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=1.426e^-24)
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	0.09802

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
wolba	2.7135	0.0995

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
3L	7300051	3L_7300051_SNP [dm3] 3L_7306951_SNP [dm6]	T	G	1.640e^-6	0.928	INTRON unc-13-4A
X	18531878	X_18531878_INS [dm3] X_18637845_INS [dm6]	G	GAGG	1.746e^-6	0.928	INTRON Rip11	TF binding site mE1_TFBS_cad
2R	18066056	2R_18066056_SNP [dm3] 2R_22178551_SNP [dm6]	G	C	2.378e^-6	0.928	INTRON CG11170	TF binding site BDTNP1_TFBS_twi
2L	10774719	2L_10774719_DEL [dm3] 2L_10774719_DEL [dm6]	TGCAGCAT	T	2.381e^-6	0.928	INTRON CG31869
3R	15854656	3R_15854656_SNP [dm3] 3R_20028934_SNP [dm6]	G	T	3.256e^-6	0.928	SYNONYMOUS_CODING CG4854 UPSTREAM CG4424 DOWNSTREAM trem	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med
3R	15177463	3R_15177463_SNP [dm3] 3R_19351741_SNP [dm6]	A	C	3.574e^-6	0.928	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi
2R	18066632	2R_18066632_SNP [dm3] 2R_22179127_SNP [dm6]	C	A	5.580e^-6	0.928	UPSTREAM CG11170 & 1 other INTRON CG11170	TF binding site BDTNP1_TFBS_twi
3R	15588617	3R_15588617_SNP [dm3] 3R_19762895_SNP [dm6]	C	A	5.825e^-6	0.928	INTRON GluClalpha
X	20464341	X_20464341_DEL [dm3] X_20593314_DEL [dm6]	TTT	T	6.844e^-6	0.928	INTRON RunxA
X	20464347	X_20464347_INS [dm3] X_20593320_INS [dm6]	A	AA	6.844e^-6	0.928	INTRON RunxA
X	13508094	X_13508094_SNP [dm3] X_13614061_SNP [dm6]	C	A	7.219e^-6	0.928	UTR_3_PRIME tth DOWNSTREAM BthD
3L	17480449	3L_17480449_SNP [dm3] 3L_17487349_SNP [dm6]	C	T	8.090e^-6	0.928	UPSTREAM Oatp74D INTRON Oatp74D	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl mE1_TFBS_zfh1
2R	14761088	2R_14761088_SNP [dm3] 2R_18873583_SNP [dm6]	G	A	8.240e^-6	0.928	INTERGENIC
X	20643540	X_20643540_SNP [dm3] X_20772513_SNP [dm6]	A	G	1.074e^-5	0.928	UTR_3_PRIME shakB
3L	21875246	3L_21875246_DEL [dm3] 3L_21882146_DEL [dm6]	TAATT	T	1.236e^-5	0.928	INTRON mub
X	20464339	X_20464339_SNP [dm3] X_20593312_SNP [dm6]	T	C	1.303e^-5	0.928	INTRON RunxA
3R	19406737	3R_19406737_SNP [dm3] 3R_23581015_SNP [dm6]	T	G	1.324e^-5	0.928	DOWNSTREAM beat-IV INTERGENIC
3R	15177422	3R_15177422_SNP [dm3] 3R_19351700_SNP [dm6]	G	A	1.406e^-5	0.928	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi
X	20017198	X_20017198_SNP [dm3] X_20123165_SNP [dm6]	T	A	1.454e^-5	0.928	DOWNSTREAM CG34331 INTRON CG34331
3R	19406738	3R_19406738_SNP [dm3] 3R_23581016_SNP [dm6]	T	A	1.561e^-5	0.928	DOWNSTREAM beat-IV INTERGENIC
2L	6891014	2L_6891014_SNP [dm3] 2L_6891014_SNP [dm6]	A	T	1.653e^-5	0.928	INTRON Nlg2
3R	19406716	3R_19406716_DEL [dm3] 3R_23580994_DEL [dm6]	AGTTATTTAAGGAATACTTG...	A	1.701e^-5	0.928	DOWNSTREAM beat-IV INTERGENIC
2R	14761004	2R_14761004_SNP [dm3] 2R_18873499_SNP [dm6]	G	T	1.706e^-5	0.928	INTERGENIC
2L	12379846	2L_12379846_SNP [dm3] 2L_12379846_SNP [dm6]	G	T	1.745e^-5	0.928	INTRON bru-2
X	20464273	X_20464273_SNP [dm3] X_20593246_SNP [dm6]	A	C	1.768e^-5	0.928	INTRON RunxA
3R	24021172	3R_24021172_SNP [dm3] 3R_28195450_SNP [dm6]	T	G	1.953e^-5	0.928	INTRON CG34354
2L	15093810	2L_15093810_SNP [dm3] 2L_15093810_SNP [dm6]	C	A	1.999e^-5	0.928	INTRON CG15270
3L	7291511	3L_7291511_SNP [dm3] 3L_7298411_SNP [dm6]	T	G	2.023e^-5	0.928	INTRON unc-13-4A
X	19387046	X_19387046_SNP [dm3] X_19493013_SNP [dm6]	G	A	2.089e^-5	0.928	DOWNSTREAM CG12204 INTRON CG12203	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_slp1 mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
X	3890661	X_3890661_DEL [dm3] X_3996628_DEL [dm6]	TGCCCATTGATACGT...	T	2.224e^-5	0.928	INTERGENIC
X	13449367	X_13449367_SNP [dm3] X_13555334_SNP [dm6]	A	T	2.237e^-5	0.928	UTR_5_PRIME CG11816
X	4223747	X_4223747_INS [dm3] X_4329714_INS [dm6]	C	CC	2.290e^-5	0.928	UPSTREAM CG12693 INTRON norpA
3L	7300053	3L_7300053_SNP [dm3] 3L_7306953_SNP [dm6]	G	A	2.376e^-5	0.928	INTRON unc-13-4A
3L	18117510	3L_18117510_SNP [dm3] 3L_18124410_SNP [dm6]	G	A	2.431e^-5	0.928	INTERGENIC
3L	947106	3L_947106_SNP [dm3] 3L_947106_SNP [dm6]	C	A	2.436e^-5	0.928	INTRON Glut1
2L	16011789	2L_16011789_SNP [dm3] 2L_16011789_SNP [dm6]	A	G	2.445e^-5	0.928	INTRON beat-Ic
X	18255037	X_18255037_SNP [dm3] X_18361004_SNP [dm6]	A	G	2.481e^-5	0.928	INTRON CG6106
3L	9525834	3L_9525834_SNP [dm3] 3L_9532734_SNP [dm6]	T	C	2.560e^-5	0.928	INTERGENIC
2L	3142277	2L_3142277_SNP [dm3] 2L_3142277_SNP [dm6]	A	G	2.703e^-5	0.928	INTRON toc
3L	21869633	3L_21869633_SNP [dm3] 3L_21876533_SNP [dm6]	G	A	2.737e^-5	0.928	INTRON mub
X	4284571	X_4284571_SNP [dm3] X_4390538_SNP [dm6]	A	G	2.754e^-5	0.928	INTRON CR32773	TF binding site mE1_TFBS_Kr
2L	14346737	2L_14346737_INS [dm3] 2L_14346737_INS [dm6]	A	AA	2.759e^-5	0.928	UPSTREAM Send2 DOWNSTREAM CG33090 & 1 other INTERGENIC
2L	6890913	2L_6890913_SNP [dm3] 2L_6890913_SNP [dm6]	T	A	2.763e^-5	0.928	INTRON Nlg2
2R	17419550	2R_17419550_SNP [dm3] 2R_21532045_SNP [dm6]	T	A	2.875e^-5	0.928	INTRON Egfr EXON CR44725
3L	1035418	3L_1035418_SNP [dm3] 3L_1035418_SNP [dm6]	G	A	3.083e^-5	0.928	SYNONYMOUS_CODING CG9205 UPSTREAM trio DOWNSTREAM bab1	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
X	18038392	X_18038392_SNP [dm3] X_18144359_SNP [dm6]	A	C	3.109e^-5	0.928	INTERGENIC
2L	14346984	2L_14346984_SNP [dm3] 2L_14346984_SNP [dm6]	G	T	3.163e^-5	0.928	UPSTREAM Send2 DOWNSTREAM mTTF INTERGENIC
X	4609555	X_4609555_SNP [dm3] X_4715522_SNP [dm6]	C	T	3.173e^-5	0.928	INTRON Proc-R
2R	1919997	2R_1919997_SNP [dm3] 2R_6032492_SNP [dm6]	C	A	3.224e^-5	0.928	NON_SYNONYMOUS_CODING SCAP
X	13449365	X_13449365_SNP [dm3] X_13555332_SNP [dm6]	G	T	3.270e^-5	0.928	UTR_5_PRIME CG11816
3L	15643669	3L_15643669_SNP [dm3] 3L_15650569_SNP [dm6]	A	G	3.320e^-5	0.928	UPSTREAM Eig71Ea & 1 other DOWNSTREAM Eig71Ec & 1 other INTERGENIC
2L	10535826	2L_10535826_SNP [dm3] 2L_10535826_SNP [dm6]	C	T	3.331e^-5	0.928	SYNONYMOUS_CODING CG18302
X	3967535	X_3967535_SNP [dm3] X_4073502_SNP [dm6]	C	A	3.337e^-5	0.928	INTERGENIC	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2R	2741145	2R_2741145_DEL [dm3] 2R_6853640_DEL [dm6]	CGC	C	3.425e^-5	0.928	INTERGENIC
2R	14895284	2R_14895284_SNP [dm3] 2R_19007779_SNP [dm6]	T	G	3.438e^-5	0.928	INTRON tn
2L	14232440	2L_14232440_SNP [dm3] 2L_14232440_SNP [dm6]	T	C	3.527e^-5	0.928	INTRON Dyrk2	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
3R	26353068	3R_26353068_SNP [dm3] 3R_30527346_SNP [dm6]	T	A	3.580e^-5	0.928	UPSTREAM jdp DOWNSTREAM CR45552 INTERGENIC
2L	7937829	2L_7937829_SNP [dm3] 2L_7937829_SNP [dm6]	C	A	3.659e^-5	0.928	INTRON Snoo
3L	21876795	3L_21876795_SNP [dm3] 3L_21883695_SNP [dm6]	G	T	3.692e^-5	0.928	DOWNSTREAM CR43878 INTRON mub
2R	3089077	2R_3089077_SNP [dm3] 2R_7201572_SNP [dm6]	C	A	3.699e^-5	0.928	INTRON pk
X	17315731	X_17315731_SNP [dm3] X_17421698_SNP [dm6]	C	T	3.726e^-5	0.928	NON_SYNONYMOUS_CODING CG8611 DOWNSTREAM CG12994	TF binding site BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad
2L	8441041	2L_8441041_SNP [dm3] 2L_8441041_SNP [dm6]	T	A	3.798e^-5	0.928	SYNONYMOUS_CODING mus201
2R	15725074	2R_15725074_SNP [dm3] 2R_19837569_SNP [dm6]	A	G	3.882e^-5	0.928	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	7274733	3R_7274733_SNP [dm3] 3R_11449011_SNP [dm6]	C	A	3.895e^-5	0.928	INTRON CG17230 & 1 other
2R	16245437	2R_16245437_SNP [dm3] 2R_20357932_SNP [dm6]	G	A	3.970e^-5	0.928	INTERGENIC
2R	17473635	2R_17473635_SNP [dm3] 2R_21586130_SNP [dm6]	G	A	4.085e^-5	0.928	DOWNSTREAM CG30222 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	20708485	3R_20708485_SNP [dm3] 3R_24882763_SNP [dm6]	A	G	4.089e^-5	0.928	SYNONYMOUS_CODING CG31121	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
X	4283726	X_4283726_SNP [dm3] X_4389693_SNP [dm6]	G	A	4.153e^-5	0.928	INTRON CR32773
2R	13931235	2R_13931235_SNP [dm3] 2R_18043730_SNP [dm6]	G	C	4.198e^-5	0.928	START_GAINED CG5773 UTR_5_PRIME CG5773 UPSTREAM CG5773 DOWNSTREAM CG5770
X	14704819	X_14704819_SNP [dm3] X_14810786_SNP [dm6]	C	T	4.257e^-5	0.928	INTRON rut
2L	18425707	2L_18425707_SNP [dm3] 2L_18425707_SNP [dm6]	T	G	4.316e^-5	0.928	INTERGENIC
3L	10759146	3L_10759146_SNP [dm3] 3L_10766046_SNP [dm6]	T	A	4.350e^-5	0.928	INTERGENIC
3R	15849272	3R_15849272_SNP [dm3] 3R_20023550_SNP [dm6]	G	A	4.374e^-5	0.928	SYNONYMOUS_CODING psidin	TF binding site mE1_TFBS_cad
2R	17473629	2R_17473629_SNP [dm3] 2R_21586124_SNP [dm6]	C	G	4.374e^-5	0.928	DOWNSTREAM CG30222 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	17473630	2R_17473630_SNP [dm3] 2R_21586125_SNP [dm6]	C	G	4.374e^-5	0.928	DOWNSTREAM CG30222 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
X	4282991	X_4282991_SNP [dm3] X_4388958_SNP [dm6]	T	C	4.420e^-5	0.928	INTRON CR32773	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
X	4283300	X_4283300_SNP [dm3] X_4389267_SNP [dm6]	A	G	4.420e^-5	0.928	INTRON CR32773
3L	12804100	3L_12804100_SNP [dm3] 3L_12811000_SNP [dm6]	C	A	4.505e^-5	0.928	SYNONYMOUS_CODING Sap130 DOWNSTREAM CG32110	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	1693269	2L_1693269_SNP [dm3] 2L_1693269_SNP [dm6]	T	A	4.507e^-5	0.928	INTRON chinmo
2L	1384489	2L_1384489_SNP [dm3] 2L_1384489_SNP [dm6]	G	T	4.558e^-5	0.928	INTRON lea
3L	10759151	3L_10759151_SNP [dm3] 3L_10766051_SNP [dm6]	A	C	4.628e^-5	0.928	INTERGENIC
2R	17473583	2R_17473583_SNP [dm3] 2R_21586078_SNP [dm6]	C	G	4.649e^-5	0.928	DOWNSTREAM CG30222 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	14895282	2R_14895282_SNP [dm3] 2R_19007777_SNP [dm6]	G	C	4.755e^-5	0.928	INTRON tn
2L	16192863	2L_16192863_SNP [dm3] 2L_16192863_SNP [dm6]	T	A	4.802e^-5	0.928	INTERGENIC
2L	7223283	2L_7223283_SNP [dm3] 2L_7223283_SNP [dm6]	C	A	4.804e^-5	0.928	UPSTREAM ico DOWNSTREAM Ndae1 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 mE1_TFBS_HSA
3R	22751210	3R_22751210_SNP [dm3] 3R_26925488_SNP [dm6]	G	A	4.811e^-5	0.928	INTRON sda
X	6194927	X_6194927_SNP [dm3] X_6300894_SNP [dm6]	G	A	4.826e^-5	0.928	SYNONYMOUS_CODING CG12219	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3L	10759161	3L_10759161_INS [dm3] 3L_10766061_INS [dm6]	A	AC	4.885e^-5	0.928	INTERGENIC
3L	10759167	3L_10759167_INS [dm3] 3L_10766067_INS [dm6]	G	GA	4.885e^-5	0.928	INTERGENIC
3L	15402265	3L_15402265_SNP [dm3] 3L_15409165_SNP [dm6]	T	A	4.970e^-5	0.928	DOWNSTREAM CG33259 INTERGENIC
3R	4239750	3R_4239750_SNP [dm3] 3R_8414028_SNP [dm6]	T	G	4.985e^-5	0.928	INTRON CG45263
2L	19263814	2L_19263814_DEL [dm3] 2L_19263814_DEL [dm6]	TTG	C	5.196e^-5	0.928	DOWNSTREAM CR44191 INTERGENIC
3L	10759158	3L_10759158_SNP [dm3] 3L_10766058_SNP [dm6]	A	C	5.275e^-5	0.928	INTERGENIC
3R	22751207	3R_22751207_SNP [dm3] 3R_26925485_SNP [dm6]	A	G	5.303e^-5	0.928	INTRON sda
X	4050143	X_4050143_INS [dm3] X_4156110_INS [dm6]	T	TTGGGT	5.384e^-5	0.928	INTRON Fas2
X	9644615	X_9644615_SNP [dm3] X_9750582_SNP [dm6]	G	A	5.386e^-5	0.928	INTRON Sp1	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3L	15646689	3L_15646689_SNP [dm3] 3L_15653589_SNP [dm6]	C	G	5.404e^-5	0.928	DOWNSTREAM Eig71Ed & 1 other INTERGENIC	TF binding site mE1_TFBS_HSA
3R	8378747	3R_8378747_SNP [dm3] 3R_12553025_SNP [dm6]	C	T	5.443e^-5	0.928	SYNONYMOUS_CODING Octbeta2R	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3L	10759165	3L_10759165_SNP [dm3] 3L_10766065_SNP [dm6]	T	A	5.444e^-5	0.928	INTERGENIC
X	17538165	X_17538165_SNP [dm3] X_17644132_SNP [dm6]	A	G	5.506e^-5	0.928	SYNONYMOUS_CODING RhoGAPp190 INTRON RhoGAPp190

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Missing results

By genomic position
Variant impact
Gene name

se_GenomeSize phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results