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=2.470e^-15)
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
No significant result.

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1653 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	3636656	3L_3636656_SNP [dm3] 3L_3636656_SNP [dm6]	C	T	5.742e^-8	0.092	INTRON dar1
3L	3636625	3L_3636625_SNP [dm3] 3L_3636625_SNP [dm6]	G	A	9.760e^-8	0.092	INTRON dar1
3L	1524467	3L_1524467_SNP [dm3] 3L_1524467_SNP [dm6]	C	T	3.169e^-7	0.198	SYNONYMOUS_CODING CG12090
2L	5581237	2L_5581237_SNP [dm3] 2L_5581237_SNP [dm6]	T	A	7.806e^-7	0.366	UPSTREAM CG14011 INTERGENIC
2L	12588491	2L_12588491_SNP [dm3] 2L_12588491_SNP [dm6]	A	G	3.355e^-6	1	INTRON nub
2L	21065643	2L_21065643_SNP [dm3] 2L_21065643_SNP [dm6]	T	A	4.424e^-6	1	INTRON CG9265
X	16002170	X_16002170_SNP [dm3] X_16108137_SNP [dm6]	G	T	5.181e^-6	1	INTERGENIC
2R	8419563	2R_8419563_SNP [dm3] 2R_12532058_SNP [dm6]	G	A	5.618e^-6	1	INTRON fra	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	13915974	3R_13915974_SNP [dm3] 3R_18090252_SNP [dm6]	T	C	6.910e^-6	1	UPSTREAM sr INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	6576444	3L_6576444_SNP [dm3] 3L_6583344_SNP [dm6]	T	C	7.178e^-6	1	INTRON CG18769 & 1 other
2L	12588616	2L_12588616_SNP [dm3] 2L_12588616_SNP [dm6]	A	G	8.608e^-6	1	INTRON nub
X	13668881	X_13668881_SNP [dm3] X_13774848_SNP [dm6]	A	C	1.025e^-5	1	UTR_3_PRIME rdgB INTRON rdgB	TF binding site BDTNP1_TFBS_dl
X	13668882	X_13668882_SNP [dm3] X_13774849_SNP [dm6]	T	A	1.025e^-5	1	UTR_3_PRIME rdgB INTRON rdgB	TF binding site BDTNP1_TFBS_dl
3L	7000779	3L_7000779_SNP [dm3] 3L_7007679_SNP [dm6]	C	T	1.056e^-5	1	INTRON Mp
2R	18596308	2R_18596308_SNP [dm3] 2R_22708803_SNP [dm6]	T	G	1.075e^-5	1	SYNONYMOUS_CODING CG30275 UPSTREAM CR43735
3L	14358347	3L_14358347_SNP [dm3] 3L_14365247_SNP [dm6]	G	A	1.125e^-5	1	INTRON fz	TF binding site BDTNP1_TFBS_dl
2L	12588606	2L_12588606_SNP [dm3] 2L_12588606_SNP [dm6]	A	C	1.162e^-5	1	INTRON nub
3R	15728462	3R_15728462_SNP [dm3] 3R_19902740_SNP [dm6]	G	C	1.269e^-5	1	DOWNSTREAM Surf6 INTRON CG4538	TF binding site BDTNP1_TFBS_dl mE1_TFBS_sens
2L	12588462	2L_12588462_SNP [dm3] 2L_12588462_SNP [dm6]	T	A	1.329e^-5	1	INTRON nub
3L	12166312	3L_12166312_SNP [dm3] 3L_12173212_SNP [dm6]	A	C	1.414e^-5	1	INTRON Rh7
3L	1871663	3L_1871663_DEL [dm3] 3L_1871663_DEL [dm6]	GG	G	1.436e^-5	1	UTR_3_PRIME dre4 DOWNSTREAM CG13924	TF binding site mE1_TFBS_cad
2L	8048314	2L_8048314_SNP [dm3] 2L_8048314_SNP [dm6]	G	A	1.785e^-5	1	SYNONYMOUS_CODING CG7466	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	18270393	3L_18270393_SNP [dm3] 3L_18277293_SNP [dm6]	T	G	1.869e^-5	1	INTERGENIC
2R	11946074	2R_11946074_SNP [dm3] 2R_16058569_SNP [dm6]	T	C	1.882e^-5	1	NON_SYNONYMOUS_CODING CG8405	TF binding site mE1_TFBS_inv
2L	14869117	2L_14869117_SNP [dm3] 2L_14869117_SNP [dm6]	A	T	1.915e^-5	1	INTERGENIC
2L	9060671	2L_9060671_SNP [dm3] 2L_9060671_SNP [dm6]	A	C	2.043e^-5	1	INTRON CG31708	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2R	12635359	2R_12635359_SNP [dm3] 2R_16747854_SNP [dm6]	T	C	2.263e^-5	1	UTR_3_PRIME Acp53C14a DOWNSTREAM Acp53C14a & 1 other
2L	12588627	2L_12588627_SNP [dm3] 2L_12588627_SNP [dm6]	T	C	2.282e^-5	1	INTRON nub
3L	3636022	3L_3636022_SNP [dm3] 3L_3636022_SNP [dm6]	T	A	2.317e^-5	1	INTRON dar1	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
X	3800941	X_3800941_SNP [dm3] X_3906908_SNP [dm6]	G	A	2.419e^-5	1	NON_SYNONYMOUS_CODING CG42541	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3L	6576458	3L_6576458_SNP [dm3] 3L_6583358_SNP [dm6]	C	T	2.434e^-5	1	INTRON CG18769 & 1 other
3L	22459977	3L_22459977_SNP [dm3] 3L_22466877_SNP [dm6]	G	A	2.628e^-5	1	UTR_5_PRIME CG11438	TF binding site BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_inv
2L	19195125	2L_19195125_SNP [dm3] 2L_19195125_SNP [dm6]	C	T	2.770e^-5	1	INTRON drl	regulatory region REDfly_CRMs
2R	12635348	2R_12635348_SNP [dm3] 2R_16747843_SNP [dm6]	A	C	2.837e^-5	1	UTR_3_PRIME Acp53C14a DOWNSTREAM Acp53C14a & 1 other
2L	7971545	2L_7971545_SNP [dm3] 2L_7971545_SNP [dm6]	G	T	2.957e^-5	1	INTRON Snoo
3R	16991774	3R_16991774_SNP [dm3] 3R_21166052_SNP [dm6]	C	T	3.015e^-5	1	DOWNSTREAM CG5810 INTRON SNF4Agamma & 1 other
3L	7920699	3L_7920699_SNP [dm3] 3L_7927599_SNP [dm6]	T	C	3.091e^-5	1	INTRON syd	TF binding site mE1_TFBS_cad
3L	18315019	3L_18315019_SNP [dm3] 3L_18321919_SNP [dm6]	T	A	3.167e^-5	1	INTERGENIC
3L	10372098	3L_10372098_INS [dm3] 3L_10378998_INS [dm6]	C	CAC	3.253e^-5	1	INTERGENIC
3L	6501555	3L_6501555_SNP [dm3] 3L_6508455_SNP [dm6]	G	C	3.409e^-5	1	INTRON sfl
3R	10914917	3R_10914917_SNP [dm3] 3R_15089195_SNP [dm6]	T	C	3.458e^-5	1	INTRON CG6966	TF binding site mE1_TFBS_Trl
3R	15732910	3R_15732910_SNP [dm3] 3R_19907188_SNP [dm6]	T	C	3.622e^-5	1	UPSTREAM CR45047 INTRON RhoGAP92B
2L	779494	2L_779494_SNP [dm3] 2L_779494_SNP [dm6]	C	T	3.672e^-5	1	SYNONYMOUS_CODING CG13947 UPSTREAM Gr21a	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	11349498	3R_11349498_DEL [dm3] 3R_15523776_DEL [dm6]	CCGTGTTC	C	3.727e^-5	1	INTERGENIC
3R	24993584	3R_24993584_SNP [dm3] 3R_29167862_SNP [dm6]	C	T	3.738e^-5	1	SYNONYMOUS_CODING CG11898	TF binding site mE1_TFBS_chinmo
2L	10679099	2L_10679099_SNP [dm3] 2L_10679099_SNP [dm6]	C	A	4.030e^-5	1	NON_SYNONYMOUS_CODING CG17104
3L	6873078	3L_6873078_SNP [dm3] 3L_6879978_SNP [dm6]	T	C	4.138e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	17903812	2R_17903812_SNP [dm3] 2R_22016307_SNP [dm6]	A	G	4.166e^-5	1	INTRON CG34370
3R	16538766	3R_16538766_SNP [dm3] 3R_20713044_SNP [dm6]	A	T	4.209e^-5	1	INTRON Oamb
2R	8313070	2R_8313070_SNP [dm3] 2R_12425565_SNP [dm6]	T	C	4.412e^-5	1	UTR_5_PRIME CG8525 UPSTREAM CG8525 DOWNSTREAM CG8520	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Ubx
3R	16538764	3R_16538764_SNP [dm3] 3R_20713042_SNP [dm6]	C	G	4.473e^-5	1	INTRON Oamb
2R	14694384	2R_14694384_SNP [dm3] 2R_18806879_SNP [dm6]	A	T	4.652e^-5	1	INTRON CR44468 EXON CR44468	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
2R	5591064	2R_5591064_SNP [dm3] 2R_9703559_SNP [dm6]	G	T	4.727e^-5	1	UPSTREAM CG30002 INTERGENIC	TF binding site BDTNP1_TFBS_da
3L	18314994	3L_18314994_SNP [dm3] 3L_18321894_SNP [dm6]	G	A	4.790e^-5	1	INTERGENIC
2R	8305892	2R_8305892_SNP [dm3] 2R_12418387_SNP [dm6]	G	T	4.796e^-5	1	DOWNSTREAM CG42782 & 1 other INTERGENIC
3R	11387837	3R_11387837_SNP [dm3] 3R_15562115_SNP [dm6]	T	C	4.939e^-5	1	INTERGENIC
2R	17525449	2R_17525449_SNP [dm3] 2R_21637944_SNP [dm6]	A	G	4.945e^-5	1	SYNONYMOUS_CODING CG10321 UTR_3_PRIME CG10321	TF binding site mE1_TFBS_cad
2L	12154207	2L_12154207_SNP [dm3] 2L_12154207_SNP [dm6]	A	G	4.949e^-5	1	INTRON CG31760
3L	18269978	3L_18269978_SNP [dm3] 3L_18276878_SNP [dm6]	G	T	5.003e^-5	1	INTERGENIC
2L	12588283	2L_12588283_SNP [dm3] 2L_12588283_SNP [dm6]	T	A	5.064e^-5	1	INTRON nub
3L	6983385	3L_6983385_SNP [dm3] 3L_6990285_SNP [dm6]	C	G	5.200e^-5	1	UPSTREAM bin INTERGENIC	TF binding site mE1_TFBS_Trl
2L	4259586	2L_4259586_SNP [dm3] 2L_4259586_SNP [dm6]	A	C	5.213e^-5	1	DOWNSTREAM CR44080 INTERGENIC
2L	7113783	2L_7113783_SNP [dm3] 2L_7113783_SNP [dm6]	G	T	5.372e^-5	1	INTRON Pvf3
X	16002012	X_16002012_SNP [dm3] X_16107979_SNP [dm6]	T	C	5.463e^-5	1	INTERGENIC
3R	11617750	3R_11617750_SNP [dm3] 3R_15792028_SNP [dm6]	G	A	5.471e^-5	1	NON_SYNONYMOUS_CODING c_3_G UPSTREAM Acyp2	TF binding site BDTNP1_TFBS_dl
2L	12880644	2L_12880644_SNP [dm3] 2L_12880644_SNP [dm6]	G	A	5.479e^-5	1	INTERGENIC
3R	16991750	3R_16991750_DEL [dm3] 3R_21166028_DEL [dm6]	AA	A	5.508e^-5	1	DOWNSTREAM CG5810 INTRON SNF4Agamma & 1 other
X	13483090	X_13483090_DEL [dm3] X_13589057_DEL [dm6]	CA	T	5.555e^-5	1	INTRON Tango13
3R	9986269	3R_9986269_SNP [dm3] 3R_14160547_SNP [dm6]	G	A	5.567e^-5	1	UPSTREAM CG31327 INTERGENIC
2R	9761176	2R_9761176_SNP [dm3] 2R_13873671_SNP [dm6]	T	A	5.617e^-5	1	SYNONYMOUS_CODING shot	TF binding site mE1_TFBS_cad
2R	8305890	2R_8305890_SNP [dm3] 2R_12418385_SNP [dm6]	G	T	5.642e^-5	1	DOWNSTREAM CG42782 & 1 other INTERGENIC
2R	15894081	2R_15894081_SNP [dm3] 2R_20006576_SNP [dm6]	G	A	5.983e^-5	1	UPSTREAM CR44628 INTERGENIC
3R	12897470	3R_12897470_SNP [dm3] 3R_17071748_SNP [dm6]	G	A	6.000e^-5	1	SYNONYMOUS_CODING Ns1 UPSTREAM mRpS11	TF binding site mE1_TFBS_HSA
2R	14156232	2R_14156232_SNP [dm3] 2R_18268727_SNP [dm6]	A	G	6.013e^-5	1	INTERGENIC	TF binding site mE1_TFBS_chinmo
2L	14887713	2L_14887713_SNP [dm3] 2L_14887713_SNP [dm6]	A	G	6.025e^-5	1	INTERGENIC
2L	851442	2L_851442_SNP [dm3] 2L_851442_SNP [dm6]	C	T	6.090e^-5	1	UTR_3_PRIME CG4291 UPSTREAM drongo DOWNSTREAM CR44060	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_h
X	3376485	X_3376485_SNP [dm3] X_3482452_SNP [dm6]	T	C	6.177e^-5	1	UPSTREAM CG10802 & 1 other INTRON CR44999	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_hkb mE1_TFBS_HSA mE1_TFBS_run mE1_TFBS_sens mE1_TFBS_Trl mE1_TFBS_Ubx
2R	5391781	2R_5391781_SNP [dm3] 2R_9504276_SNP [dm6]	T	A	6.264e^-5	1	INTRON brp
2L	2822715	2L_2822715_SNP [dm3] 2L_2822715_SNP [dm6]	C	T	6.500e^-5	1	DOWNSTREAM CG3123 INTRON Duox
2L	4276571	2L_4276571_SNP [dm3] 2L_4276571_SNP [dm6]	T	A	6.614e^-5	1	INTERGENIC
3R	18862991	3R_18862991_SNP [dm3] 3R_23037269_SNP [dm6]	G	A	6.661e^-5	1	INTERGENIC
2L	12759117	2L_12759117_SNP [dm3] 2L_12759117_SNP [dm6]	A	T	6.712e^-5	1	INTERGENIC
2L	5497343	2L_5497343_SNP [dm3] 2L_5497343_SNP [dm6]	T	G	6.724e^-5	1	INTERGENIC
2R	18474864	2R_18474864_SNP [dm3] 2R_22587359_SNP [dm6]	G	T	6.729e^-5	1	INTRON dnr1
3R	27170694	3R_27170694_SNP [dm3] 3R_31344972_SNP [dm6]	G	C	6.742e^-5	1	INTRON CG34347	TF binding site mE1_TFBS_chinmo
X	18660957	X_18660957_SNP [dm3] X_18766924_SNP [dm6]	T	C	6.800e^-5	1	INTRON CCKLR-17D3	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_zfh1
3L	14761296	3L_14761296_SNP [dm3] 3L_14768196_SNP [dm6]	T	C	7.124e^-5	1	SYNONYMOUS_CODING CG17173 DOWNSTREAM CG9384	TF binding site mE1_TFBS_sens
X	4774504	X_4774504_SNP [dm3] X_4880471_SNP [dm6]	G	T	7.154e^-5	1	INTRON CG42594	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	6877152	3L_6877152_SNP [dm3] 3L_6884052_SNP [dm6]	G	A	7.196e^-5	1	UPSTREAM CR45416 INTERGENIC
2R	15894085	2R_15894085_SNP [dm3] 2R_20006580_SNP [dm6]	G	T	7.242e^-5	1	UPSTREAM CR44628 INTERGENIC
3R	20067007	3R_20067007_SNP [dm3] 3R_24241285_SNP [dm6]	G	T	7.369e^-5	1	INTRON mask	TF binding site mE1_TFBS_cad
3L	7547381	3L_7547381_SNP [dm3] 3L_7554281_SNP [dm6]	G	T	7.377e^-5	1	INTERGENIC
2L	10744988	2L_10744988_SNP [dm3] 2L_10744988_SNP [dm6]	G	A	7.528e^-5	1	UTR_3_PRIME CG17124 DOWNSTREAM CG17124
2R	14156160	2R_14156160_SNP [dm3] 2R_18268655_SNP [dm6]	G	T	7.586e^-5	1	INTERGENIC	TF binding site mE1_TFBS_chinmo
2L	852466	2L_852466_SNP [dm3] 2L_852466_SNP [dm6]	G	A	7.600e^-5	1	UPSTREAM kraken INTRON CG4291	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	12187671	2L_12187671_SNP [dm3] 2L_12187671_SNP [dm6]	T	G	7.649e^-5	1	INTRON aret
X	10549758	X_10549758_SNP [dm3] X_10655725_SNP [dm6]	C	T	7.725e^-5	1	INTRON X11Lbeta
2L	4271794	2L_4271794_SNP [dm3] 2L_4271794_SNP [dm6]	C	A	7.864e^-5	1	INTERGENIC
2R	8305905	2R_8305905_SNP [dm3] 2R_12418400_SNP [dm6]	G	A	8.048e^-5	1	DOWNSTREAM CG42782 & 1 other INTERGENIC
3L	22946407	3L_22946407_SNP [dm3] 3L_22953307_SNP [dm6]	C	G	8.167e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA

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By genomic position
Variant impact
Gene name

Sample.size Experience 4 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results