Mad BDTNP1_TFBS_sna mE1_TFBS_chinmo mE1_TFBS_HSA
3R	22305982	3R_22305982_SNP [dm3] 3R_26480260_SNP [dm6]	A	G	8.468e^-6	0.733	INTRON plum
2R	16649085	2R_16649085_SNP [dm3] 2R_20761580_SNP [dm6]	A	G	9.092e^-6	0.733	INTERGENIC	TF binding site mE1_TFBS_eve mE1_TFBS_HSA
3R	17557672	3R_17557672_SNP [dm3] 3R_21731950_SNP [dm6]	A	T	9.319e^-6	0.733	INTERGENIC
3R	17557656	3R_17557656_SNP [dm3] 3R_21731934_SNP [dm6]	C	T	9.718e^-6	0.733	INTERGENIC
3L	15002874	3L_15002874_SNP [dm3] 3L_15009774_SNP [dm6]	A	G	1.127e^-5	0.733	INTRON Reck
2R	13852021	2R_13852021_SNP [dm3] 2R_17964516_SNP [dm6]	A	G	1.128e^-5	0.733	INTERGENIC
3R	22305848	3R_22305848_SNP [dm3] 3R_26480126_SNP [dm6]	T	C	1.128e^-5	0.733	INTRON plum
3L	17249403	3L_17249403_INS [dm3] 3L_17256303_INS [dm6]	T	TT	1.153e^-5	0.733	INTRON CR43870
3L	18274222	3L_18274222_DEL [dm3] 3L_18281122_DEL [dm6]	ACGATCT	A	1.155e^-5	0.733	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
3L	11802950	3L_11802950_SNP [dm3] 3L_11809850_SNP [dm6]	A	G	1.196e^-5	0.733	SYNONYMOUS_CODING CG42255	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3L	3446253	3L_3446253_SNP [dm3] 3L_3446253_SNP [dm6]	G	C	1.248e^-5	0.733	INTRON eIF5B
2R	16254800	2R_16254800_SNP [dm3] 2R_20367295_SNP [dm6]	G	A	1.269e^-5	0.733	INTERGENIC
3L	3446277	3L_3446277_SNP [dm3] 3L_3446277_SNP [dm6]	A	T	1.272e^-5	0.733	INTRON eIF5B
2R	19876961	2R_19876961_SNP [dm3] 2R_23989438_SNP [dm6]	C	T	1.276e^-5	0.733	SYNONYMOUS_CODING Pask UPSTREAM Phm	TF binding site mE1_TFBS_sens
X	13478687	X_13478687_SNP [dm3] X_13584654_SNP [dm6]	G	C	1.276e^-5	0.733	INTRON Tango13
3R	19655061	3R_19655061_SNP [dm3] 3R_23829339_SNP [dm6]	T	A	1.315e^-5	0.733	INTRON CG34355
X	5545351	X_5545351_SNP [dm3] X_5651318_SNP [dm6]	T	G	1.356e^-5	0.733	UTR_3_PRIME CG42265
2L	16810787	2L_16810787_SNP [dm3] 2L_16810787_SNP [dm6]	G	T	1.391e^-5	0.733	INTRON CG13280 & 1 other
3R	22751911	3R_22751911_SNP [dm3] 3R_26926189_SNP [dm6]	C	T	1.408e^-5	0.733	INTRON sda
X	20707599	X_20707599_SNP [dm3] X_20836572_SNP [dm6]	T	C	1.550e^-5	0.779	INTRON shakB
3R	9018365	3R_9018365_SNP [dm3] 3R_13192643_SNP [dm6]	A	G	1.634e^-5	0.779	DOWNSTREAM CG8141 INTERGENIC
3R	17521224	3R_17521224_SNP [dm3] 3R_21695502_SNP [dm6]	T	A	1.662e^-5	0.779	INTRON CG31176
3L	5858021	3L_5858021_SNP [dm3] 3L_5864921_SNP [dm6]	C	T	1.664e^-5	0.779	INTERGENIC	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3L	7468654	3L_7468654_SNP [dm3] 3L_7475554_SNP [dm6]	G	T	1.703e^-5	0.779	UPSTREAM CG43292 INTERGENIC
X	13956412	X_13956412_SNP [dm3] X_14062379_SNP [dm6]	T	A	1.778e^-5	0.783	UPSTREAM Ste:CG33236 INTERGENIC
2R	18716599	2R_18716599_INS [dm3] 2R_22829076_INS [dm6]	G	GCTTG	1.804e^-5	0.783	UPSTREAM CG30272 DOWNSTREAM CG30274 & 1 other INTERGENIC
3R	17557655	3R_17557655_SNP [dm3] 3R_21731933_SNP [dm6]	A	G	1.875e^-5	0.783	INTERGENIC
2L	11070741	2L_11070741_SNP [dm3] 2L_11070741_SNP [dm6]	G	A	1.902e^-5	0.783	UPSTREAM CG14915 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad
2R	18712995	2R_18712995_SNP [dm3] 2R_22825472_SNP [dm6]	C	A	1.991e^-5	0.783	INTRON CG42284 & 1 other
2R	19890547	2R_19890547_SNP [dm3] 2R_24003024_SNP [dm6]	T	A	2.005e^-5	0.783	INTRON Unc-89	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2R	19890623	2R_19890623_SNP [dm3] 2R_24003100_SNP [dm6]	C	A	2.005e^-5	0.783	SYNONYMOUS_CODING Unc-89	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	19655060	3R_19655060_SNP [dm3] 3R_23829338_SNP [dm6]	A	G	2.082e^-5	0.797	INTRON CG34355
3L	13890646	3L_13890646_SNP [dm3] 3L_13897546_SNP [dm6]	A	T	2.374e^-5	0.831	INTRON dysc
2R	14136737	2R_14136737_SNP [dm3] 2R_18249232_SNP [dm6]	C	A	2.435e^-5	0.831	INTERGENIC	TF binding site mE1_TFBS_chinmo mE1_TFBS_inv
3L	5331534	3L_5331534_SNP [dm3] 3L_5338434_SNP [dm6]	G	A	2.474e^-5	0.831	INTERGENIC
2R	11286523	2R_11286523_SNP [dm3] 2R_15399018_SNP [dm6]	A	C	2.536e^-5	0.831	INTERGENIC
2L	2341641	2L_2341641_SNP [dm3] 2L_2341641_SNP [dm6]	T	A	2.569e^-5	0.831	INTRON CG9967 & 1 other
2L	16941270	2L_16941270_SNP [dm3] 2L_16941270_SNP [dm6]	C	A	2.681e^-5	0.831	INTERGENIC
3L	15002979	3L_15002979_DEL [dm3] 3L_15009879_DEL [dm6]	ATTCAGT	A	2.695e^-5	0.831	INTRON Reck
2L	19526516	2L_19526516_SNP [dm3] 2L_19526516_SNP [dm6]	C	A	2.733e^-5	0.831	UPSTREAM CG10137 & 1 other DOWNSTREAM CG10165 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_Ubx
X	46269	X_46269_SNP [dm3] X_149882_SNP [dm6]	G	A	2.844e^-5	0.831	INTRON tyn
3R	19655066	3R_19655066_SNP [dm3] 3R_23829344_SNP [dm6]	T	G	2.936e^-5	0.831	INTRON CG34355
2L	2341647	2L_2341647_SNP [dm3] 2L_2341647_SNP [dm6]	T	C	2.937e^-5	0.831	INTRON CG9967 & 1 other
2L	3153569	2L_3153569_SNP [dm3] 2L_3153569_SNP [dm6]	A	G	3.165e^-5	0.831	UPSTREAM Mad INTRON Mad
X	10855548	X_10855548_SNP [dm3] X_10961515_SNP [dm6]	C	T	3.247e^-5	0.831	INTRON Myo10A
2R	16254819	2R_16254819_SNP [dm3] 2R_20367314_SNP [dm6]	A	C	3.330e^-5	0.831	INTERGENIC
3R	9018366	3R_9018366_SNP [dm3] 3R_13192644_SNP [dm6]	A	C	3.334e^-5	0.831	DOWNSTREAM CG8141 INTERGENIC
3R	17195296	3R_17195296_SNP [dm3] 3R_21369574_SNP [dm6]	T	C	3.337e^-5	0.831	SYNONYMOUS_CODING pre-mod_mdg4_-U DOWNSTREAM mod_mdg4_ & 2 others INTRON mod_mdg4_
2R	7102822	2R_7102822_SNP [dm3] 2R_11215317_SNP [dm6]	C	G	3.378e^-5	0.831	SYNONYMOUS_CODING shn	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3L	3270631	3L_3270631_SNP [dm3] 3L_3270631_SNP [dm6]	G	A	3.415e^-5	0.831	UPSTREAM CG14960 INTERGENIC
3R	20226832	3R_20226832_SNP [dm3] 3R_24401110_SNP [dm6]	C	T	3.461e^-5	0.831	UTR_3_PRIME nAChRalpha1
3R	5367593	3R_5367593_SNP [dm3] 3R_9541871_SNP [dm6]	C	T	3.461e^-5	0.831	NON_SYNONYMOUS_CODING mura
2L	9722503	2L_9722503_SNP [dm3] 2L_9722503_SNP [dm6]	C	T	3.466e^-5	0.831	INTRON Nckx30C	TF binding site mE1_TFBS_sens
3L	15001599	3L_15001599_SNP [dm3] 3L_15008499_SNP [dm6]	T	C	3.471e^-5	0.831	INTRON Reck	TF binding site BDTNP1_TFBS_twi
3L	6879674	3L_6879674_SNP [dm3] 3L_6886574_SNP [dm6]	A	T	3.473e^-5	0.831	INTERGENIC
X	13478742	X_13478742_SNP [dm3] X_13584709_SNP [dm6]	G	T	3.492e^-5	0.831	INTRON Tango13
2L	6513173	2L_6513173_SNP [dm3] 2L_6513173_SNP [dm6]	A	G	3.509e^-5	0.831	INTRON CG31637	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi
3L	15015059	3L_15015059_SNP [dm3] 3L_15021959_SNP [dm6]	G	A	3.543e^-5	0.831	INTRON Sytbeta	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_prd BDTNP1_TFBS_twi
2R	9387307	2R_9387307_SNP [dm3] 2R_13499802_SNP [dm6]	C	A	3.573e^-5	0.831	UPSTREAM mars INTRON drk	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	4583132	2L_4583132_SNP [dm3] 2L_4583132_SNP [dm6]	C	T	3.638e^-5	0.831	UPSTREAM CR43716 INTRON dp
3R	17462967	3R_17462967_SNP [dm3] 3R_21637245_SNP [dm6]	C	T	3.731e^-5	0.831	INTRON E2f	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
X	10956562	X_10956562_SNP [dm3] X_11062529_SNP [dm6]	T	G	3.778e^-5	0.831	INTRON CG1537
3R	18304913	3R_18304913_SNP [dm3] 3R_22479191_SNP [dm6]	T	C	3.839e^-5	0.831	SYNONYMOUS_CODING Nrx-1	TF binding site mE1_TFBS_chinmo
X	15357163	X_15357163_SNP [dm3] X_15463130_SNP [dm6]	A	T	3.942e^-5	0.831	SYNONYMOUS_CODING CG6294 UTR_5_PRIME CG6299 UPSTREAM shtd	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_Mad BDTNP1_TFBS_sna mE1_TFBS_chinmo mE1_TFBS_HSA
X	53148	X_53148_SNP [dm3] X_156761_SNP [dm6]	A	T	4.014e^-5	0.831	INTRON tyn
X	20707620	X_20707620_SNP [dm3] X_20836593_SNP [dm6]	G	A	4.073e^-5	0.831	INTRON shakB
3R	18657407	3R_18657407_SNP [dm3] 3R_22831685_SNP [dm6]	T	A	4.142e^-5	0.831	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2R	4300358	2R_4300358_SNP [dm3] 2R_8412853_SNP [dm6]	A	T	4.215e^-5	0.831	INTERGENIC
2L	4360305	2L_4360305_SNP [dm3] 2L_4360305_SNP [dm6]	T	C	4.303e^-5	0.831	INTERGENIC	regulatory region REDfly_CRMs TF binding site mE1_TFBS_sens
3R	6438883	3R_6438883_SNP [dm3] 3R_10613161_SNP [dm6]	A	G	4.325e^-5	0.831	UTR_5_PRIME hth	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
X	15420819	X_15420819_DEL [dm3] X_15526786_DEL [dm6]	AC	A	4.352e^-5	0.831	INTRON Ac13E
X	20707607	X_20707607_SNP [dm3] X_20836580_SNP [dm6]	A	T	4.384e^-5	0.831	INTRON shakB
3R	12359282	3R_12359282_SNP [dm3] 3R_16533560_SNP [dm6]	A	C	4.396e^-5	0.831	INTRON CG42342	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad mE1_TFBS_HSA
X	13956399	X_13956399_INS [dm3] X_14062366_INS [dm6]	C	CATTTGGCCGCCAACC...	4.574e^-5	0.831	UPSTREAM Ste:CG33236 INTERGENIC
2R	20119278	2R_20119278_SNP [dm3] 2R_24231755_SNP [dm6]	C	T	4.585e^-5	0.831	INTERGENIC
X	8355696	X_8355696_SNP [dm3] X_8461663_SNP [dm6]	A	C	4.614e^-5	0.831	SYNONYMOUS_CODING Es2 UPSTREAM CG15347
3R	25372754	3R_25372754_INS [dm3] 3R_29547032_INS [dm6]	A	AAATA	4.679e^-5	0.831	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_sens
3L	11028841	3L_11028841_SNP [dm3] 3L_11035741_SNP [dm6]	G	A	4.687e^-5	0.831	DOWNSTREAM CG43693 EXON CR44547	TF binding site mE1_TFBS_HSA
X	71569	X_71569_SNP [dm3] X_175182_SNP [dm6]	G	T	4.778e^-5	0.831	UPSTREAM tyn INTRON tyn	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	4178767	2R_4178767_SNP [dm3] 2R_8291262_SNP [dm6]	A	T	4.813e^-5	0.831	INTERGENIC
3R	9018353	3R_9018353_SNP [dm3] 3R_13192631_SNP [dm6]	A	G	4.959e^-5	0.831	DOWNSTREAM CG8141 INTERGENIC
2R	19890263	2R_19890263_SNP [dm3] 2R_24002740_SNP [dm6]	G	T	5.015e^-5	0.831	NON_SYNONYMOUS_CODING Unc-89	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2R	18714993	2R_18714993_SNP [dm3] 2R_22827470_SNP [dm6]	G	T	5.022e^-5	0.831	INTRON CG30274 & 1 other

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Missing results

By genomic position
Variant impact
Gene name

Branching_O2_5pc phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results