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=1.070e^-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_2L_t	0.03335
In_3R_P	0.04555
In_3R_K	4.581e-05

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	5.4138	0.0667
In_3R_K	15.7123	0.0004

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2148 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
3R	8220563	3R_8220563_SNP [dm3] 3R_12394841_SNP [dm6]	A	G	3.098e^-9	0.006	NON_SYNONYMOUS_CODING CG10097 UTR_5_PRIME CG10096 INTRON CG34402
3R	8221499	3R_8221499_SNP [dm3] 3R_12395777_SNP [dm6]	G	A	3.336e^-8	0.031	SYNONYMOUS_CODING CG10097 UTR_5_PRIME CG10096 DOWNSTREAM Cyp9f3Psi INTRON CG34402
3R	8220292	3R_8220292_SNP [dm3] 3R_12394570_SNP [dm6]	T	C	6.304e^-8	0.039	SYNONYMOUS_CODING CG10097 START_GAINED CG10096 UTR_5_PRIME CG10096 INTRON CG34402
2R	15172123	2R_15172123_SNP [dm3] 2R_19284618_SNP [dm6]	T	C	6.011e^-7	0.222	NON_SYNONYMOUS_CODING CG10476 UPSTREAM CG11906 DOWNSTREAM CG10474	TF binding site mE1_TFBS_HSA
3R	8235851	3R_8235851_SNP [dm3] 3R_12410129_SNP [dm6]	A	G	6.581e^-7	0.222	INTRON CG5196	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_HSA
3R	8235861	3R_8235861_SNP [dm3] 3R_12410139_SNP [dm6]	T	A	7.138e^-7	0.222	INTRON CG5196	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_HSA
3R	8165817	3R_8165817_SNP [dm3] 3R_12340095_SNP [dm6]	G	A	8.835e^-7	0.222	DOWNSTREAM CR44941 INTERGENIC
2L	15400980	2L_15400980_SNP [dm3] 2L_15400980_SNP [dm6]	A	G	9.463e^-7	0.222	UPSTREAM CR45374 INTERGENIC
2R	5031932	2R_5031932_SNP [dm3] 2R_9144427_SNP [dm6]	A	T	1.111e^-6	0.228	SYNONYMOUS_CODING Prp38 UPSTREAM shrb & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_sens mE1_TFBS_ttk
3R	8242073	3R_8242073_SNP [dm3] 3R_12416351_SNP [dm6]	C	A	1.263e^-6	0.228	SYNONYMOUS_CODING pps	TF binding site mE1_TFBS_chinmo mE1_TFBS_sens
3R	25079389	3R_25079389_SNP [dm3] 3R_29253667_SNP [dm6]	T	G	1.385e^-6	0.228	SYNONYMOUS_CODING stg	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3R	8214104	3R_8214104_SNP [dm3] 3R_12388382_SNP [dm6]	G	A	1.644e^-6	0.228	SYNONYMOUS_CODING CG33098 UTR_3_PRIME CG33098 UPSTREAM CG34402 INTRON CG34402	TF binding site mE1_TFBS_cad
3R	14503318	3R_14503318_SNP [dm3] 3R_18677596_SNP [dm6]	G	C	1.663e^-6	0.228	UPSTREAM CG7706 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cnc mE1_TFBS_HSA
2L	528292	2L_528292_SNP [dm3] 2L_528292_SNP [dm6]	C	G	1.700e^-6	0.228	INTRON ush	regulatory region REDfly_CRMs
X	8201781	X_8201781_SNP [dm3] X_8307748_SNP [dm6]	G	A	1.925e^-6	0.241	INTRON nAChRalpha3
3L	6546938	3L_6546938_SNP [dm3] 3L_6553838_SNP [dm6]	C	T	2.773e^-6	0.325	INTRON CG18769
3R	8235744	3R_8235744_SNP [dm3] 3R_12410022_SNP [dm6]	C	A	3.106e^-6	0.343	INTRON CG5196	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_HSA
2L	15400979	2L_15400979_SNP [dm3] 2L_15400979_SNP [dm6]	G	T	3.478e^-6	0.353	UPSTREAM CR45374 INTERGENIC
3R	25078873	3R_25078873_SNP [dm3] 3R_29253151_SNP [dm6]	C	T	3.575e^-6	0.353	SYNONYMOUS_CODING stg	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Mad BDTNP1_TFBS_sna mE1_TFBS_HSA mE1_TFBS_sens
3R	8235953	3R_8235953_SNP [dm3] 3R_12410231_SNP [dm6]	A	G	3.826e^-6	0.359	INTRON CG5196	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad mE1_TFBS_HSA
2L	528267	2L_528267_SNP [dm3] 2L_528267_SNP [dm6]	T	A	4.026e^-6	0.36	INTRON ush	regulatory region REDfly_CRMs
2R	5022135	2R_5022135_SNP [dm3] 2R_9134630_SNP [dm6]	C	T	4.570e^-6	0.39	SYNONYMOUS_CODING Hydr1 DOWNSTREAM alc	TF binding site BDTNP1_TFBS_prd BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3R	8236552	3R_8236552_SNP [dm3] 3R_12410830_SNP [dm6]	T	C	4.821e^-6	0.393	SYNONYMOUS_CODING CG5196 DOWNSTREAM Dip-C	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	8235993	3R_8235993_SNP [dm3] 3R_12410271_SNP [dm6]	T	G	5.730e^-6	0.428	SPLICE_SITE_REGION CG5196 INTRON CG5196	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad mE1_TFBS_HSA
2L	8372130	2L_8372130_SNP [dm3] 2L_8372130_SNP [dm6]	C	T	6.145e^-6	0.428	UPSTREAM CG17292 INTRON CG17292
3R	8221792	3R_8221792_SNP [dm3] 3R_12396070_SNP [dm6]	T	G	6.250e^-6	0.428	UPSTREAM CG10096 & 1 other INTRON CG34402 EXON Cyp9f3Psi
2R	5028335	2R_5028335_SNP [dm3] 2R_9140830_SNP [dm6]	G	A	6.275e^-6	0.428	UTR_5_PRIME CG44286 UPSTREAM CG44286 INTRON CG8788 & 1 other
2L	13886448	2L_13886448_SNP [dm3] 2L_13886448_SNP [dm6]	A	G	6.385e^-6	0.428	INTRON CenG1A	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_Kr
3R	8234140	3R_8234140_SNP [dm3] 3R_12408418_SNP [dm6]	C	G	6.755e^-6	0.437	NON_SYNONYMOUS_CODING CG5196 UPSTREAM CG5196 DOWNSTREAM CG5167	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 mE1_TFBS_cad
3R	8234276	3R_8234276_SNP [dm3] 3R_12408554_SNP [dm6]	C	G	7.718e^-6	0.462	UPSTREAM CG5196 DOWNSTREAM CG5167 INTRON CG5196	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 mE1_TFBS_cad
3L	6546745	3L_6546745_SNP [dm3] 3L_6553645_SNP [dm6]	T	C	7.736e^-6	0.462	INTRON CG18769
2L	19251673	2L_19251673_SNP [dm3] 2L_19251673_SNP [dm6]	A	T	8.126e^-6	0.462	INTERGENIC
2R	5976584	2R_5976584_DEL [dm3] 2R_10089079_DEL [dm6]	CACA	C	8.431e^-6	0.462	INTRON CG2269
2L	8371979	2L_8371979_SNP [dm3] 2L_8371979_SNP [dm6]	A	G	8.742e^-6	0.462	UPSTREAM CG17292 INTRON CG17292
2R	19244649	2R_19244649_SNP [dm3] 2R_23357126_SNP [dm6]	G	T	8.938e^-6	0.462	SYNONYMOUS_CODING CG3500 UPSTREAM CG9875 DOWNSTREAM Rpi	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	8137315	2R_8137315_SNP [dm3] 2R_12249810_SNP [dm6]	G	A	9.324e^-6	0.462	INTERGENIC
3R	17214297	3R_17214297_SNP [dm3] 3R_21388575_SNP [dm6]	G	T	9.331e^-6	0.462	UPSTREAM bap INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_Trl
X	13606673	X_13606673_SNP [dm3] X_13712640_SNP [dm6]	G	T	9.367e^-6	0.462	SYNONYMOUS_CODING NnaD INTRON CG9940
2R	5024966	2R_5024966_SNP [dm3] 2R_9137461_SNP [dm6]	C	T	9.890e^-6	0.471	NON_SYNONYMOUS_CODING alc UPSTREAM alc	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad
2R	8089970	2R_8089970_SNP [dm3] 2R_12202465_SNP [dm6]	A	G	1.004e^-5	0.471	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	8221349	3R_8221349_SNP [dm3] 3R_12395627_SNP [dm6]	A	G	1.033e^-5	0.471	DOWNSTREAM Cyp9f3Psi INTRON CG34402 & 2 others
3R	8511738	3R_8511738_SNP [dm3] 3R_12686016_SNP [dm6]	C	T	1.098e^-5	0.471	INTRON kar	TF binding site mE1_TFBS_cad
3L	9526161	3L_9526161_SNP [dm3] 3L_9533061_SNP [dm6]	A	T	1.108e^-5	0.471	INTERGENIC
2R	15171997	2R_15171997_SNP [dm3] 2R_19284492_SNP [dm6]	T	G	1.109e^-5	0.471	UPSTREAM CG11906 DOWNSTREAM CG10476 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	9933853	2R_9933853_SNP [dm3] 2R_14046348_SNP [dm6]	G	A	1.145e^-5	0.471	INTRON mam
3L	8631682	3L_8631682_INS [dm3] 3L_8638582_INS [dm6]	A	ATA	1.202e^-5	0.471	UTR_3_PRIME Zasp66	TF binding site mE1_TFBS_cnc
3R	15041244	3R_15041244_SNP [dm3] 3R_19215522_SNP [dm6]	C	T	1.235e^-5	0.471	UTR_3_PRIME vib DOWNSTREAM cry
3R	11639782	3R_11639782_SNP [dm3] 3R_15814060_SNP [dm6]	C	T	1.270e^-5	0.471	INTRON alpha-Man-IIb
3R	8224915	3R_8224915_SNP [dm3] 3R_12399193_SNP [dm6]	A	T	1.284e^-5	0.471	SYNONYMOUS_CODING lig3 UPSTREAM Cyp9f3Psi INTRON CG34402	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	15172241	2R_15172241_SNP [dm3] 2R_19284736_SNP [dm6]	G	A	1.286e^-5	0.471	SYNONYMOUS_CODING CG10476 UPSTREAM CG11906 DOWNSTREAM CG10474	TF binding site mE1_TFBS_HSA
3R	12325612	3R_12325612_SNP [dm3] 3R_16499890_SNP [dm6]	T	G	1.297e^-5	0.471	SYNONYMOUS_CODING decay UPSTREAM Gr89a
2L	7072903	2L_7072903_SNP [dm3] 2L_7072903_SNP [dm6]	C	T	1.342e^-5	0.471	INTRON Pvf2
2L	15401192	2L_15401192_SNP [dm3] 2L_15401192_SNP [dm6]	A	G	1.352e^-5	0.471	UPSTREAM CR45374 INTERGENIC
2R	15172245	2R_15172245_SNP [dm3] 2R_19284740_SNP [dm6]	A	G	1.356e^-5	0.471	SYNONYMOUS_CODING CG10476 UPSTREAM CG11906 DOWNSTREAM CG10474	TF binding site mE1_TFBS_HSA
3R	7633296	3R_7633296_SNP [dm3] 3R_11807574_SNP [dm6]	G	T	1.425e^-5	0.48	INTRON ClC-a
2L	15790236	2L_15790236_DEL [dm3] 2L_15790236_DEL [dm6]	TTAATCTCTTTCAGTGGCAG...	T	1.433e^-5	0.48	DOWNSTREAM CG18109 INTERGENIC
3R	8236387	3R_8236387_SNP [dm3] 3R_12410665_SNP [dm6]	G	A	1.469e^-5	0.484	SYNONYMOUS_CODING CG5196	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	25079138	3R_25079138_SNP [dm3] 3R_29253416_SNP [dm6]	G	A	1.615e^-5	0.51	NON_SYNONYMOUS_CODING stg	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
2L	19251790	2L_19251790_SNP [dm3] 2L_19251790_SNP [dm6]	A	G	1.619e^-5	0.51	INTERGENIC
3R	23161744	3R_23161744_SNP [dm3] 3R_27336022_SNP [dm6]	A	G	1.650e^-5	0.51	INTERGENIC
3R	23161801	3R_23161801_SNP [dm3] 3R_27336079_SNP [dm6]	G	A	1.657e^-5	0.51	INTERGENIC
2R	15172026	2R_15172026_SNP [dm3] 2R_19284521_SNP [dm6]	T	A	1.764e^-5	0.529	UPSTREAM CG11906 DOWNSTREAM CG10476 & 1 other INTERGENIC	TF binding site mE1_TFBS_HSA
3R	8511590	3R_8511590_SNP [dm3] 3R_12685868_SNP [dm6]	T	C	1.832e^-5	0.529	INTRON kar	TF binding site mE1_TFBS_cad
3R	13328042	3R_13328042_SNP [dm3] 3R_17502320_SNP [dm6]	T	G	1.897e^-5	0.529	INTRON Dscam3
2R	5027061	2R_5027061_SNP [dm3] 2R_9139556_SNP [dm6]	C	T	1.912e^-5	0.529	UTR_5_PRIME CG8788 & 1 other INTRON CG8788 & 1 other	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi
2R	5025853	2R_5025853_SNP [dm3] 2R_9138348_SNP [dm6]	A	G	2.021e^-5	0.529	UPSTREAM alc & 2 others INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_Trl mE1_TFBS_Ubx
3R	23161749	3R_23161749_SNP [dm3] 3R_27336027_SNP [dm6]	G	A	2.040e^-5	0.529	INTERGENIC
3R	8221282	3R_8221282_SNP [dm3] 3R_12395560_SNP [dm6]	A	C	2.087e^-5	0.529	NON_SYNONYMOUS_CODING CG10097 UTR_5_PRIME CG10096 DOWNSTREAM Cyp9f3Psi INTRON CG34402
3R	8215726	3R_8215726_SNP [dm3] 3R_12390004_SNP [dm6]	T	C	2.107e^-5	0.529	SYNONYMOUS_CODING CG34402 DOWNSTREAM CG10096 & 1 other
2R	8173388	2R_8173388_SNP [dm3] 2R_12285883_SNP [dm6]	T	C	2.110e^-5	0.529	UPSTREAM CG42700 INTRON CG42700
3R	8511699	3R_8511699_SNP [dm3] 3R_12685977_SNP [dm6]	A	T	2.121e^-5	0.529	INTRON kar	TF binding site mE1_TFBS_cad
2L	15735651	2L_15735651_SNP [dm3] 2L_15735651_SNP [dm6]	C	T	2.138e^-5	0.529	INTRON CycE	regulatory region FlyBase REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3R	25078765	3R_25078765_SNP [dm3] 3R_29253043_SNP [dm6]	G	A	2.147e^-5	0.529	SYNONYMOUS_CODING stg	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Mad BDTNP1_TFBS_sna mE1_TFBS_HSA mE1_TFBS_sens
2L	14926231	2L_14926231_SNP [dm3] 2L_14926231_SNP [dm6]	A	G	2.151e^-5	0.529	SYNONYMOUS_CODING CG3491 INTRON CG42313
3L	9634257	3L_9634257_SNP [dm3] 3L_9641157_SNP [dm6]	G	T	2.172e^-5	0.529	SYNONYMOUS_CODING CG18180 INTRON fry	TF binding site mE1_TFBS_cad
3L	5361684	3L_5361684_INS [dm3] 3L_5368584_INS [dm6]	T	TG	2.194e^-5	0.529	UPSTREAM CG10635 & 1 other INTERGENIC
2L	15764094	2L_15764094_SNP [dm3] 2L_15764094_SNP [dm6]	T	G	2.201e^-5	0.529	UPSTREAM CG3793 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad
3R	8231349	3R_8231349_SNP [dm3] 3R_12405627_SNP [dm6]	T	C	2.231e^-5	0.529	UPSTREAM CG5167 INTRON Cyp9f2	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	5034213	2R_5034213_SNP [dm3] 2R_9146708_SNP [dm6]	G	A	2.264e^-5	0.529	SYNONYMOUS_CODING CG30344
2R	15171741	2R_15171741_SNP [dm3] 2R_19284236_SNP [dm6]	T	A	2.267e^-5	0.529	UPSTREAM CG11906 DOWNSTREAM CG10476 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_GATAe mE1_TFBS_HSA
2L	7073756	2L_7073756_SNP [dm3] 2L_7073756_SNP [dm6]	T	A	2.283e^-5	0.529	INTRON Pvf2
X	9455415	X_9455415_SNP [dm3] X_9561382_SNP [dm6]	C	T	2.311e^-5	0.529	SYNONYMOUS_CODING Cubn	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3R	8219408	3R_8219408_SNP [dm3] 3R_12393686_SNP [dm6]	G	A	2.518e^-5	0.569	UTR_5_PRIME CG10096 UTR_3_PRIME CG10097 UPSTREAM CG10096 DOWNSTREAM CG10097 INTRON CG34402
3R	8237029	3R_8237029_SNP [dm3] 3R_12411307_SNP [dm6]	T	C	2.614e^-5	0.579	SYNONYMOUS_CODING CG5196 DOWNSTREAM Dip-C	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	9731081	3L_9731081_SNP [dm3] 3L_9737981_SNP [dm6]	G	A	2.624e^-5	0.579	INTRON CG42268
3R	6542668	3R_6542668_SNP [dm3] 3R_10716946_SNP [dm6]	T	C	2.672e^-5	0.583	INTERGENIC
2L	15735639	2L_15735639_SNP [dm3] 2L_15735639_SNP [dm6]	C	A	2.707e^-5	0.584	INTRON CycE	regulatory region FlyBase REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
X	13606664	X_13606664_SNP [dm3] X_13712631_SNP [dm6]	G	T	2.741e^-5	0.584	SPLICE_SITE_REGION NnaD SYNONYMOUS_CODING NnaD INTRON CG9940
3R	8235840	3R_8235840_SNP [dm3] 3R_12410118_SNP [dm6]	T	C	2.807e^-5	0.587	INTRON CG5196	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_HSA
3R	17213941	3R_17213941_SNP [dm3] 3R_21388219_SNP [dm6]	T	A	2.817e^-5	0.587	UPSTREAM bap INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
2R	17990646	2R_17990646_SNP [dm3] 2R_22103141_SNP [dm6]	T	C	2.953e^-5	0.597	UPSTREAM CG6613 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	8234936	3R_8234936_SNP [dm3] 3R_12409214_SNP [dm6]	A	G	2.955e^-5	0.597	UTR_5_PRIME CG5196 INTRON CG5196	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_Med BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	11719656	3R_11719656_INS [dm3] 3R_15893934_INS [dm6]	C	CC	2.962e^-5	0.597	INTRON CG14877
2L	19253260	2L_19253260_SNP [dm3] 2L_19253260_SNP [dm6]	C	T	3.007e^-5	0.6	INTERGENIC
3L	5343409	3L_5343409_SNP [dm3] 3L_5350309_SNP [dm6]	C	A	3.041e^-5	0.6	INTRON lama
2R	17990624	2R_17990624_SNP [dm3] 2R_22103119_SNP [dm6]	T	A	3.091e^-5	0.604	UPSTREAM CG6613 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	7473528	2R_7473528_SNP [dm3] 2R_11586023_SNP [dm6]	G	A	3.165e^-5	0.607	SYNONYMOUS_CODING tou
2R	8179555	2R_8179555_SNP [dm3] 2R_12292050_SNP [dm6]	T	G	3.172e^-5	0.607	INTRON CG42700
3R	7633242	3R_7633242_SNP [dm3] 3R_11807520_SNP [dm6]	A	G	3.204e^-5	0.607	UPSTREAM ClC-a INTRON ClC-a
2R	15172244	2R_15172244_SNP [dm3] 2R_19284739_SNP [dm6]	G	T	3.273e^-5	0.61	NON_SYNONYMOUS_CODING CG10476 UPSTREAM CG11906 DOWNSTREAM CG10474	TF binding site mE1_TFBS_HSA

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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=1.524e^-7)
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
In_3R_P	0.086051
In_3R_K	0.009244

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_3R_K	12.2532	0.0022

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2001 significant hits at p-value < 0.001. The 1000 top results are displayed in the table below.

Variant impact HIGH MODERATE LOW MODIFIER

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Chromosome	Position	ID	Reference	Variant	p-value	FDR_BH	Transcript annotation	Binding site annotation
2L	22820712	2L_22820712_SNP [dm3] 2L_22927980_SNP [dm6]	T	A	1.240e^-6	0.632	INTRON lt
3R	8214104	3R_8214104_SNP [dm3] 3R_12388382_SNP [dm6]	G	A	2.523e^-6	0.632	SYNONYMOUS_CODING CG33098 UTR_3_PRIME CG33098 UPSTREAM CG34402 INTRON CG34402	TF binding site mE1_TFBS_cad
2R	7834712	2R_7834712_SNP [dm3] 2R_11947207_SNP [dm6]	T	C	2.837e^-6	0.632	INTRON CG13188
2L	22709561	2L_22709561_SNP [dm3] 2L_22816829_SNP [dm6]	G	A	2.901e^-6	0.632	INTERGENIC
2L	22644486	2L_22644486_SNP [dm3] 2L_22751754_SNP [dm6]	C	A	3.119e^-6	0.632	INTRON CG40006 EXON CR43927
X	3983424	X_3983424_SNP [dm3] X_4089391_SNP [dm6]	G	A	3.919e^-6	0.632	INTRON CG43689	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
2L	22618160	2L_22618160_SNP [dm3] 2L_22725428_SNP [dm6]	T	A	4.165e^-6	0.632	INTRON CG40006
2L	6581293	2L_6581293_SNP [dm3] 2L_6581293_SNP [dm6]	C	G	4.177e^-6	0.632	INTRON CG11319
2L	22613358	2L_22613358_SNP [dm3] 2L_22720626_SNP [dm6]	T	C	4.388e^-6	0.632	INTRON CG40006
2L	22637027	2L_22637027_DEL [dm3] 2L_22744295_DEL [dm6]	GTGCC	AA	4.545e^-6	0.632	INTRON CG40006
2L	22596763	2L_22596763_SNP [dm3] 2L_22704031_SNP [dm6]	A	C	4.583e^-6	0.632	INTRON CG40006
3L	9870970	3L_9870970_SNP [dm3] 3L_9877870_SNP [dm6]	C	T	4.657e^-6	0.632	INTERGENIC
2L	22617684	2L_22617684_SNP [dm3] 2L_22724952_SNP [dm6]	T	C	4.677e^-6	0.632	INTRON CG40006
3R	8220563	3R_8220563_SNP [dm3] 3R_12394841_SNP [dm6]	A	G	5.657e^-6	0.632	NON_SYNONYMOUS_CODING CG10097 UTR_5_PRIME CG10096 INTRON CG34402
2L	8524326	2L_8524326_SNP [dm3] 2L_8524326_SNP [dm6]	C	T	5.939e^-6	0.632	SYNONYMOUS_CODING Acer DOWNSTREAM lmgA & 1 other	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2L	22733760	2L_22733760_SNP [dm3] 2L_22841028_SNP [dm6]	A	T	6.276e^-6	0.632	INTERGENIC
X	21178791	X_21178791_SNP [dm3] X_21307764_SNP [dm6]	C	T	6.629e^-6	0.632	SYNONYMOUS_CODING CG1801	TF binding site BDTNP1_TFBS_twi
2L	22609381	2L_22609381_SNP [dm3] 2L_22716649_SNP [dm6]	A	G	6.923e^-6	0.632	INTRON CG40006
2L	22652211	2L_22652211_SNP [dm3] 2L_22759479_SNP [dm6]	G	T	7.012e^-6	0.632	INTERGENIC
2L	22630715	2L_22630715_SNP [dm3] 2L_22737983_SNP [dm6]	C	G	7.907e^-6	0.632	INTRON CG40006
2L	22631833	2L_22631833_SNP [dm3] 2L_22739101_SNP [dm6]	A	T	8.342e^-6	0.632	INTRON CG40006
2L	22631818	2L_22631818_SNP [dm3] 2L_22739086_SNP [dm6]	T	C	8.457e^-6	0.632	INTRON CG40006
2L	22625225	2L_22625225_SNP [dm3] 2L_22732493_SNP [dm6]	C	A	8.510e^-6	0.632	INTRON CG40006
2L	22626351	2L_22626351_DEL [dm3] 2L_22733619_DEL [dm6]	GG	G	8.885e^-6	0.632	INTRON CG40006
3R	8210917	3R_8210917_SNP [dm3] 3R_12385195_SNP [dm6]	T	G	9.431e^-6	0.632	INTRON GstD11
3R	8221499	3R_8221499_SNP [dm3] 3R_12395777_SNP [dm6]	G	A	9.620e^-6	0.632	SYNONYMOUS_CODING CG10097 UTR_5_PRIME CG10096 DOWNSTREAM Cyp9f3Psi INTRON CG34402
2L	22704228	2L_22704228_SNP [dm3] 2L_22811496_SNP [dm6]	C	A	9.961e^-6	0.632	INTERGENIC
2L	22714814	2L_22714814_SNP [dm3] 2L_22822082_SNP [dm6]	A	G	9.961e^-6	0.632	INTERGENIC
3R	23903399	3R_23903399_SNP [dm3] 3R_28077677_SNP [dm6]	G	A	1.130e^-5	0.632	INTRON CG34362
2R	5783798	2R_5783798_SNP [dm3] 2R_9896293_SNP [dm6]	G	T	1.136e^-5	0.632	NON_SYNONYMOUS_CODING CG30007
2R	5783795	2R_5783795_SNP [dm3] 2R_9896290_SNP [dm6]	C	A	1.235e^-5	0.632	NON_SYNONYMOUS_CODING CG30007
2L	8311282	2L_8311282_SNP [dm3] 2L_8311282_SNP [dm6]	A	T	1.298e^-5	0.632	UPSTREAM CG7806 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_HSA
2L	22626562	2L_22626562_SNP [dm3] 2L_22733830_SNP [dm6]	A	T	1.339e^-5	0.632	INTRON CG40006
3R	24262915	3R_24262915_SNP [dm3] 3R_28437193_SNP [dm6]	T	G	1.357e^-5	0.632	INTRON beat-VI
2L	22639394	2L_22639394_SNP [dm3] 2L_22746662_SNP [dm6]	G	A	1.390e^-5	0.632	INTRON CG40006
2L	22617799	2L_22617799_SNP [dm3] 2L_22725067_SNP [dm6]	C	T	1.418e^-5	0.632	INTRON CG40006
3R	8213155	3R_8213155_SNP [dm3] 3R_12387433_SNP [dm6]	G	T	1.448e^-5	0.632	UPSTREAM CG33098 INTRON CG34402 & 1 other
2R	9967141	2R_9967141_SNP [dm3] 2R_14079636_SNP [dm6]	T	A	1.486e^-5	0.632	INTRON Prosap
2L	22701799	2L_22701799_SNP [dm3] 2L_22809067_SNP [dm6]	G	A	1.566e^-5	0.632	INTERGENIC
3R	23901645	3R_23901645_SNP [dm3] 3R_28075923_SNP [dm6]	A	C	1.687e^-5	0.632	INTRON CG34362	TF binding site mE1_TFBS_inv
2L	8521447	2L_8521447_SNP [dm3] 2L_8521447_SNP [dm6]	C	T	1.692e^-5	0.632	UPSTREAM Acer INTRON CG13091	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_h mE1_TFBS_sens mE1_TFBS_Ubx
2L	22610844	2L_22610844_INS [dm3] 2L_22718112_INS [dm6]	A	ACCTA	1.694e^-5	0.632	INTRON CG40006
2L	22637098	2L_22637098_SNP [dm3] 2L_22744366_SNP [dm6]	A	C	1.735e^-5	0.632	INTRON CG40006
2L	8372639	2L_8372639_SNP [dm3] 2L_8372639_SNP [dm6]	C	T	1.814e^-5	0.632	INTRON CG17292
2L	4917163	2L_4917163_SNP [dm3] 2L_4917163_SNP [dm6]	T	A	1.828e^-5	0.632	INTRON hoe1
2L	10691093	2L_10691093_SNP [dm3] 2L_10691093_SNP [dm6]	C	T	1.848e^-5	0.632	INTERGENIC
2L	22682289	2L_22682289_SNP [dm3] 2L_22789557_SNP [dm6]	C	A	1.849e^-5	0.632	INTERGENIC
2L	6581270	2L_6581270_SNP [dm3] 2L_6581270_SNP [dm6]	A	T	1.864e^-5	0.632	INTRON CG11319
3L	14109818	3L_14109818_SNP [dm3] 3L_14116718_SNP [dm6]	C	A	1.880e^-5	0.632	INTRON Sox21b
2L	22640780	2L_22640780_SNP [dm3] 2L_22748048_SNP [dm6]	A	G	1.906e^-5	0.632	INTRON CG40006
2L	22715265	2L_22715265_SNP [dm3] 2L_22822533_SNP [dm6]	G	A	1.938e^-5	0.632	INTERGENIC
2L	8521314	2L_8521314_SNP [dm3] 2L_8521314_SNP [dm6]	G	C	1.942e^-5	0.632	NON_SYNONYMOUS_CODING CG13091 UPSTREAM Acer	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_h mE1_TFBS_sens mE1_TFBS_Ubx
X	4293765	X_4293765_SNP [dm3] X_4399732_SNP [dm6]	A	G	1.997e^-5	0.632	INTRON CR32773
2L	22596883	2L_22596883_SNP [dm3] 2L_22704151_SNP [dm6]	T	A	2.004e^-5	0.632	INTRON CG40006
3R	24263324	3R_24263324_SNP [dm3] 3R_28437602_SNP [dm6]	T	G	2.005e^-5	0.632	INTRON beat-VI
2L	22697318	2L_22697318_INS [dm3] 2L_22804586_INS [dm6]	A	AG	2.018e^-5	0.632	INTERGENIC
2L	22636266	2L_22636266_SNP [dm3] 2L_22743534_SNP [dm6]	G	T	2.035e^-5	0.632	INTRON CG40006
2L	7572459	2L_7572459_SNP [dm3] 2L_7572459_SNP [dm6]	A	G	2.131e^-5	0.632	INTRON RapGAP1
2L	22732809	2L_22732809_SNP [dm3] 2L_22840077_SNP [dm6]	A	G	2.145e^-5	0.632	INTERGENIC
3R	9642047	3R_9642047_SNP [dm3] 3R_13816325_SNP [dm6]	T	C	2.157e^-5	0.632	DOWNSTREAM CR43641 EXON CR43642
2L	10691095	2L_10691095_SNP [dm3] 2L_10691095_SNP [dm6]	A	C	2.164e^-5	0.632	INTERGENIC
3R	8213161	3R_8213161_INS [dm3] 3R_12387439_INS [dm6]	T	TTGATA	2.179e^-5	0.632	UPSTREAM CG33098 INTRON CG34402 & 1 other
2R	5777267	2R_5777267_SNP [dm3] 2R_9889762_SNP [dm6]	G	A	2.197e^-5	0.632	UPSTREAM CG30008 DOWNSTREAM CG12923 INTRON CG1513
2L	22626360	2L_22626360_SNP [dm3] 2L_22733628_SNP [dm6]	T	G	2.205e^-5	0.632	INTRON CG40006
2L	22683141	2L_22683141_SNP [dm3] 2L_22790409_SNP [dm6]	A	T	2.207e^-5	0.632	INTERGENIC
2L	22655837	2L_22655837_SNP [dm3] 2L_22763105_SNP [dm6]	C	A	2.249e^-5	0.632	INTERGENIC
3R	13307719	3R_13307719_SNP [dm3] 3R_17481997_SNP [dm6]	G	A	2.273e^-5	0.632	SPLICE_SITE_REGION Dscam3 DOWNSTREAM Dscam3 INTRON Dscam3
2L	8372098	2L_8372098_SNP [dm3] 2L_8372098_SNP [dm6]	G	A	2.330e^-5	0.632	UPSTREAM CG17292 INTRON CG17292
2L	8521332	2L_8521332_SNP [dm3] 2L_8521332_SNP [dm6]	A	C	2.431e^-5	0.632	SYNONYMOUS_CODING CG13091 UPSTREAM Acer	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_h mE1_TFBS_sens mE1_TFBS_Ubx
3R	13856908	3R_13856908_SNP [dm3] 3R_18031186_SNP [dm6]	T	C	2.446e^-5	0.632	INTERGENIC
2L	22640804	2L_22640804_SNP [dm3] 2L_22748072_SNP [dm6]	G	A	2.485e^-5	0.632	INTRON CG40006
2L	22627816	2L_22627816_SNP [dm3] 2L_22735084_SNP [dm6]	T	C	2.509e^-5	0.632	INTRON CG40006
2L	7572449	2L_7572449_SNP [dm3] 2L_7572449_SNP [dm6]	A	G	2.515e^-5	0.632	INTRON RapGAP1
2L	22613344	2L_22613344_SNP [dm3] 2L_22720612_SNP [dm6]	T	C	2.624e^-5	0.632	INTRON CG40006
2L	22636855	2L_22636855_SNP [dm3] 2L_22744123_SNP [dm6]	G	A	2.656e^-5	0.632	INTRON CG40006
3R	16771739	3R_16771739_DEL [dm3] 3R_20946017_DEL [dm6]	CG	C	2.676e^-5	0.632	UPSTREAM CG31191 INTERGENIC	TF binding site mE1_TFBS_cad
3L	1982820	3L_1982820_SNP [dm3] 3L_1982820_SNP [dm6]	G	T	2.699e^-5	0.632	INTERGENIC
3R	8215726	3R_8215726_SNP [dm3] 3R_12390004_SNP [dm6]	T	C	2.726e^-5	0.632	SYNONYMOUS_CODING CG34402 DOWNSTREAM CG10096 & 1 other
2L	19557847	2L_19557847_DEL [dm3] 2L_19557847_DEL [dm6]	TTTTTGT	T	2.767e^-5	0.632	UPSTREAM Tep5 INTERGENIC
2L	22579668	2L_22579668_SNP [dm3] 2L_22686936_SNP [dm6]	G	C	2.782e^-5	0.632	INTRON CG40006
2R	5783305	2R_5783305_SNP [dm3] 2R_9895800_SNP [dm6]	C	A	2.813e^-5	0.632	NON_SYNONYMOUS_CODING CG30007
2L	22594273	2L_22594273_SNP [dm3] 2L_22701541_SNP [dm6]	T	A	2.885e^-5	0.632	INTRON CG40006
3R	7370337	3R_7370337_SNP [dm3] 3R_11544615_SNP [dm6]	C	T	2.940e^-5	0.632	INTERGENIC	TF binding site BDTNP1_TFBS_dl
2L	22692875	2L_22692875_SNP [dm3] 2L_22800143_SNP [dm6]	A	G	2.951e^-5	0.632	INTERGENIC
2L	22678220	2L_22678220_SNP [dm3] 2L_22785488_SNP [dm6]	T	A	2.964e^-5	0.632	INTERGENIC	TF binding site mE1_TFBS_inv mE1_TFBS_Trl
3R	23971143	3R_23971143_SNP [dm3] 3R_28145421_SNP [dm6]	G	C	2.977e^-5	0.632	INTERGENIC
3R	17215667	3R_17215667_SNP [dm3] 3R_21389945_SNP [dm6]	T	C	3.012e^-5	0.632	SYNONYMOUS_CODING bap	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3R	22346051	3R_22346051_SNP [dm3] 3R_26520329_SNP [dm6]	T	C	3.023e^-5	0.632	INTRON plum EXON CR45226
2L	10792123	2L_10792123_SNP [dm3] 2L_10792123_SNP [dm6]	C	A	3.029e^-5	0.632	DOWNSTREAM CG31870 INTRON CG31869
2L	22692351	2L_22692351_SNP [dm3] 2L_22799619_SNP [dm6]	C	T	3.084e^-5	0.632	INTERGENIC
X	22232347	X_22232347_DEL [dm3] X_22830511_DEL [dm6]	GCTGCTG	G	3.123e^-5	0.632	INTRON fog	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_eve mE1_TFBS_HSA mE1_TFBS_inv
2L	8311265	2L_8311265_SNP [dm3] 2L_8311265_SNP [dm6]	G	T	3.162e^-5	0.632	UPSTREAM CG7806 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_HSA
2L	22637965	2L_22637965_SNP [dm3] 2L_22745233_SNP [dm6]	A	G	3.165e^-5	0.632	INTRON CG40006
2R	12026902	2R_12026902_SNP [dm3] 2R_16139397_SNP [dm6]	C	G	3.167e^-5	0.632	INTRON Got1
3L	4889607	3L_4889607_SNP [dm3] 3L_4889607_SNP [dm6]	G	A	3.217e^-5	0.635	SPLICE_SITE_REGION CG17150 INTRON CG17150
2L	8529077	2L_8529077_SNP [dm3] 2L_8529077_SNP [dm6]	G	C	3.325e^-5	0.638	UPSTREAM CG17834 & 2 others INTERGENIC	TF binding site BDTNP1_TFBS_dl
2L	8372130	2L_8372130_SNP [dm3] 2L_8372130_SNP [dm6]	C	T	3.376e^-5	0.638	UPSTREAM CG17292 INTRON CG17292
3R	13856909	3R_13856909_SNP [dm3] 3R_18031187_SNP [dm6]	G	A	3.433e^-5	0.638	INTERGENIC
3L	1529646	3L_1529646_SNP [dm3] 3L_1529646_SNP [dm6]	G	T	3.436e^-5	0.638	SYNONYMOUS_CODING Ir62a INTRON CG12090
3R	23884531	3R_23884531_SNP [dm3] 3R_28058809_SNP [dm6]	G	A	3.463e^-5	0.638	INTRON CG34362

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By genomic position
Variant impact
Gene name

Cuticul_n_C23 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results