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=3.553e^-11)
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_K	0.05057

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_3R_K	8.8714	0.0118

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1815 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	8314568	3L_8314568_SNP [dm3] 3L_8321468_SNP [dm6]	A	G	4.091e^-7	0.767	INTRON CG13670	TF binding site mE1_TFBS_cad
3L	8314503	3L_8314503_SNP [dm3] 3L_8321403_SNP [dm6]	A	T	3.456e^-6	0.979	INTRON CG13670	TF binding site mE1_TFBS_cad
X	10078498	X_10078498_SNP [dm3] X_10184465_SNP [dm6]	A	G	3.948e^-6	0.979	INTRON CG43902 & 1 other
3L	10571829	3L_10571829_DEL [dm3] 3L_10578729_DEL [dm6]	GG	A	5.512e^-6	0.979	INTRON A2bp1	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3R	21337061	3R_21337061_SNP [dm3] 3R_25511339_SNP [dm6]	A	T	6.299e^-6	0.979	INTERGENIC
3L	10571834	3L_10571834_SNP [dm3] 3L_10578734_SNP [dm6]	A	G	8.030e^-6	0.979	INTRON A2bp1	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3L	18882553	3L_18882553_SNP [dm3] 3L_18889453_SNP [dm6]	T	C	9.657e^-6	0.979	INTRON CG3961
3R	11580407	3R_11580407_SNP [dm3] 3R_15754685_SNP [dm6]	A	G	9.888e^-6	0.979	INTERGENIC
2R	18474107	2R_18474107_SNP [dm3] 2R_22586602_SNP [dm6]	G	T	1.047e^-5	0.979	INTRON dnr1
X	13221413	X_13221413_SNP [dm3] X_13327380_SNP [dm6]	T	C	1.063e^-5	0.979	SYNONYMOUS_CODING IP3K2
3L	7889244	3L_7889244_DEL [dm3] 3L_7896144_DEL [dm6]	TATTAACTTAAACATCTTCA...	T	1.651e^-5	0.979	UTR_3_PRIME pbl DOWNSTREAM eIF4E-5
X	19301615	X_19301615_SNP [dm3] X_19407582_SNP [dm6]	A	C	1.685e^-5	0.979	INTRON kek5
3L	18889880	3L_18889880_SNP [dm3] 3L_18896780_SNP [dm6]	C	T	1.802e^-5	0.979	UPSTREAM snoRNA:Psi28S-2566 INTRON CG3902	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
3L	10695016	3L_10695016_SNP [dm3] 3L_10701916_SNP [dm6]	G	A	2.007e^-5	0.979	INTERGENIC
3L	10695012	3L_10695012_SNP [dm3] 3L_10701912_SNP [dm6]	G	T	2.019e^-5	0.979	INTERGENIC
X	2244201	X_2244201_SNP [dm3] X_2350168_SNP [dm6]	C	A	2.087e^-5	0.979	UPSTREAM ptr INTRON ptr	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	7889240	3L_7889240_SNP [dm3] 3L_7896140_SNP [dm6]	C	T	2.115e^-5	0.979	UTR_3_PRIME pbl DOWNSTREAM eIF4E-5
3L	18560093	3L_18560093_SNP [dm3] 3L_18566993_SNP [dm6]	T	A	2.192e^-5	0.979	INTRON AstC-R1
3L	10292364	3L_10292364_SNP [dm3] 3L_10299264_SNP [dm6]	G	A	2.342e^-5	0.979	INTERGENIC	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2L	12231602	2L_12231602_SNP [dm3] 2L_12231602_SNP [dm6]	G	T	2.450e^-5	0.979	INTRON aret
2R	8856210	2R_8856210_SNP [dm3] 2R_12968705_SNP [dm6]	G	T	2.515e^-5	0.979	SYNONYMOUS_CODING Psc	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	21998515	3R_21998515_SNP [dm3] 3R_26172793_SNP [dm6]	A	G	2.683e^-5	0.979	INTRON CG31323
X	19301541	X_19301541_SNP [dm3] X_19407508_SNP [dm6]	T	C	2.706e^-5	0.979	INTRON kek5
3L	4163845	3L_4163845_SNP [dm3] 3L_4163845_SNP [dm6]	T	C	2.717e^-5	0.979	SYNONYMOUS_CODING mas	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	1530819	2L_1530819_INS [dm3] 2L_1530819_INS [dm6]	T	TT	2.883e^-5	0.979	INTERGENIC
3L	7298516	3L_7298516_SNP [dm3] 3L_7305416_SNP [dm6]	T	C	3.184e^-5	0.979	INTRON unc-13-4A
3L	8314617	3L_8314617_SNP [dm3] 3L_8321517_SNP [dm6]	A	C	3.192e^-5	0.979	INTRON CG13670
2R	14318503	2R_14318503_SNP [dm3] 2R_18430998_SNP [dm6]	T	C	3.352e^-5	0.979	UTR_3_PRIME CG30118 DOWNSTREAM CG12263 INTRON CG30118
X	11392200	X_11392200_SNP [dm3] X_11498167_SNP [dm6]	T	G	3.375e^-5	0.979	INTRON Drak
3R	20877075	3R_20877075_SNP [dm3] 3R_25051353_SNP [dm6]	C	T	3.378e^-5	0.979	NON_SYNONYMOUS_CODING CG11791	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	16071344	2R_16071344_SNP [dm3] 2R_20183839_SNP [dm6]	G	A	3.509e^-5	0.979	INTERGENIC
3R	13368067	3R_13368067_SNP [dm3] 3R_17542345_SNP [dm6]	A	G	3.696e^-5	0.979	INTRON SF1
2L	9624477	2L_9624477_SNP [dm3] 2L_9624477_SNP [dm6]	C	A	3.733e^-5	0.979	UTR_3_PRIME CG31882
X	12751137	X_12751137_SNP [dm3] X_12857104_SNP [dm6]	A	G	3.735e^-5	0.979	SYNONYMOUS_CODING CG4661 INTRON Pde9
2L	2809799	2L_2809799_SNP [dm3] 2L_2809799_SNP [dm6]	C	G	3.745e^-5	0.979	SYNONYMOUS_CODING daw	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3L	18914817	3L_18914817_SNP [dm3] 3L_18921717_SNP [dm6]	T	C	3.780e^-5	0.979	DOWNSTREAM CG32204 INTRON CG3819
X	15989787	X_15989787_SNP [dm3] X_16095754_SNP [dm6]	A	C	3.801e^-5	0.979	INTRON CG42354 & 1 other
X	5034832	X_5034832_SNP [dm3] X_5140799_SNP [dm6]	G	C	3.897e^-5	0.979	INTRON rg & 1 other	TF binding site mE1_TFBS_inv
2R	20588700	2R_20588700_SNP [dm3] 2R_24701177_SNP [dm6]	T	A	3.926e^-5	0.979	SYNONYMOUS_CODING Mid1
3L	18889911	3L_18889911_DEL [dm3] 3L_18896811_DEL [dm6]	GTAAATTATTATTATTATCA...	G	3.971e^-5	0.979	UPSTREAM snoRNA:Psi28S-2566 INTRON CG3902	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
X	11565934	X_11565934_SNP [dm3] X_11671901_SNP [dm6]	G	A	4.073e^-5	0.979	INTRON Ptp10D	TF binding site mE1_TFBS_cad
3L	18906963	3L_18906963_SNP [dm3] 3L_18913863_SNP [dm6]	T	C	4.212e^-5	0.979	NON_SYNONYMOUS_CODING CG14077
3L	12414308	3L_12414308_SNP [dm3] 3L_12421208_SNP [dm6]	T	G	4.277e^-5	0.979	INTERGENIC
3R	14529535	3R_14529535_SNP [dm3] 3R_18703813_SNP [dm6]	A	G	4.383e^-5	0.979	INTERGENIC
3R	3774604	3R_3774604_SNP [dm3] 3R_7948882_SNP [dm6]	G	A	4.468e^-5	0.979	INTRON dsx
X	4448661	X_4448661_DEL [dm3] X_4554628_DEL [dm6]	GC	G	4.514e^-5	0.979	UPSTREAM CG11444 INTRON CR32773	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	18882775	3L_18882775_SNP [dm3] 3L_18889675_SNP [dm6]	A	C	4.613e^-5	0.979	INTRON CG3961	TF binding site BDTNP1_TFBS_dl
X	8807753	X_8807753_SNP [dm3] X_8913720_SNP [dm6]	G	C	4.615e^-5	0.979	INTRON rdgA
X	18730754	X_18730754_SNP [dm3] X_18836721_SNP [dm6]	G	T	4.636e^-5	0.979	INTRON Pvf1
X	22108291	X_22108291_SNP [dm3] X_22706455_SNP [dm6]	T	A	4.704e^-5	0.979	INTRON CR44997
3R	7904600	3R_7904600_SNP [dm3] 3R_12078878_SNP [dm6]	A	T	4.734e^-5	0.979	INTRON CG14741	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
X	9092040	X_9092040_SNP [dm3] X_9198007_SNP [dm6]	C	T	5.027e^-5	0.979	SYNONYMOUS_CODING su_r_	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_sna mE1_TFBS_chinmo mE1_TFBS_HSA
3R	11089295	3R_11089295_SNP [dm3] 3R_15263573_SNP [dm6]	C	T	5.027e^-5	0.979	START_GAINED Set UTR_5_PRIME Set UPSTREAM eIF-2gamma & 1 other	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Mad BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_ttk
3L	18913570	3L_18913570_SNP [dm3] 3L_18920470_SNP [dm6]	A	T	5.031e^-5	0.979	UTR_3_PRIME CG3819 UPSTREAM CG18223 DOWNSTREAM CG3819
3R	9679238	3R_9679238_SNP [dm3] 3R_13853516_SNP [dm6]	T	C	5.079e^-5	0.979	INTERGENIC	TF binding site mE1_TFBS_inv
2L	12619135	2L_12619135_SNP [dm3] 2L_12619135_SNP [dm6]	T	C	5.132e^-5	0.979	INTRON Ref2 & 1 other	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_Trl
3L	1363400	3L_1363400_DEL [dm3] 3L_1363400_DEL [dm6]	GGGTG	G	5.141e^-5	0.979	INTRON Ptp61F	TF binding site BDTNP1_TFBS_dl
X	2769334	X_2769334_SNP [dm3] X_2875301_SNP [dm6]	T	A	5.146e^-5	0.979	DOWNSTREAM CG14417 INTRON kirre
2L	12254919	2L_12254919_SNP [dm3] 2L_12254919_SNP [dm6]	T	C	5.180e^-5	0.979	INTRON aret
3L	18882719	3L_18882719_SNP [dm3] 3L_18889619_SNP [dm6]	C	A	5.331e^-5	0.979	INTRON CG3961	TF binding site BDTNP1_TFBS_dl
X	4448664	X_4448664_SNP [dm3] X_4554631_SNP [dm6]	C	T	5.384e^-5	0.979	UPSTREAM CG11444 INTRON CR32773	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	18881979	3L_18881979_SNP [dm3] 3L_18888879_SNP [dm6]	A	T	5.450e^-5	0.979	INTRON CG3961
2L	4111492	2L_4111492_DEL [dm3] 2L_4111492_DEL [dm6]	GG	G	5.510e^-5	0.979	INTRON ed
3L	4160872	3L_4160872_SNP [dm3] 3L_4160872_SNP [dm6]	G	A	5.578e^-5	0.979	UTR_5_PRIME nab DOWNSTREAM mas	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_sens mE1_TFBS_Trl
3L	13239228	3L_13239228_SNP [dm3] 3L_13246128_SNP [dm6]	A	G	5.627e^-5	0.979	DOWNSTREAM CG32119 INTRON caps
2L	2266078	2L_2266078_SNP [dm3] 2L_2266078_SNP [dm6]	A	T	5.648e^-5	0.979	UPSTREAM CG34049 INTERGENIC
3L	10695068	3L_10695068_SNP [dm3] 3L_10701968_SNP [dm6]	A	G	5.765e^-5	0.979	INTERGENIC
X	2245169	X_2245169_DEL [dm3] X_2351136_DEL [dm6]	TT	T	5.789e^-5	0.979	INTRON ptr
2R	12498356	2R_12498356_SNP [dm3] 2R_16610851_SNP [dm6]	A	G	5.835e^-5	0.979	INTRON CG5065
3L	18903040	3L_18903040_SNP [dm3] 3L_18909940_SNP [dm6]	G	A	6.033e^-5	0.979	INTRON Ir75d & 1 other
3L	4163863	3L_4163863_SNP [dm3] 3L_4163863_SNP [dm6]	C	T	6.345e^-5	0.979	SYNONYMOUS_CODING mas	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	16246938	2L_16246938_DEL [dm3] 2L_16246938_DEL [dm6]	TAGTT	T	6.350e^-5	0.979	UTR_3_PRIME PRL-1
X	4954059	X_4954059_INS [dm3] X_5060026_INS [dm6]	G	GG	6.371e^-5	0.979	INTRON CR44833 & 1 other
3L	9806771	3L_9806771_SNP [dm3] 3L_9813671_SNP [dm6]	T	A	6.495e^-5	0.979	UPSTREAM CG43897 INTERGENIC	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
X	7776511	X_7776511_SNP [dm3] X_7882478_SNP [dm6]	C	G	6.562e^-5	0.979	NON_SYNONYMOUS_CODING Ir7f UPSTREAM Ir7e
3L	10741113	3L_10741113_SNP [dm3] 3L_10748013_SNP [dm6]	C	A	6.600e^-5	0.979	INTERGENIC
2R	2874740	2R_2874740_SNP [dm3] 2R_6987235_SNP [dm6]	T	A	6.653e^-5	0.979	INTRON CG17002	TF binding site mE1_TFBS_cad
3R	11580337	3R_11580337_SNP [dm3] 3R_15754615_SNP [dm6]	C	G	6.705e^-5	0.979	INTERGENIC
3L	10109271	3L_10109271_SNP [dm3] 3L_10116171_SNP [dm6]	A	G	6.733e^-5	0.979	INTRON dpr6
X	4539562	X_4539562_SNP [dm3] X_4645529_SNP [dm6]	C	A	6.738e^-5	0.979	UTR_3_PRIME HLH4C UPSTREAM CG3062	TF binding site mE1_TFBS_chinmo
3R	25499425	3R_25499425_SNP [dm3] 3R_29673703_SNP [dm6]	T	C	6.801e^-5	0.979	DOWNSTREAM Bub3 INTRON ppk19
X	22370049	X_22370049_SNP [dm3] X_22968213_SNP [dm6]	T	G	6.882e^-5	0.979	INTERGENIC
3L	10109277	3L_10109277_SNP [dm3] 3L_10116177_SNP [dm6]	G	C	6.891e^-5	0.979	INTRON dpr6
2R	18177092	2R_18177092_SNP [dm3] 2R_22289587_SNP [dm6]	G	T	6.967e^-5	0.979	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sbb
X	5588315	X_5588315_SNP [dm3] X_5694282_SNP [dm6]	A	G	6.986e^-5	0.979	SYNONYMOUS_CODING CG3149	TF binding site BDTNP1_TFBS_twi mE1_TFBS_chinmo
2R	10404253	2R_10404253_SNP [dm3] 2R_14516748_SNP [dm6]	C	A	6.997e^-5	0.979	INTERGENIC
2R	9974008	2R_9974008_SNP [dm3] 2R_14086503_SNP [dm6]	G	A	7.010e^-5	0.979	INTRON Prosap
3R	12146903	3R_12146903_SNP [dm3] 3R_16321181_SNP [dm6]	G	A	7.022e^-5	0.979	UPSTREAM tRNA:F2:89BC & 2 others INTRON Sulf1
2L	1928454	2L_1928454_SNP [dm3] 2L_1928454_SNP [dm6]	C	T	7.043e^-5	0.979	UTR_5_PRIME CG7337 INTRON CG7337
3L	18914844	3L_18914844_SNP [dm3] 3L_18921744_SNP [dm6]	T	A	7.050e^-5	0.979	DOWNSTREAM CG32204 INTRON CG3819
X	22371736	X_22371736_SNP [dm3] X_22969900_SNP [dm6]	A	T	7.080e^-5	0.979	INTERGENIC	transposable element FlyBase
2L	4281093	2L_4281093_SNP [dm3] 2L_4281093_SNP [dm6]	A	T	7.103e^-5	0.979	INTRON Art2	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	7220390	3L_7220390_SNP [dm3] 3L_7227290_SNP [dm6]	A	T	7.242e^-5	0.979	INTERGENIC
X	2244180	X_2244180_SNP [dm3] X_2350147_SNP [dm6]	A	T	7.272e^-5	0.979	UPSTREAM ptr INTRON ptr	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	2158923	2L_2158923_SNP [dm3] 2L_2158923_SNP [dm6]	A	G	7.498e^-5	0.979	SYNONYMOUS_CODING aop	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2R	13081965	2R_13081965_SNP [dm3] 2R_17194460_SNP [dm6]	T	A	7.574e^-5	0.979	UPSTREAM CG10950 INTERGENIC
3L	13864106	3L_13864106_SNP [dm3] 3L_13871006_SNP [dm6]	T	C	7.597e^-5	0.979	UTR_3_PRIME dysc
3L	15696722	3L_15696722_SNP [dm3] 3L_15703622_SNP [dm6]	T	C	7.619e^-5	0.979	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_ftz BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	12086776	3R_12086776_SNP [dm3] 3R_16261054_SNP [dm6]	G	A	7.709e^-5	0.979	DOWNSTREAM tara & 1 other INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_zfh1
3R	7229494	3R_7229494_SNP [dm3] 3R_11403772_SNP [dm6]	T	C	7.751e^-5	0.979	UTR_3_PRIME pros

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Missing results

By genomic position
Variant impact
Gene name

Cuticul_13_11_Me_C25 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results