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=1.296e^-2)
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	0.02872
In_3R_K	9.861e-05

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	8.8052	0.0122

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2411 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	14439953	2R_14439953_SNP [dm3] 2R_18552448_SNP [dm6]	A	G	1.283e^-6	0.658	INTERGENIC
3L	12746288	3L_12746288_SNP [dm3] 3L_12753188_SNP [dm6]	A	C	1.970e^-6	0.658	UTR_3_PRIME CG10984 DOWNSTREAM CG10973
3R	17535726	3R_17535726_SNP [dm3] 3R_21710004_SNP [dm6]	A	C	2.338e^-6	0.658	INTRON CG31176
2L	9982629	2L_9982629_SNP [dm3] 2L_9982629_SNP [dm6]	T	G	2.641e^-6	0.658	INTERGENIC	regulatory region REDfly_CRMs
2L	11971634	2L_11971634_SNP [dm3] 2L_11971634_SNP [dm6]	C	T	2.949e^-6	0.658	UPSTREAM CR43314 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
3R	9900597	3R_9900597_SNP [dm3] 3R_14074875_SNP [dm6]	A	C	3.135e^-6	0.658	INTRON foxo
X	20891586	X_20891586_SNP [dm3] X_21020559_SNP [dm6]	G	A	3.161e^-6	0.658	INTERGENIC
3R	17537127	3R_17537127_SNP [dm3] 3R_21711405_SNP [dm6]	G	A	3.384e^-6	0.658	INTRON CG31176
2L	20934671	2L_20934671_SNP [dm3] 2L_20934671_SNP [dm6]	G	A	3.526e^-6	0.658	UPSTREAM CG9270 INTERGENIC
3L	12751160	3L_12751160_SNP [dm3] 3L_12758060_SNP [dm6]	C	A	3.596e^-6	0.658	SYNONYMOUS_CODING CG32113	TF binding site mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens
3R	17536443	3R_17536443_DEL [dm3] 3R_21710721_DEL [dm6]	GGCAGAACTGATTG...	G	3.857e^-6	0.658	INTRON CG31176
2L	14865403	2L_14865403_SNP [dm3] 2L_14865403_SNP [dm6]	C	A	4.805e^-6	0.704	INTERGENIC
3R	25818024	3R_25818024_SNP [dm3] 3R_29992302_SNP [dm6]	A	G	5.608e^-6	0.704	SYNONYMOUS_CODING Acph-1	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2L	14865404	2L_14865404_SNP [dm3] 2L_14865404_SNP [dm6]	C	A	5.863e^-6	0.704	INTERGENIC
2R	14439785	2R_14439785_SNP [dm3] 2R_18552280_SNP [dm6]	A	C	6.227e^-6	0.704	INTERGENIC
2R	14428637	2R_14428637_SNP [dm3] 2R_18541132_SNP [dm6]	C	G	6.996e^-6	0.704	INTRON Rgk2	TF binding site mE1_TFBS_chinmo
3R	10077896	3R_10077896_SNP [dm3] 3R_14252174_SNP [dm6]	C	A	7.170e^-6	0.704	INTRON Aats-met
3L	5903135	3L_5903135_SNP [dm3] 3L_5910035_SNP [dm6]	G	A	7.400e^-6	0.704	DOWNSTREAM CG13288 INTRON CG13288
3L	12746313	3L_12746313_SNP [dm3] 3L_12753213_SNP [dm6]	C	T	7.998e^-6	0.704	UTR_3_PRIME CG10984 DOWNSTREAM CG10973
3L	12751154	3L_12751154_SNP [dm3] 3L_12758054_SNP [dm6]	A	C	8.161e^-6	0.704	SYNONYMOUS_CODING CG32113	TF binding site mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens
3L	11039110	3L_11039110_SNP [dm3] 3L_11046010_SNP [dm6]	A	G	9.464e^-6	0.704	INTRON CG43693	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Trl
2R	14428646	2R_14428646_SNP [dm3] 2R_18541141_SNP [dm6]	A	G	1.054e^-5	0.704	INTRON Rgk2	TF binding site mE1_TFBS_chinmo
3L	9423062	3L_9423062_SNP [dm3] 3L_9429962_SNP [dm6]	C	A	1.104e^-5	0.704	UPSTREAM MTF-1 & 2 others INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Ubx
2L	11971518	2L_11971518_SNP [dm3] 2L_11971518_SNP [dm6]	G	A	1.266e^-5	0.704	UPSTREAM CR43314 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_eve mE1_TFBS_HSA mE1_TFBS_Trl
3L	5903378	3L_5903378_SNP [dm3] 3L_5910278_SNP [dm6]	C	T	1.300e^-5	0.704	DOWNSTREAM CG13288 INTRON CG13288
2R	19063283	2R_19063283_SNP [dm3] 2R_23175760_SNP [dm6]	C	A	1.490e^-5	0.704	INTRON CG34371
2R	16678625	2R_16678625_SNP [dm3] 2R_20791120_SNP [dm6]	G	T	1.615e^-5	0.704	UTR_5_PRIME CG43677 UPSTREAM CG43667 DOWNSTREAM CG43668
2R	12105168	2R_12105168_DEL [dm3] 2R_16217663_DEL [dm6]	AA	A	1.625e^-5	0.704	INTRON mrj	TF binding site BDTNP1_TFBS_da
2R	9143376	2R_9143376_SNP [dm3] 2R_13255871_SNP [dm6]	T	A	1.745e^-5	0.704	UPSTREAM CR44343 & 1 other INTERGENIC
2L	20934675	2L_20934675_SNP [dm3] 2L_20934675_SNP [dm6]	C	G	1.773e^-5	0.704	UPSTREAM CG9270 INTERGENIC
2R	8341093	2R_8341093_SNP [dm3] 2R_12453588_SNP [dm6]	A	G	1.816e^-5	0.704	SYNONYMOUS_CODING Lac DOWNSTREAM Dyb	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2R	6807246	2R_6807246_SNP [dm3] 2R_10919741_SNP [dm6]	G	T	1.833e^-5	0.704	INTERGENIC	TF binding site mE1_TFBS_inv
3R	19282495	3R_19282495_SNP [dm3] 3R_23456773_SNP [dm6]	C	A	1.845e^-5	0.704	INTRON CG4374
2L	529905	2L_529905_SNP [dm3] 2L_529905_SNP [dm6]	T	G	1.891e^-5	0.704	INTRON ush	regulatory region REDfly_CRMs
3L	11798983	3L_11798983_SNP [dm3] 3L_11805883_SNP [dm6]	G	A	1.905e^-5	0.704	SPLICE_SITE_REGION CG42255 SYNONYMOUS_CODING CG42255
3L	12743868	3L_12743868_SNP [dm3] 3L_12750768_SNP [dm6]	T	C	1.905e^-5	0.704	UPSTREAM Klc INTRON CG10984	TF binding site BDTNP1_TFBS_dl mE1_TFBS_ttk
2L	1605945	2L_1605945_SNP [dm3] 2L_1605945_SNP [dm6]	G	C	1.963e^-5	0.704	INTRON CG31935 & 1 other
3R	24165640	3R_24165640_INS [dm3] 3R_28339918_INS [dm6]	T	TT	2.032e^-5	0.704	UPSTREAM Moca-cyp & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	15310274	2R_15310274_SNP [dm3] 2R_19422769_SNP [dm6]	A	C	2.039e^-5	0.704	INTRON hts	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_Trl
X	12421844	X_12421844_SNP [dm3] X_12527811_SNP [dm6]	A	T	2.040e^-5	0.704	INTRON CG43921	TF binding site BDTNP1_TFBS_dl
2L	11922449	2L_11922449_SNP [dm3] 2L_11922449_SNP [dm6]	T	A	2.041e^-5	0.704	INTRON Pde1c
2L	14845093	2L_14845093_SNP [dm3] 2L_14845093_SNP [dm6]	T	A	2.089e^-5	0.704	UTR_3_PRIME CG15279
3R	16101081	3R_16101081_SNP [dm3] 3R_20275359_SNP [dm6]	C	T	2.134e^-5	0.704	INTRON cic
2R	16972214	2R_16972214_SNP [dm3] 2R_21084709_SNP [dm6]	C	T	2.243e^-5	0.704	INTRON Treh	TF binding site mE1_TFBS_cad
X	12421798	X_12421798_SNP [dm3] X_12527765_SNP [dm6]	C	T	2.279e^-5	0.704	INTRON CG43921	TF binding site BDTNP1_TFBS_dl
3R	27086228	3R_27086228_SNP [dm3] 3R_31260506_SNP [dm6]	T	A	2.362e^-5	0.704	DOWNSTREAM CG3669 INTRON CG18672
X	12421912	X_12421912_SNP [dm3] X_12527879_SNP [dm6]	A	T	2.392e^-5	0.704	INTRON CG43921
3R	7924718	3R_7924718_DEL [dm3] 3R_12098996_DEL [dm6]	TGGCTT	T	2.431e^-5	0.704	INTRON dpr17	TF binding site mE1_TFBS_HSA
3R	10910192	3R_10910192_SNP [dm3] 3R_15084470_SNP [dm6]	G	T	2.453e^-5	0.704	INTRON CG6966
2R	14222071	2R_14222071_SNP [dm3] 2R_18334566_SNP [dm6]	A	G	2.602e^-5	0.704	INTRON sbb	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
3R	23321143	3R_23321143_SNP [dm3] 3R_27495421_SNP [dm6]	C	A	2.611e^-5	0.704	INTERGENIC
3L	9514910	3L_9514910_SNP [dm3] 3L_9521810_SNP [dm6]	G	A	2.688e^-5	0.704	INTRON CG33700
2R	15310115	2R_15310115_SNP [dm3] 2R_19422610_SNP [dm6]	C	A	2.700e^-5	0.704	INTRON hts	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	14844884	2L_14844884_DEL [dm3] 2L_14844884_DEL [dm6]	GGG	G	2.749e^-5	0.704	DOWNSTREAM CG15279 INTERGENIC
3L	12751118	3L_12751118_SNP [dm3] 3L_12758018_SNP [dm6]	G	A	2.783e^-5	0.704	SYNONYMOUS_CODING CG32113	TF binding site mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens
2L	7555667	2L_7555667_SNP [dm3] 2L_7555667_SNP [dm6]	G	A	2.833e^-5	0.704	INTRON RapGAP1
3R	16428632	3R_16428632_SNP [dm3] 3R_20602910_SNP [dm6]	T	C	2.868e^-5	0.704	INTRON bon
3R	8888424	3R_8888424_SNP [dm3] 3R_13062702_SNP [dm6]	G	T	2.880e^-5	0.704	UTR_5_PRIME sim INTRON sim
X	20891561	X_20891561_SNP [dm3] X_21020534_SNP [dm6]	C	G	2.887e^-5	0.704	INTERGENIC
2R	14218128	2R_14218128_SNP [dm3] 2R_18330623_SNP [dm6]	T	A	2.936e^-5	0.704	INTRON sbb
2L	7680333	2L_7680333_DEL [dm3] 2L_7680333_DEL [dm6]	ATCTATATA	A	2.944e^-5	0.704	INTRON Myo28B1
3R	16101208	3R_16101208_SNP [dm3] 3R_20275486_SNP [dm6]	C	G	2.956e^-5	0.704	INTRON cic	TF binding site BDTNP1_TFBS_twi
2R	14222063	2R_14222063_SNP [dm3] 2R_18334558_SNP [dm6]	C	T	2.962e^-5	0.704	INTRON sbb	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
2L	11209332	2L_11209332_SNP [dm3] 2L_11209332_SNP [dm6]	A	T	2.962e^-5	0.704	INTERGENIC	silencer mE1_HDAC_PRE
X	13750063	X_13750063_SNP [dm3] X_13856030_SNP [dm6]	G	A	2.982e^-5	0.704	SYNONYMOUS_CODING mamo	TF binding site BDTNP1_TFBS_sna mE1_TFBS_chinmo mE1_TFBS_HSA
3L	17098153	3L_17098153_SNP [dm3] 3L_17105053_SNP [dm6]	A	C	3.013e^-5	0.704	INTRON Rbp6
2R	14219663	2R_14219663_SNP [dm3] 2R_18332158_SNP [dm6]	A	T	3.032e^-5	0.704	INTRON sbb	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_inv
3L	9423064	3L_9423064_SNP [dm3] 3L_9429964_SNP [dm6]	C	T	3.106e^-5	0.704	UPSTREAM MTF-1 & 2 others INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Ubx
2L	11971458	2L_11971458_SNP [dm3] 2L_11971458_SNP [dm6]	A	T	3.140e^-5	0.704	UPSTREAM CR43314 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_eve mE1_TFBS_HSA mE1_TFBS_Trl
X	8914043	X_8914043_SNP [dm3] X_9020010_SNP [dm6]	T	A	3.176e^-5	0.704	SYNONYMOUS_CODING rdgA INTRON CR43836
3L	19285729	3L_19285729_SNP [dm3] 3L_19292629_SNP [dm6]	G	A	3.185e^-5	0.704	UTR_5_PRIME Gbs-76A UPSTREAM Gbs-76A	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_Trl
2L	14845112	2L_14845112_SNP [dm3] 2L_14845112_SNP [dm6]	A	T	3.223e^-5	0.704	UTR_3_PRIME CG15279
3L	9423034	3L_9423034_SNP [dm3] 3L_9429934_SNP [dm6]	A	T	3.287e^-5	0.704	UPSTREAM MTF-1 & 2 others INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Ubx
2R	3896214	2R_3896214_SNP [dm3] 2R_8008709_SNP [dm6]	T	A	3.293e^-5	0.704	DOWNSTREAM CG14762 INTRON Odc2	TF binding site mE1_TFBS_cad
3R	16101062	3R_16101062_DEL [dm3] 3R_20275340_DEL [dm6]	CGCCTACTGGCG...	C	3.364e^-5	0.704	INTRON cic
2R	14221804	2R_14221804_SNP [dm3] 2R_18334299_SNP [dm6]	A	T	3.376e^-5	0.704	INTRON sbb
3R	9730205	3R_9730205_SNP [dm3] 3R_13904483_SNP [dm6]	A	T	3.462e^-5	0.704	UTR_3_PRIME ems
3R	16428653	3R_16428653_SNP [dm3] 3R_20602931_SNP [dm6]	G	A	3.509e^-5	0.704	INTRON bon
3L	7307650	3L_7307650_SNP [dm3] 3L_7314550_SNP [dm6]	A	T	3.601e^-5	0.704	INTERGENIC
2L	11209417	2L_11209417_SNP [dm3] 2L_11209417_SNP [dm6]	C	T	3.608e^-5	0.704	INTERGENIC	silencer mE1_HDAC_PRE
2R	9343449	2R_9343449_SNP [dm3] 2R_13455944_SNP [dm6]	T	C	3.652e^-5	0.704	INTRON arr
2R	9143032	2R_9143032_INS [dm3] 2R_13255527_INS [dm6]	T	TATTT	3.714e^-5	0.704	UPSTREAM CR44343 INTERGENIC
2R	9601281	2R_9601281_SNP [dm3] 2R_13713776_SNP [dm6]	A	G	3.769e^-5	0.704	SYNONYMOUS_CODING fas
2R	14219961	2R_14219961_SNP [dm3] 2R_18332456_SNP [dm6]	T	C	3.772e^-5	0.704	INTRON sbb	TF binding site mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_run
2L	14845108	2L_14845108_SNP [dm3] 2L_14845108_SNP [dm6]	G	A	3.787e^-5	0.704	UTR_3_PRIME CG15279
2R	11585720	2R_11585720_SNP [dm3] 2R_15698215_SNP [dm6]	T	G	3.795e^-5	0.704	DOWNSTREAM CG30080 & 2 others INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA
3L	11426987	3L_11426987_SNP [dm3] 3L_11433887_SNP [dm6]	C	T	3.796e^-5	0.704	DOWNSTREAM CG6149 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_Kr
3L	9423024	3L_9423024_SNP [dm3] 3L_9429924_SNP [dm6]	G	A	3.920e^-5	0.704	UPSTREAM MTF-1 & 2 others INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Ubx
3R	10910191	3R_10910191_SNP [dm3] 3R_15084469_SNP [dm6]	A	G	3.933e^-5	0.704	INTRON CG6966
2L	8499587	2L_8499587_SNP [dm3] 2L_8499587_SNP [dm6]	C	T	3.952e^-5	0.704	INTRON Dh31
2R	7458085	2R_7458085_SNP [dm3] 2R_11570580_SNP [dm6]	A	G	3.981e^-5	0.704	INTERGENIC
3L	7777775	3L_7777775_SNP [dm3] 3L_7784675_SNP [dm6]	T	A	4.000e^-5	0.704	INTRON CG32369
2L	14844900	2L_14844900_SNP [dm3] 2L_14844900_SNP [dm6]	C	A	4.055e^-5	0.704	DOWNSTREAM CG15279 INTERGENIC
X	21870030	X_21870030_SNP [dm3] X_22468194_SNP [dm6]	G	C	4.073e^-5	0.704	UTR_3_PRIME CG14619
2R	3578052	2R_3578052_SNP [dm3] 2R_7690547_SNP [dm6]	A	T	4.111e^-5	0.704	INTRON CG1399
3R	22731664	3R_22731664_SNP [dm3] 3R_26905942_SNP [dm6]	T	C	4.114e^-5	0.704	INTRON T48	regulatory region REDfly_CRMs
3R	9900625	3R_9900625_SNP [dm3] 3R_14074903_SNP [dm6]	A	G	4.118e^-5	0.704	INTRON foxo
2L	17098035	2L_17098035_SNP [dm3] 2L_17098035_SNP [dm6]	T	A	4.120e^-5	0.704	INTERGENIC
3L	12750071	3L_12750071_SNP [dm3] 3L_12756971_SNP [dm6]	G	A	4.156e^-5	0.704	SYNONYMOUS_CODING CG32113	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	12289675	3R_12289675_SNP [dm3] 3R_16463953_SNP [dm6]	A	C	4.187e^-5	0.704	NON_SYNONYMOUS_CODING CG42232	TF binding site mE1_TFBS_sens

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Missing results

By genomic position
Variant impact
Gene name

Cuticul_2_Me_C26_C27 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results