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=1.343e^-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	0.03456

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_3R_K	6.6371	0.0362

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1724 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	11017597	3L_11017597_SNP [dm3] 3L_11024497_SNP [dm6]	T	C	7.232e^-10	0.001	NON_SYNONYMOUS_CODING Fad2
3L	11016619	3L_11016619_SNP [dm3] 3L_11023519_SNP [dm6]	T	A	1.822e^-8	0.017	UPSTREAM Fad2 INTERGENIC	TF binding site BDTNP1_TFBS_twi
X	15262429	X_15262429_SNP [dm3] X_15368396_SNP [dm6]	C	A	7.554e^-7	0.334	INTRON acj6
3L	11016871	3L_11016871_SNP [dm3] 3L_11023771_SNP [dm6]	C	T	8.385e^-7	0.334	NON_SYNONYMOUS_CODING Fad2	TF binding site BDTNP1_TFBS_twi mE1_TFBS_sens
3L	11004879	3L_11004879_SNP [dm3] 3L_11011779_SNP [dm6]	A	G	1.055e^-6	0.334	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_inv
3L	4134805	3L_4134805_SNP [dm3] 3L_4134805_SNP [dm6]	A	T	1.069e^-6	0.334	UPSTREAM ens DOWNSTREAM RfC4 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_jumu mE1_TFBS_sens mE1_TFBS_Trl
3L	11020960	3L_11020960_SNP [dm3] 3L_11027860_SNP [dm6]	G	A	2.439e^-6	0.653	NON_SYNONYMOUS_CODING CG32081 DOWNSTREAM CG32079
2L	5410137	2L_5410137_SNP [dm3] 2L_5410137_SNP [dm6]	T	C	3.443e^-6	0.75	INTRON H15	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	16903274	3L_16903274_SNP [dm3] 3L_16910174_SNP [dm6]	C	A	3.598e^-6	0.75	INTRON Lmpt
X	8530718	X_8530718_SNP [dm3] X_8636685_SNP [dm6]	C	A	4.083e^-6	0.766	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	10599209	3R_10599209_SNP [dm3] 3R_14773487_SNP [dm6]	T	G	5.861e^-6	0.999	INTRON jvl	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	3473916	3L_3473916_SNP [dm3] 3L_3473916_SNP [dm6]	T	C	8.405e^-6	1	INTRON CG42324
3R	20255768	3R_20255768_SNP [dm3] 3R_24430046_SNP [dm6]	C	G	1.153e^-5	1	INTRON nAChRalpha1
3L	4135617	3L_4135617_SNP [dm3] 3L_4135617_SNP [dm6]	C	T	1.153e^-5	1	SYNONYMOUS_CODING RfC4 DOWNSTREAM Rop	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_ttk
3R	12951187	3R_12951187_SNP [dm3] 3R_17125465_SNP [dm6]	G	C	1.190e^-5	1	UPSTREAM cher DOWNSTREAM CG45079 & 1 other INTERGENIC
3L	18217503	3L_18217503_SNP [dm3] 3L_18224403_SNP [dm6]	C	T	1.380e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens
2L	17441436	2L_17441436_SNP [dm3] 2L_17441436_SNP [dm6]	T	C	1.434e^-5	1	SYNONYMOUS_CODING dl INTRON dl	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	3785713	3L_3785713_SNP [dm3] 3L_3785713_SNP [dm6]	T	A	1.437e^-5	1	INTRON CG32264	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Ubx
2L	17567159	2L_17567159_SNP [dm3] 2L_17567159_SNP [dm6]	G	A	1.470e^-5	1	DOWNSTREAM mir-124 INTERGENIC
2L	15378351	2L_15378351_SNP [dm3] 2L_15378351_SNP [dm6]	C	T	1.535e^-5	1	INTERGENIC
3L	4133100	3L_4133100_SNP [dm3] 3L_4133100_SNP [dm6]	A	T	1.649e^-5	1	INTRON ens	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi
3L	11527986	3L_11527986_SNP [dm3] 3L_11534886_SNP [dm6]	C	T	1.739e^-5	1	UPSTREAM Mob2 INTRON Mob2	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
3L	5159041	3L_5159041_SNP [dm3] 3L_5165941_SNP [dm6]	T	C	1.784e^-5	1	INTRON shep
2R	13834707	2R_13834707_DEL [dm3] 2R_17947202_DEL [dm6]	GG	G	1.792e^-5	1	INTERGENIC
3R	22073468	3R_22073468_SNP [dm3] 3R_26247746_SNP [dm6]	T	C	1.802e^-5	1	INTRON CR42745	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad
3L	11018550	3L_11018550_INS [dm3] 3L_11025450_INS [dm6]	G	GCT	1.819e^-5	1	UPSTREAM CG32079 DOWNSTREAM Fad2 INTERGENIC
3L	3525165	3L_3525165_SNP [dm3] 3L_3525165_SNP [dm6]	G	T	1.820e^-5	1	INTRON Eip63E
3L	11015542	3L_11015542_SNP [dm3] 3L_11022442_SNP [dm6]	A	C	1.957e^-5	1	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	4133158	3L_4133158_SNP [dm3] 3L_4133158_SNP [dm6]	T	A	2.051e^-5	1	INTRON ens	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi
3L	14012858	3L_14012858_SNP [dm3] 3L_14019758_SNP [dm6]	T	A	2.082e^-5	1	UTR_3_PRIME upSET DOWNSTREAM ptip	TF binding site mE1_TFBS_kn
3R	26700986	3R_26700986_SNP [dm3] 3R_30875264_SNP [dm6]	A	G	2.232e^-5	1	NON_SYNONYMOUS_CODING CG15546	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	763551	3R_763551_SNP [dm3] 3R_4937829_SNP [dm6]	C	T	2.249e^-5	1	SYNONYMOUS_CODING Cdep INTRON Cdep	TF binding site mE1_TFBS_cad mE1_TFBS_sens
3R	10599213	3R_10599213_SNP [dm3] 3R_14773491_SNP [dm6]	T	G	2.335e^-5	1	INTRON jvl	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	13600615	3L_13600615_SNP [dm3] 3L_13607515_SNP [dm6]	T	C	2.467e^-5	1	INTRON bru-3
2L	19060630	2L_19060630_SNP [dm3] 2L_19060630_SNP [dm6]	G	A	2.539e^-5	1	SYNONYMOUS_CODING Phlpp
3R	27273730	3R_27273730_SNP [dm3] 3R_31448008_SNP [dm6]	C	T	2.635e^-5	1	INTRON Gprk2
3L	14701513	3L_14701513_SNP [dm3] 3L_14708413_SNP [dm6]	G	A	2.685e^-5	1	INTRON ome	TF binding site mE1_TFBS_inv
3R	26699273	3R_26699273_SNP [dm3] 3R_30873551_SNP [dm6]	T	C	2.693e^-5	1	DOWNSTREAM CG15546 INTERGENIC
3L	6311594	3L_6311594_SNP [dm3] 3L_6318494_SNP [dm6]	A	G	2.747e^-5	1	INTERGENIC	regulatory region REDfly_CRMs
3R	10599198	3R_10599198_SNP [dm3] 3R_14773476_SNP [dm6]	A	T	2.748e^-5	1	INTRON jvl	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	5714099	2R_5714099_SNP [dm3] 2R_9826594_SNP [dm6]	A	C	2.758e^-5	1	NON_SYNONYMOUS_CODING dila	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
X	11005612	X_11005612_SNP [dm3] X_11111579_SNP [dm6]	T	C	2.766e^-5	1	SYNONYMOUS_CODING Hsp60 DOWNSTREAM CG11122	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	10599194	3R_10599194_SNP [dm3] 3R_14773472_SNP [dm6]	C	A	2.963e^-5	1	INTRON jvl	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	12372621	3L_12372621_SNP [dm3] 3L_12379521_SNP [dm6]	A	T	3.050e^-5	1	UTR_5_PRIME Ncc69	TF binding site BDTNP1_TFBS_twi
2R	8148163	2R_8148163_SNP [dm3] 2R_12260658_SNP [dm6]	G	A	3.181e^-5	1	INTRON Cam EXON CR43900	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_Trl
3R	20255911	3R_20255911_SNP [dm3] 3R_24430189_SNP [dm6]	T	G	3.207e^-5	1	INTRON nAChRalpha1
3L	11019915	3L_11019915_SNP [dm3] 3L_11026815_SNP [dm6]	A	G	3.221e^-5	1	NON_SYNONYMOUS_CODING CG32079 UPSTREAM CG32081
2L	2368987	2L_2368987_SNP [dm3] 2L_2368987_SNP [dm6]	A	C	3.312e^-5	1	UTR_3_PRIME Axud1	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	17145961	3L_17145961_SNP [dm3] 3L_17152861_SNP [dm6]	C	T	3.419e^-5	1	INTRON Rbp6
2R	14269072	2R_14269072_SNP [dm3] 2R_18381567_SNP [dm6]	C	T	3.497e^-5	1	SYNONYMOUS_CODING CG43202	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	2362706	3L_2362706_SNP [dm3] 3L_2362706_SNP [dm6]	G	A	3.612e^-5	1	DOWNSTREAM CG13801 INTERGENIC
3L	16998745	3L_16998745_SNP [dm3] 3L_17005645_SNP [dm6]	A	G	3.625e^-5	1	INTRON CG3764
2R	7067517	2R_7067517_SNP [dm3] 2R_11180012_SNP [dm6]	G	A	3.691e^-5	1	INTRON shn
3R	22916337	3R_22916337_SNP [dm3] 3R_27090615_SNP [dm6]	T	G	3.710e^-5	1	INTRON Cpr97Eb
2L	2368984	2L_2368984_SNP [dm3] 2L_2368984_SNP [dm6]	T	C	3.730e^-5	1	UTR_3_PRIME Axud1	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	11015320	3L_11015320_INS [dm3] 3L_11022220_INS [dm6]	T	TT	3.772e^-5	1	INTERGENIC	TF binding site mE1_TFBS_cad
2L	10964824	2L_10964824_INS [dm3] 2L_10964824_INS [dm6]	G	GGCAA	3.890e^-5	1	UPSTREAM dpr2 DOWNSTREAM CG33129 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_z mE1_TFBS_bab1 mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_ttk
3L	18216196	3L_18216196_DEL [dm3] 3L_18223096_DEL [dm6]	TG	T	3.903e^-5	1	INTERGENIC
3R	765962	3R_765962_SNP [dm3] 3R_4940240_SNP [dm6]	A	C	4.009e^-5	1	DOWNSTREAM Cdep INTRON Cdep
3R	10599218	3R_10599218_SNP [dm3] 3R_14773496_SNP [dm6]	T	C	4.073e^-5	1	INTRON jvl	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	17159830	2L_17159830_SNP [dm3] 2L_17159830_SNP [dm6]	T	A	4.335e^-5	1	INTRON beat-IIIa & 1 other
3L	11004941	3L_11004941_SNP [dm3] 3L_11011841_SNP [dm6]	T	G	4.340e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_inv
3L	11055479	3L_11055479_SNP [dm3] 3L_11062379_SNP [dm6]	T	G	4.424e^-5	1	SYNONYMOUS_CODING CG32069 DOWNSTREAM CG32075 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_ttk mE1_TFBS_Ubx
2R	18540699	2R_18540699_SNP [dm3] 2R_22653194_SNP [dm6]	G	A	4.576e^-5	1	UTR_3_PRIME nsr DOWNSTREAM nsr INTRON Cyp6d2	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	13897245	3R_13897245_SNP [dm3] 3R_18071523_SNP [dm6]	T	A	4.604e^-5	1	INTERGENIC	TF binding site mE1_TFBS_cad
2R	16934511	2R_16934511_INS [dm3] 2R_21047006_INS [dm6]	C	CA	4.608e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3L	3784507	3L_3784507_SNP [dm3] 3L_3784507_SNP [dm6]	A	C	4.776e^-5	1	INTRON CG32264	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad
X	13868221	X_13868221_SNP [dm3] X_13974188_SNP [dm6]	C	T	4.785e^-5	1	INTRON mamo
3L	2362702	3L_2362702_SNP [dm3] 3L_2362702_SNP [dm6]	T	G	4.856e^-5	1	DOWNSTREAM CG13801 INTERGENIC
2L	10703202	2L_10703202_SNP [dm3] 2L_10703202_SNP [dm6]	C	T	4.901e^-5	1	UPSTREAM CG6415 INTRON Lip2	TF binding site BDTNP1_TFBS_dl
3R	10599189	3R_10599189_SNP [dm3] 3R_14773467_SNP [dm6]	G	A	4.917e^-5	1	INTRON jvl	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	8334648	2R_8334648_SNP [dm3] 2R_12447143_SNP [dm6]	G	A	4.944e^-5	1	INTRON Dyb
3L	4133239	3L_4133239_SNP [dm3] 3L_4133239_SNP [dm6]	G	C	4.948e^-5	1	INTRON ens	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
X	21353347	X_21353347_SNP [dm3] X_21482320_SNP [dm6]	T	A	4.953e^-5	1	DOWNSTREAM CR45511 INTERGENIC
X	21353349	X_21353349_SNP [dm3] X_21482322_SNP [dm6]	C	T	4.953e^-5	1	DOWNSTREAM CR45511 INTERGENIC
3L	14376821	3L_14376821_SNP [dm3] 3L_14383721_SNP [dm6]	A	G	4.954e^-5	1	DOWNSTREAM CG43120 INTERGENIC
X	4839089	X_4839089_SNP [dm3] X_4945056_SNP [dm6]	A	G	4.993e^-5	1	INTRON Ptp4E
2L	10703207	2L_10703207_SNP [dm3] 2L_10703207_SNP [dm6]	T	A	5.089e^-5	1	UPSTREAM CG6415 INTRON Lip2	TF binding site BDTNP1_TFBS_dl
3L	4132916	3L_4132916_SNP [dm3] 3L_4132916_SNP [dm6]	A	T	5.094e^-5	1	INTRON ens
2R	15271284	2R_15271284_SNP [dm3] 2R_19383779_SNP [dm6]	T	C	5.127e^-5	1	SYNONYMOUS_CODING CG10073
3L	4133373	3L_4133373_SNP [dm3] 3L_4133373_SNP [dm6]	G	T	5.240e^-5	1	INTRON ens	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
3R	25440367	3R_25440367_DEL [dm3] 3R_29614645_DEL [dm6]	CG	C	5.244e^-5	1	INTRON alph
2R	3475163	2R_3475163_SNP [dm3] 2R_7587658_SNP [dm6]	C	T	5.247e^-5	1	UPSTREAM blow DOWNSTREAM CG1360 INTERGENIC	TF binding site mE1_TFBS_Trl
2R	17583811	2R_17583811_SNP [dm3] 2R_21696306_SNP [dm6]	T	C	5.369e^-5	1	UPSTREAM CngB INTRON CngB	TF binding site mE1_TFBS_cad
2R	17583833	2R_17583833_SNP [dm3] 2R_21696328_SNP [dm6]	G	A	5.369e^-5	1	UPSTREAM CngB INTRON CngB	TF binding site mE1_TFBS_cad
2R	17761005	2R_17761005_DEL [dm3] 2R_21873500_DEL [dm6]	ACCTC	T	5.414e^-5	1	INTRON Fili
3R	12327399	3R_12327399_SNP [dm3] 3R_16501677_SNP [dm6]	C	A	5.430e^-5	1	UPSTREAM decay INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_jumu mE1_TFBS_Trl
3L	3789043	3L_3789043_SNP [dm3] 3L_3789043_SNP [dm6]	T	C	5.768e^-5	1	INTRON CG32264	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_cad
3L	3789288	3L_3789288_SNP [dm3] 3L_3789288_SNP [dm6]	A	C	5.854e^-5	1	INTRON CG32264	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_cad
3L	6311605	3L_6311605_SNP [dm3] 3L_6318505_SNP [dm6]	G	A	5.857e^-5	1	INTERGENIC	regulatory region REDfly_CRMs
3L	14702295	3L_14702295_SNP [dm3] 3L_14709195_SNP [dm6]	T	C	5.885e^-5	1	INTRON ome
2R	14894192	2R_14894192_SNP [dm3] 2R_19006687_SNP [dm6]	T	G	5.949e^-5	1	INTRON tn	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3L	11018459	3L_11018459_SNP [dm3] 3L_11025359_SNP [dm6]	T	A	5.981e^-5	1	UPSTREAM CG32079 DOWNSTREAM Fad2 INTERGENIC
2L	4671984	2L_4671984_SNP [dm3] 2L_4671984_SNP [dm6]	T	C	6.039e^-5	1	INTERGENIC
3L	7585045	3L_7585045_SNP [dm3] 3L_7591945_SNP [dm6]	C	T	6.082e^-5	1	UPSTREAM CG7716 INTERGENIC
2R	15464290	2R_15464290_SNP [dm3] 2R_19576785_SNP [dm6]	G	A	6.104e^-5	1	INTRON sm
2L	10703180	2L_10703180_SNP [dm3] 2L_10703180_SNP [dm6]	T	A	6.185e^-5	1	UPSTREAM CG6415 INTRON Lip2	TF binding site BDTNP1_TFBS_dl
2R	10637411	2R_10637411_SNP [dm3] 2R_14749906_SNP [dm6]	G	A	6.200e^-5	1	SYNONYMOUS_CODING AttB DOWNSTREAM Rpn6
3L	11017325	3L_11017325_SNP [dm3] 3L_11024225_SNP [dm6]	C	G	6.206e^-5	1	SYNONYMOUS_CODING Fad2	TF binding site BDTNP1_TFBS_twi mE1_TFBS_sens
2L	2357469	2L_2357469_SNP [dm3] 2L_2357469_SNP [dm6]	C	A	6.247e^-5	1	UPSTREAM CG9967 INTRON eys

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Missing results

By genomic position
Variant impact
Gene name

Cuticul_9_13_C27_2 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results