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=5.472e^-6)
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_2L_t	0.03985
In_3R_Mo	0.04026

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	9.3701	0.0092
In_3R_Mo	5.735	0.0568

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1882 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	3801353	3R_3801353_SNP [dm3] 3R_7975631_SNP [dm6]	T	C	2.222e^-7	0.417	SYNONYMOUS_CODING CD98hc	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	8113408	2R_8113408_SNP [dm3] 2R_12225903_SNP [dm6]	G	T	1.011e^-6	0.748	SYNONYMOUS_CODING CG8854	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_inv
3R	6659878	3R_6659878_SNP [dm3] 3R_10834156_SNP [dm6]	G	C	1.302e^-6	0.748	INTRON Cad86C	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	4047994	2L_4047994_SNP [dm3] 2L_4047994_SNP [dm6]	T	A	1.904e^-6	0.748	INTRON ed	TF binding site mE1_TFBS_chinmo
2R	1072336	2R_1072336_INS [dm3] 2R_5184831_INS [dm6]	C	CGCC	2.688e^-6	0.748	INTRON Nipped-A
3R	6659901	3R_6659901_SNP [dm3] 3R_10834179_SNP [dm6]	A	C	3.152e^-6	0.748	INTRON Cad86C	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	6659902	3R_6659902_DEL [dm3] 3R_10834180_DEL [dm6]	GCTCCAG	G	3.280e^-6	0.748	INTRON Cad86C	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	13188174	3L_13188174_SNP [dm3] 3L_13195074_SNP [dm6]	C	G	3.544e^-6	0.748	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
X	13210675	X_13210675_SNP [dm3] X_13316642_SNP [dm6]	G	A	3.983e^-6	0.748	INTRON IP3K2
2R	1072326	2R_1072326_INS [dm3] 2R_5184821_INS [dm6]	T	TT	4.447e^-6	0.748	INTRON Nipped-A
3L	13188081	3L_13188081_SNP [dm3] 3L_13194981_SNP [dm6]	C	A	5.399e^-6	0.748	INTERGENIC
3L	13188049	3L_13188049_SNP [dm3] 3L_13194949_SNP [dm6]	C	A	6.256e^-6	0.748	INTERGENIC
3L	9191571	3L_9191571_SNP [dm3] 3L_9198471_SNP [dm6]	G	A	6.949e^-6	0.748	INTERGENIC
2L	10803280	2L_10803280_SNP [dm3] 2L_10803280_SNP [dm6]	G	A	7.232e^-6	0.748	UPSTREAM CR44581 DOWNSTREAM Nos INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2R	8112670	2R_8112670_SNP [dm3] 2R_12225165_SNP [dm6]	C	T	7.318e^-6	0.748	SYNONYMOUS_CODING CG8854	TF binding site mE1_TFBS_chinmo
X	5014312	X_5014312_SNP [dm3] X_5120279_SNP [dm6]	G	A	7.689e^-6	0.748	INTRON rg & 1 other
2L	10803278	2L_10803278_SNP [dm3] 2L_10803278_SNP [dm6]	C	T	8.591e^-6	0.748	UPSTREAM CR44581 DOWNSTREAM Nos INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
3L	13188077	3L_13188077_SNP [dm3] 3L_13194977_SNP [dm6]	A	G	8.920e^-6	0.748	INTERGENIC
3L	13188083	3L_13188083_SNP [dm3] 3L_13194983_SNP [dm6]	C	T	8.920e^-6	0.748	INTERGENIC
3L	13188084	3L_13188084_SNP [dm3] 3L_13194984_SNP [dm6]	C	T	8.920e^-6	0.748	INTERGENIC
X	13210651	X_13210651_SNP [dm3] X_13316618_SNP [dm6]	G	C	8.972e^-6	0.748	INTRON IP3K2
3L	13188108	3L_13188108_SNP [dm3] 3L_13195008_SNP [dm6]	G	C	9.164e^-6	0.748	INTERGENIC	TF binding site mE1_TFBS_HSA
X	12422708	X_12422708_SNP [dm3] X_12528675_SNP [dm6]	A	C	9.187e^-6	0.748	INTRON CG43921
3R	3841967	3R_3841967_SNP [dm3] 3R_8016245_SNP [dm6]	C	T	9.575e^-6	0.748	UTR_3_PRIME Pbp95 & 1 other DOWNSTREAM CG2747	TF binding site mE1_TFBS_sbb
3R	13364199	3R_13364199_SNP [dm3] 3R_17538477_SNP [dm6]	C	T	1.019e^-5	0.765	SYNONYMOUS_CODING l_3_07882	TF binding site mE1_TFBS_sens
3R	13364203	3R_13364203_SNP [dm3] 3R_17538481_SNP [dm6]	G	A	1.069e^-5	0.771	NON_SYNONYMOUS_CODING l_3_07882	TF binding site mE1_TFBS_sens
2L	10803270	2L_10803270_SNP [dm3] 2L_10803270_SNP [dm6]	A	T	1.201e^-5	0.823	UPSTREAM CR44581 INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
3L	10373469	3L_10373469_SNP [dm3] 3L_10380369_SNP [dm6]	T	C	1.228e^-5	0.823	INTERGENIC
2L	10803285	2L_10803285_SNP [dm3] 2L_10803285_SNP [dm6]	T	G	1.381e^-5	0.834	UPSTREAM CR44581 DOWNSTREAM Nos INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
3R	13364202	3R_13364202_SNP [dm3] 3R_17538480_SNP [dm6]	G	A	1.394e^-5	0.834	SYNONYMOUS_CODING l_3_07882	TF binding site mE1_TFBS_sens
3R	14342260	3R_14342260_SNP [dm3] 3R_18516538_SNP [dm6]	A	G	1.465e^-5	0.834	INTRON fru	TF binding site BDTNP1_TFBS_twi
2L	900071	2L_900071_SNP [dm3] 2L_900071_SNP [dm6]	A	G	1.526e^-5	0.834	SYNONYMOUS_CODING Lsp1beta	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2L	10803300	2L_10803300_SNP [dm3] 2L_10803300_SNP [dm6]	T	G	1.555e^-5	0.834	UPSTREAM CR44581 DOWNSTREAM Nos INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2L	10803261	2L_10803261_SNP [dm3] 2L_10803261_SNP [dm6]	G	A	1.608e^-5	0.834	UPSTREAM CR44581 INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2R	3356245	2R_3356245_SNP [dm3] 2R_7468740_SNP [dm6]	C	A	1.802e^-5	0.834	INTRON Aldh-III
2L	18684237	2L_18684237_SNP [dm3] 2L_18684237_SNP [dm6]	G	A	1.837e^-5	0.834	UTR_3_PRIME msl-1 DOWNSTREAM CG31751 & 1 other
3R	14342166	3R_14342166_SNP [dm3] 3R_18516444_SNP [dm6]	T	C	1.864e^-5	0.834	INTRON fru	TF binding site BDTNP1_TFBS_twi
2L	15402084	2L_15402084_SNP [dm3] 2L_15402084_SNP [dm6]	T	C	1.874e^-5	0.834	INTERGENIC
3R	8606136	3R_8606136_SNP [dm3] 3R_12780414_SNP [dm6]	T	G	1.944e^-5	0.834	INTRON beat-Vc
2R	8109912	2R_8109912_SNP [dm3] 2R_12222407_SNP [dm6]	C	A	1.962e^-5	0.834	INTERGENIC
2R	8106282	2R_8106282_SNP [dm3] 2R_12218777_SNP [dm6]	A	C	1.969e^-5	0.834	INTERGENIC
3L	13188525	3L_13188525_SNP [dm3] 3L_13195425_SNP [dm6]	G	A	1.972e^-5	0.834	INTERGENIC
3R	15402898	3R_15402898_SNP [dm3] 3R_19577176_SNP [dm6]	C	T	2.132e^-5	0.834	INTRON Dys
2R	15381439	2R_15381439_INS [dm3] 2R_19493934_INS [dm6]	A	ATTTT	2.143e^-5	0.834	UTR_3_PRIME Rep DOWNSTREAM hpo
3L	10378650	3L_10378650_SNP [dm3] 3L_10385550_SNP [dm6]	C	A	2.143e^-5	0.834	UPSTREAM CR45245 INTERGENIC
2L	10803301	2L_10803301_SNP [dm3] 2L_10803301_SNP [dm6]	A	C	2.242e^-5	0.834	UPSTREAM CR44581 DOWNSTREAM Nos INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
3R	6669804	3R_6669804_SNP [dm3] 3R_10844082_SNP [dm6]	C	T	2.279e^-5	0.834	SYNONYMOUS_CODING Cad86C	TF binding site mE1_TFBS_cad mE1_TFBS_inv
3R	6669810	3R_6669810_SNP [dm3] 3R_10844088_SNP [dm6]	G	A	2.279e^-5	0.834	SYNONYMOUS_CODING Cad86C	TF binding site mE1_TFBS_cad mE1_TFBS_inv
2R	8109725	2R_8109725_SNP [dm3] 2R_12222220_SNP [dm6]	G	C	2.302e^-5	0.834	INTERGENIC
3R	14342272	3R_14342272_SNP [dm3] 3R_18516550_SNP [dm6]	A	T	2.327e^-5	0.834	INTRON fru	TF binding site BDTNP1_TFBS_twi
2L	10092491	2L_10092491_SNP [dm3] 2L_10092491_SNP [dm6]	A	T	2.337e^-5	0.834	UPSTREAM CG13133 INTRON CG44153
2R	8109605	2R_8109605_SNP [dm3] 2R_12222100_SNP [dm6]	C	A	2.387e^-5	0.834	INTERGENIC
2R	7534789	2R_7534789_SNP [dm3] 2R_11647284_SNP [dm6]	T	C	2.397e^-5	0.834	INTRON CG9003	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2R	15381433	2R_15381433_DEL [dm3] 2R_19493928_DEL [dm6]	TACA	T	2.404e^-5	0.834	UTR_3_PRIME Rep DOWNSTREAM hpo
3R	6539705	3R_6539705_INS [dm3] 3R_10713983_INS [dm6]	C	CGC	2.446e^-5	0.834	UPSTREAM CG4073 INTERGENIC
3R	2167567	3R_2167567_SNP [dm3] 3R_6341845_SNP [dm6]	T	C	2.503e^-5	0.837	UPSTREAM CG17917 DOWNSTREAM Osi20 INTERGENIC
3L	18363406	3L_18363406_SNP [dm3] 3L_18370306_SNP [dm6]	T	G	2.545e^-5	0.837	INTERGENIC
2R	13121386	2R_13121386_SNP [dm3] 2R_17233881_SNP [dm6]	T	C	2.715e^-5	0.844	INTRON mbl
3L	13188344	3L_13188344_SNP [dm3] 3L_13195244_SNP [dm6]	G	A	2.758e^-5	0.844	INTERGENIC	TF binding site mE1_TFBS_HSA
3R	14342251	3R_14342251_SNP [dm3] 3R_18516529_SNP [dm6]	C	T	2.806e^-5	0.844	INTRON fru	TF binding site BDTNP1_TFBS_twi
3L	15528636	3L_15528636_DEL [dm3] 3L_15535536_DEL [dm6]	CA	C	2.888e^-5	0.844	UTR_5_PRIME CrebA	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_Trl
3R	3820434	3R_3820434_SNP [dm3] 3R_7994712_SNP [dm6]	T	C	2.903e^-5	0.844	INTRON CG2781
2L	900008	2L_900008_SNP [dm3] 2L_900008_SNP [dm6]	T	C	2.945e^-5	0.844	SYNONYMOUS_CODING Lsp1beta	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2R	8109757	2R_8109757_SNP [dm3] 2R_12222252_SNP [dm6]	A	C	3.024e^-5	0.844	INTERGENIC
X	921614	X_921614_DEL [dm3] X_1027581_DEL [dm6]	CTC	C	3.027e^-5	0.844	UPSTREAM CG32814 & 1 other DOWNSTREAM CDC45L INTRON su_w[a]_ & 1 other	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens
2L	8890223	2L_8890223_SNP [dm3] 2L_8890223_SNP [dm6]	G	A	3.037e^-5	0.844	INTERGENIC
2R	8113034	2R_8113034_DEL [dm3] 2R_12225529_DEL [dm6]	TGCGTAAA	T	3.054e^-5	0.844	INTRON CG8854
3L	15540175	3L_15540175_SNP [dm3] 3L_15547075_SNP [dm6]	C	G	3.097e^-5	0.844	INTRON CrebA
2R	10091864	2R_10091864_SNP [dm3] 2R_14204359_SNP [dm6]	A	T	3.114e^-5	0.844	INTRON Sox15	regulatory region REDfly_CRMs
3L	13188602	3L_13188602_SNP [dm3] 3L_13195502_SNP [dm6]	A	G	3.150e^-5	0.844	INTERGENIC
X	19252922	X_19252922_SNP [dm3] X_19358889_SNP [dm6]	T	G	3.306e^-5	0.872	INTRON kek5	TF binding site BDTNP1_TFBS_dl
X	12207397	X_12207397_INS [dm3] X_12313364_INS [dm6]	C	CGCCAAGTC	3.476e^-5	0.872	INTRON Ten-a
2L	13665220	2L_13665220_SNP [dm3] 2L_13665220_SNP [dm6]	G	A	3.488e^-5	0.872	UPSTREAM CG18507 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	8109780	2R_8109780_SNP [dm3] 2R_12222275_SNP [dm6]	G	A	3.510e^-5	0.872	INTERGENIC
X	4277123	X_4277123_SNP [dm3] X_4383090_SNP [dm6]	C	T	3.514e^-5	0.872	DOWNSTREAM CG12688 INTERGENIC
2R	20508703	2R_20508703_SNP [dm3] 2R_24621180_SNP [dm6]	C	A	3.544e^-5	0.872	INTRON CG13594	TF binding site mE1_TFBS_chinmo
2R	8087999	2R_8087999_SNP [dm3] 2R_12200494_SNP [dm6]	G	A	3.616e^-5	0.872	SYNONYMOUS_CODING RpS11 UPSTREAM snoRNA:Me28S-C3420a INTRON RpS11	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_sens
2R	8113161	2R_8113161_SNP [dm3] 2R_12225656_SNP [dm6]	T	A	3.639e^-5	0.872	INTRON CG8854
2R	19533110	2R_19533110_SNP [dm3] 2R_23645587_SNP [dm6]	G	A	3.746e^-5	0.872	UPSTREAM retn INTRON retn	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_kni BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_disco mE1_TFBS_HSA
X	19252948	X_19252948_SNP [dm3] X_19358915_SNP [dm6]	T	A	3.831e^-5	0.872	INTRON kek5	TF binding site BDTNP1_TFBS_dl
2R	8092915	2R_8092915_SNP [dm3] 2R_12205410_SNP [dm6]	C	G	3.831e^-5	0.872	UPSTREAM CR45276 INTERGENIC	TF binding site BDTNP1_TFBS_dl
X	3704104	X_3704104_SNP [dm3] X_3810071_SNP [dm6]	C	T	3.879e^-5	0.872	SYNONYMOUS_CODING fd3F	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
3L	18208348	3L_18208348_SNP [dm3] 3L_18215248_SNP [dm6]	T	C	3.956e^-5	0.872	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_prd mE1_TFBS_HSA
2L	5051058	2L_5051058_DEL [dm3] 2L_5051058_DEL [dm6]	CATC	C	4.070e^-5	0.872	UTR_5_PRIME CG9121 UPSTREAM CG9121 DOWNSTREAM eIF-3p40
3L	16558392	3L_16558392_SNP [dm3] 3L_16565292_SNP [dm6]	A	T	4.154e^-5	0.872	INTRON Mipp1	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl
2R	9849005	2R_9849005_DEL [dm3] 2R_13961500_DEL [dm6]	ATATTTACAAA...	A	4.158e^-5	0.872	INTRON Cp1	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med
3R	18358308	3R_18358308_SNP [dm3] 3R_22532586_SNP [dm6]	T	C	4.276e^-5	0.872	UTR_3_PRIME CG5326 UPSTREAM CG33093	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	2787480	3L_2787480_SNP [dm3] 3L_2787480_SNP [dm6]	C	T	4.508e^-5	0.872	UTR_3_PRIME CG43444	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	9394919	2R_9394919_SNP [dm3] 2R_13507414_SNP [dm6]	A	T	4.521e^-5	0.872	UPSTREAM EfTuM INTRON mip120	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	10595399	3R_10595399_SNP [dm3] 3R_14769677_SNP [dm6]	T	G	4.534e^-5	0.872	INTRON jvl
2R	8102309	2R_8102309_INS [dm3] 2R_12214804_INS [dm6]	G	GAGTG	4.636e^-5	0.872	DOWNSTREAM CG13171 INTERGENIC
3R	14342310	3R_14342310_SNP [dm3] 3R_18516588_SNP [dm6]	C	A	4.645e^-5	0.872	INTRON fru	TF binding site BDTNP1_TFBS_twi
X	16640847	X_16640847_SNP [dm3] X_16746814_SNP [dm6]	T	G	4.681e^-5	0.872	UPSTREAM CG9634 INTRON CG9634
3R	20351934	3R_20351934_SNP [dm3] 3R_24526212_SNP [dm6]	C	A	4.720e^-5	0.872	INTRON CG13618
3L	9421668	3L_9421668_SNP [dm3] 3L_9428568_SNP [dm6]	G	A	4.764e^-5	0.872	UTR_3_PRIME Shc DOWNSTREAM RpS17 & 1 other	TF binding site BDTNP1_TFBS_dl
2R	16039477	2R_16039477_SNP [dm3] 2R_20151972_SNP [dm6]	G	A	4.801e^-5	0.872	INTERGENIC	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2L	18622620	2L_18622620_SNP [dm3] 2L_18622620_SNP [dm6]	C	T	4.829e^-5	0.872	INTRON MESR3
3R	25354357	3R_25354357_SNP [dm3] 3R_29528635_SNP [dm6]	G	A	4.906e^-5	0.872	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	10707670	2L_10707670_SNP [dm3] 2L_10707670_SNP [dm6]	G	A	4.938e^-5	0.872	INTRON Lip2
2R	8084501	2R_8084501_SNP [dm3] 2R_12196996_SNP [dm6]	T	C	4.995e^-5	0.872	INTRON CG8858	TF binding site mE1_TFBS_cad

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Missing results

By genomic position
Variant impact
Gene name

Cuticul_7_11_C31_2 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results