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=9.422e^-2)
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
No significant result.

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
wolba	4.1353	0.042

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

102 significant hits at p-value < 0.001.

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

Chromosome	Position	ID	Reference	Variant	p-value	FDR_BH	Transcript annotation	Binding site annotation
2L	11052038	2L_11052038_INS [dm3] 2L_11052038_INS [dm6]	C	CGTCTTC	3.347e^-4	0.501	INTRON Samuel
2L	11295911	2L_11295911_SNP [dm3] 2L_11295911_SNP [dm6]	C	A	3.347e^-4	0.501	INTERGENIC
2L	12645756	2L_12645756_SNP [dm3] 2L_12645756_SNP [dm6]	A	G	3.347e^-4	0.501	INTRON Ref2
2L	13122123	2L_13122123_SNP [dm3] 2L_13122123_SNP [dm6]	T	G	3.347e^-4	0.501	INTERGENIC
2L	13595183	2L_13595183_SNP [dm3] 2L_13595183_SNP [dm6]	A	G	3.347e^-4	0.501	DOWNSTREAM CG9254 INTRON kuz
2L	13595194	2L_13595194_SNP [dm3] 2L_13595194_SNP [dm6]	T	G	3.347e^-4	0.501	DOWNSTREAM CG9254 INTRON kuz
2L	13595228	2L_13595228_SNP [dm3] 2L_13595228_SNP [dm6]	T	C	3.347e^-4	0.501	DOWNSTREAM CG9254 INTRON kuz
2L	13595325	2L_13595325_SNP [dm3] 2L_13595325_SNP [dm6]	T	G	3.347e^-4	0.501	DOWNSTREAM CG9254 INTRON kuz
2L	13595385	2L_13595385_DEL [dm3] 2L_13595385_DEL [dm6]	AGTTATGTCCTCGC...	A	3.347e^-4	0.501	DOWNSTREAM CG9254 INTRON kuz
2L	13595432	2L_13595432_SNP [dm3] 2L_13595432_SNP [dm6]	A	G	3.347e^-4	0.501	DOWNSTREAM CG9254 INTRON kuz
2L	13610933	2L_13610933_SNP [dm3] 2L_13610933_SNP [dm6]	A	C	3.347e^-4	0.501	DOWNSTREAM mir-2489 INTRON kuz
2L	13888975	2L_13888975_SNP [dm3] 2L_13888975_SNP [dm6]	A	C	3.347e^-4	0.501	INTRON CenG1A	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_cad
2L	13934838	2L_13934838_SNP [dm3] 2L_13934838_SNP [dm6]	C	T	3.347e^-4	0.501	UPSTREAM CG16885 INTRON Ance-3
2L	13998249	2L_13998249_SNP [dm3] 2L_13998249_SNP [dm6]	T	C	3.347e^-4	0.501	INTRON rk
2L	14079154	2L_14079154_SNP [dm3] 2L_14079154_SNP [dm6]	A	G	3.347e^-4	0.501	INTRON nAChRalpha5
2L	14090233	2L_14090233_SNP [dm3] 2L_14090233_SNP [dm6]	A	T	3.347e^-4	0.501	UTR_3_PRIME nAChRalpha5 DOWNSTREAM nAChRalpha5
2L	14323616	2L_14323616_SNP [dm3] 2L_14323616_SNP [dm6]	T	C	3.347e^-4	0.501	SYNONYMOUS_CODING wb	TF binding site mE1_TFBS_cad
2L	14323640	2L_14323640_SNP [dm3] 2L_14323640_SNP [dm6]	A	G	3.347e^-4	0.501	SYNONYMOUS_CODING wb	TF binding site mE1_TFBS_cad
2L	15229708	2L_15229708_SNP [dm3] 2L_15229708_SNP [dm6]	C	T	3.347e^-4	0.501	INTRON ZnT35C
2L	2287380	2L_2287380_SNP [dm3] 2L_2287380_SNP [dm6]	T	C	3.347e^-4	0.501	STOP_LOST CG42658 UPSTREAM CG31681
2L	4009864	2L_4009864_SNP [dm3] 2L_4009864_SNP [dm6]	T	C	3.347e^-4	0.501	DOWNSTREAM CG43774 INTERGENIC
2L	5946420	2L_5946420_SNP [dm3] 2L_5946420_SNP [dm6]	G	T	3.347e^-4	0.501	SYNONYMOUS_CODING Gpdh
2L	617739	2L_617739_SNP [dm3] 2L_617739_SNP [dm6]	G	A	3.347e^-4	0.501	INTERGENIC
2L	6768885	2L_6768885_SNP [dm3] 2L_6768885_SNP [dm6]	T	C	3.347e^-4	0.501	SYNONYMOUS_CODING CG11321 DOWNSTREAM CG11321	TF binding site mE1_TFBS_chinmo
2L	9617725	2L_9617725_SNP [dm3] 2L_9617725_SNP [dm6]	G	C	3.347e^-4	0.501	SYNONYMOUS_CODING GlcAT-S INTRON GlcAT-S	TF binding site BDTNP1_TFBS_dl mE1_TFBS_sens
2R	11522551	2R_11522551_SNP [dm3] 2R_15635046_SNP [dm6]	C	T	3.347e^-4	0.501	INTRON CG42524
2R	12432566	2R_12432566_SNP [dm3] 2R_16545061_SNP [dm6]	A	G	3.347e^-4	0.501	INTERGENIC
2R	14934199	2R_14934199_SNP [dm3] 2R_19046694_SNP [dm6]	G	A	3.347e^-4	0.501	INTERGENIC
2R	15396172	2R_15396172_SNP [dm3] 2R_19508667_SNP [dm6]	T	C	3.347e^-4	0.501	SYNONYMOUS_CODING Ir56b	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	15396184	2R_15396184_SNP [dm3] 2R_19508679_SNP [dm6]	T	C	3.347e^-4	0.501	SYNONYMOUS_CODING Ir56b	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	17323399	2R_17323399_DEL [dm3] 2R_21435894_DEL [dm6]	GG	G	3.347e^-4	0.501	INTRON Sdc
2R	17466599	2R_17466599_SNP [dm3] 2R_21579094_SNP [dm6]	C	T	3.347e^-4	0.501	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	19233439	2R_19233439_SNP [dm3] 2R_23345916_SNP [dm6]	T	A	3.347e^-4	0.501	SYNONYMOUS_CODING CG3502 UPSTREAM CG9863	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	20872329	2R_20872329_SNP [dm3] 2R_24984806_SNP [dm6]	T	G	3.347e^-4	0.501	UTR_5_PRIME emp UPSTREAM emp	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA mE1_TFBS_sens
2R	3440722	2R_3440722_SNP [dm3] 2R_7553217_SNP [dm6]	A	T	3.347e^-4	0.501	INTRON Corin
2R	3610433	2R_3610433_SNP [dm3] 2R_7722928_SNP [dm6]	T	C	3.347e^-4	0.501	UPSTREAM CG18812 INTRON CG18812	TF binding site BDTNP1_TFBS_dl mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
2R	3725850	2R_3725850_SNP [dm3] 2R_7838345_SNP [dm6]	A	G	3.347e^-4	0.501	INTRON Dgk	TF binding site mE1_TFBS_chinmo
2R	3776120	2R_3776120_SNP [dm3] 2R_7888615_SNP [dm6]	A	T	3.347e^-4	0.501	INTERGENIC	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2R	4448986	2R_4448986_SNP [dm3] 2R_8561481_SNP [dm6]	A	G	3.347e^-4	0.501	INTERGENIC
2R	4534783	2R_4534783_SNP [dm3] 2R_8647278_SNP [dm6]	A	G	3.347e^-4	0.501	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cnc mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
2R	6260838	2R_6260838_DEL [dm3] 2R_10373333_DEL [dm6]	CGTTCATATAC...	C	3.347e^-4	0.501	INTRON CG42732
2R	6798075	2R_6798075_SNP [dm3] 2R_10910570_SNP [dm6]	T	C	3.347e^-4	0.501	DOWNSTREAM Obp47a INTERGENIC
2R	8008661	2R_8008661_SNP [dm3] 2R_12121156_SNP [dm6]	A	G	3.347e^-4	0.501	INTERGENIC
2R	9374465	2R_9374465_SNP [dm3] 2R_13486960_SNP [dm6]	C	A	3.347e^-4	0.501	UTR_3_PRIME bbc DOWNSTREAM bbc & 1 other
3L	1023777	3L_1023777_SNP [dm3] 3L_1023777_SNP [dm6]	A	T	3.347e^-4	0.501	UPSTREAM trio INTRON trio
3L	10861730	3L_10861730_SNP [dm3] 3L_10868630_SNP [dm6]	C	T	3.347e^-4	0.501	INTRON tna
3L	12591606	3L_12591606_SNP [dm3] 3L_12598506_SNP [dm6]	C	T	3.347e^-4	0.501	INTERGENIC
3L	1476537	3L_1476537_SNP [dm3] 3L_1476537_SNP [dm6]	A	C	3.347e^-4	0.501	INTRON stet	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	18871364	3L_18871364_SNP [dm3] 3L_18878264_SNP [dm6]	G	A	3.347e^-4	0.501	UTR_3_PRIME CG3961 DOWNSTREAM CG3961 & 1 other
3L	18938553	3L_18938553_SNP [dm3] 3L_18945453_SNP [dm6]	G	T	3.347e^-4	0.501	INTRON CG32204
3L	18938625	3L_18938625_SNP [dm3] 3L_18945525_SNP [dm6]	T	G	3.347e^-4	0.501	INTRON CG32204
3L	18938715	3L_18938715_SNP [dm3] 3L_18945615_SNP [dm6]	G	T	3.347e^-4	0.501	INTRON CG32204
3L	18938716	3L_18938716_SNP [dm3] 3L_18945616_SNP [dm6]	C	G	3.347e^-4	0.501	INTRON CG32204
3L	18938726	3L_18938726_SNP [dm3] 3L_18945626_SNP [dm6]	C	A	3.347e^-4	0.501	INTRON CG32204
3L	18938770	3L_18938770_SNP [dm3] 3L_18945670_SNP [dm6]	T	C	3.347e^-4	0.501	INTRON CG32204
3L	18938777	3L_18938777_SNP [dm3] 3L_18945677_SNP [dm6]	G	A	3.347e^-4	0.501	INTRON CG32204
3L	18938816	3L_18938816_SNP [dm3] 3L_18945716_SNP [dm6]	C	T	3.347e^-4	0.501	INTRON CG32204
3L	18938921	3L_18938921_SNP [dm3] 3L_18945821_SNP [dm6]	G	T	3.347e^-4	0.501	UTR_5_PRIME CG32204
3L	18939003	3L_18939003_SNP [dm3] 3L_18945903_SNP [dm6]	G	A	3.347e^-4	0.501	UTR_5_PRIME CG32204
3L	19147534	3L_19147534_SNP [dm3] 3L_19154434_SNP [dm6]	A	G	3.347e^-4	0.501	INTRON fz2	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	19951432	3L_19951432_SNP [dm3] 3L_19958332_SNP [dm6]	T	C	3.347e^-4	0.501	INTRON Ac76E
3L	2186581	3L_2186581_SNP [dm3] 3L_2186581_SNP [dm6]	A	G	3.347e^-4	0.501	SYNONYMOUS_CODING CG13810	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_twi mE1_TFBS_chinmo mE1_TFBS_HSA
3L	2693141	3L_2693141_SNP [dm3] 3L_2693141_SNP [dm6]	C	T	3.347e^-4	0.501	INTRON Fife
3L	3892726	3L_3892726_SNP [dm3] 3L_3892726_SNP [dm6]	G	A	3.347e^-4	0.501	UTR_5_PRIME Fie UPSTREAM Fie & 1 other DOWNSTREAM snRNA:U11
3L	3894414	3L_3894414_SNP [dm3] 3L_3894414_SNP [dm6]	T	G	3.347e^-4	0.501	UTR_3_PRIME Fie DOWNSTREAM Gr63a
3L	4146894	3L_4146894_SNP [dm3] 3L_4146894_SNP [dm6]	G	C	3.347e^-4	0.501	DOWNSTREAM CG32260 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
3L	5691218	3L_5691218_SNP [dm3] 3L_5698118_SNP [dm6]	G	A	3.347e^-4	0.501	NON_SYNONYMOUS_CODING sif INTRON sif	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	6301502	3L_6301502_SNP [dm3] 3L_6308402_SNP [dm6]	C	G	3.347e^-4	0.501	INTERGENIC	TF binding site BDTNP1_TFBS_prd mE1_TFBS_chinmo mE1_TFBS_HSA
3L	7314673	3L_7314673_SNP [dm3] 3L_7321573_SNP [dm6]	A	C	3.347e^-4	0.501	SYNONYMOUS_CODING RhoGEF4 DOWNSTREAM CG8607
3L	7886763	3L_7886763_SNP [dm3] 3L_7893663_SNP [dm6]	G	A	3.347e^-4	0.501	SYNONYMOUS_CODING CG32365	TF binding site mE1_TFBS_cad
3L	8677557	3L_8677557_SNP [dm3] 3L_8684457_SNP [dm6]	T	G	3.347e^-4	0.501	INTERGENIC
3L	9492852	3L_9492852_SNP [dm3] 3L_9499752_SNP [dm6]	C	G	3.347e^-4	0.501	INTRON path
3R	2719671	3R_2719671_SNP [dm3] 3R_6893949_SNP [dm6]	A	G	3.347e^-4	0.501	UPSTREAM CR45559 INTERGENIC	regulatory region FlyBase REDfly_CRMs silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3R	2730232	3R_2730232_SNP [dm3] 3R_6904510_SNP [dm6]	G	C	3.347e^-4	0.501	INTRON Antp EXON CR43252	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	3409436	3R_3409436_SNP [dm3] 3R_7583714_SNP [dm6]	T	A	3.347e^-4	0.501	INTRON CG34127
3R	4418333	3R_4418333_SNP [dm3] 3R_8592611_SNP [dm6]	C	A	3.347e^-4	0.501	INTRON 5-HT2B
3R	5370332	3R_5370332_SNP [dm3] 3R_9544610_SNP [dm6]	A	T	3.347e^-4	0.501	INTRON mura	TF binding site mE1_TFBS_HSA mE1_TFBS_zfh1
3R	6078980	3R_6078980_SNP [dm3] 3R_10253258_SNP [dm6]	G	C	3.347e^-4	0.501	NON_SYNONYMOUS_CODING CG3999
X	16075006	X_16075006_SNP [dm3] X_16180973_SNP [dm6]	G	A	3.347e^-4	0.501	INTERGENIC
X	20323799	X_20323799_SNP [dm3] X_20452772_SNP [dm6]	T	C	3.347e^-4	0.501	INTRON CG32506	TF binding site BDTNP1_TFBS_twi
X	20397820	X_20397820_SNP [dm3] X_20526793_SNP [dm6]	G	C	3.347e^-4	0.501	UPSTREAM CG42579 INTERGENIC
X	2834241	X_2834241_SNP [dm3] X_2940208_SNP [dm6]	G	C	3.347e^-4	0.501	SYNONYMOUS_CODING CG14420 INTRON kirre	TF binding site mE1_TFBS_eve mE1_TFBS_HSA
X	5222817	X_5222817_SNP [dm3] X_5328784_SNP [dm6]	G	A	3.347e^-4	0.501	SYNONYMOUS_CODING CG3309	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_chinmo mE1_TFBS_HSA
X	6141091	X_6141091_SNP [dm3] X_6247058_SNP [dm6]	A	C	3.347e^-4	0.501	SYNONYMOUS_CODING Rbcn-3A	TF binding site BDTNP1_TFBS_Mad BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	12799499	2L_12799499_SNP [dm3] 2L_12799499_SNP [dm6]	C	T	6.142e^-4	0.501	INTERGENIC
3L	18848602	3L_18848602_SNP [dm3] 3L_18855502_SNP [dm6]	T	G	6.142e^-4	0.501	DOWNSTREAM CR45387 INTERGENIC	TF binding site BDTNP1_TFBS_dl
3L	18936691	3L_18936691_DEL [dm3] 3L_18943591_DEL [dm6]	AA	A	6.142e^-4	0.501	INTRON CG32204
3L	2285957	3L_2285957_DEL [dm3] 3L_2285957_DEL [dm6]	AGGCGCCATATCA...	A	6.142e^-4	0.501	INTRON MsR2
3R	2606326	3R_2606326_SNP [dm3] 3R_6780604_SNP [dm6]	A	G	6.142e^-4	0.501	DOWNSTREAM CR42721 INTERGENIC	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb mE1_TFBS_bab1 mE1_TFBS_HSA
3R	4133312	3R_4133312_SNP [dm3] 3R_8307590_SNP [dm6]	C	T	6.142e^-4	0.501	SYNONYMOUS_CODING tex DOWNSTREAM mir-4918	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
X	15273591	X_15273591_SNP [dm3] X_15379558_SNP [dm6]	G	A	6.142e^-4	0.501	UPSTREAM acj6 DOWNSTREAM CG9164 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_chinmo mE1_TFBS_HSA
2L	13595193	2L_13595193_SNP [dm3] 2L_13595193_SNP [dm6]	T	G	6.692e^-4	0.501	DOWNSTREAM CG9254 INTRON kuz
2L	13595436	2L_13595436_SNP [dm3] 2L_13595436_SNP [dm6]	A	T	6.692e^-4	0.501	DOWNSTREAM CG9254 INTRON kuz
2R	10548429	2R_10548429_SNP [dm3] 2R_14660924_SNP [dm6]	A	C	6.692e^-4	0.501	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	10548441	2R_10548441_INS [dm3] 2R_14660936_INS [dm6]	C	CAATAC	6.692e^-4	0.501	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	12851431	2R_12851431_SNP [dm3] 2R_16963926_SNP [dm6]	C	G	6.692e^-4	0.501	UPSTREAM CR44376 INTERGENIC
2R	17301190	2R_17301190_SNP [dm3] 2R_21413685_SNP [dm6]	T	A	6.692e^-4	0.501	INTRON Sdc
2R	7120624	2R_7120624_SNP [dm3] 2R_11233119_SNP [dm6]	T	A	6.692e^-4	0.501	UPSTREAM metro & 1 other DOWNSTREAM CG13218 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_Trl
3R	2726859	3R_2726859_SNP [dm3] 3R_6901137_SNP [dm6]	G	A	6.692e^-4	0.501	INTRON Antp
3R	3081448	3R_3081448_SNP [dm3] 3R_7255726_SNP [dm6]	C	T	6.692e^-4	0.501	INTRON Gld
3R	5693621	3R_5693621_SNP [dm3] 3R_9867899_SNP [dm6]	T	A	6.692e^-4	0.501	UTR_5_PRIME Teh1	TF binding site BDTNP1_TFBS_dl
3R	6078994	3R_6078994_SNP [dm3] 3R_10253272_SNP [dm6]	C	G	6.692e^-4	0.501	NON_SYNONYMOUS_CODING CG3999

By genomic position
Variant impact
Gene name

Mating_p_value phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results