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=7.371e^-8)
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

Covariate	χ²	p-value	Significance
In_3R_Mo	2.7305	0.0984

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1157 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	8809578	3L_8809578_SNP [dm3] 3L_8816478_SNP [dm6]	T	A	7.812e^-6	0.866	INTERGENIC
2R	9610105	2R_9610105_DEL [dm3] 2R_13722600_DEL [dm6]	GG	G	8.761e^-6	0.866	INTRON fas
2L	2406132	2L_2406132_SNP [dm3] 2L_2406132_SNP [dm6]	G	C	1.579e^-5	0.866	INTRON VGlut	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
X	12838031	X_12838031_SNP [dm3] X_12943998_SNP [dm6]	A	T	1.858e^-5	0.866	INTRON fne
2R	16093251	2R_16093251_SNP [dm3] 2R_20205746_SNP [dm6]	G	A	2.136e^-5	0.866	INTERGENIC
2R	16093261	2R_16093261_SNP [dm3] 2R_20205756_SNP [dm6]	G	A	2.136e^-5	0.866	INTERGENIC
2R	16093268	2R_16093268_SNP [dm3] 2R_20205763_SNP [dm6]	G	T	2.136e^-5	0.866	INTERGENIC
2R	16093269	2R_16093269_SNP [dm3] 2R_20205764_SNP [dm6]	C	A	2.136e^-5	0.866	INTERGENIC
2R	18774201	2R_18774201_SNP [dm3] 2R_22886678_SNP [dm6]	A	T	2.170e^-5	0.866	SYNONYMOUS_CODING asrij UPSTREAM CG3499 DOWNSTREAM Gmer	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Ubx
3R	18522322	3R_18522322_SNP [dm3] 3R_22696600_SNP [dm6]	T	C	2.289e^-5	0.866	SYNONYMOUS_CODING cd	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2R	16844522	2R_16844522_SNP [dm3] 2R_20957017_SNP [dm6]	T	A	2.831e^-5	0.866	INTRON hbn	TF binding site BDTNP1_TFBS_prd
2R	4203646	2R_4203646_SNP [dm3] 2R_8316141_SNP [dm6]	C	G	2.875e^-5	0.866	INTERGENIC
2R	11911376	2R_11911376_SNP [dm3] 2R_16023871_SNP [dm6]	A	G	3.021e^-5	0.866	DOWNSTREAM casp INTRON CG8399
3R	16018144	3R_16018144_SNP [dm3] 3R_20192422_SNP [dm6]	C	T	3.191e^-5	0.866	INTERGENIC
2L	16665677	2L_16665677_SNP [dm3] 2L_16665677_SNP [dm6]	G	C	3.611e^-5	0.866	INTRON Trpgamma	transposable element FlyBase
3L	13971850	3L_13971850_SNP [dm3] 3L_13978750_SNP [dm6]	C	A	3.646e^-5	0.866	UTR_3_PRIME CG17364 DOWNSTREAM Hsc70-1
3L	6649799	3L_6649799_SNP [dm3] 3L_6656699_SNP [dm6]	T	C	3.886e^-5	0.866	INTERGENIC
2L	7390125	2L_7390125_SNP [dm3] 2L_7390125_SNP [dm6]	G	A	4.395e^-5	0.866	SYNONYMOUS_CODING gudu DOWNSTREAM CG5160	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	4235576	2L_4235576_SNP [dm3] 2L_4235576_SNP [dm6]	A	T	4.528e^-5	0.866	INTERGENIC
3L	14084389	3L_14084389_SNP [dm3] 3L_14091289_SNP [dm6]	T	G	4.967e^-5	0.866	INTERGENIC
2R	15030513	2R_15030513_SNP [dm3] 2R_19143008_SNP [dm6]	T	C	5.758e^-5	0.866	INTRON ena	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
X	6455531	X_6455531_SNP [dm3] X_6561498_SNP [dm6]	G	A	5.827e^-5	0.866	SYNONYMOUS_CODING CG34417	TF binding site mE1_TFBS_sens
2L	5248343	2L_5248343_SNP [dm3] 2L_5248343_SNP [dm6]	A	C	5.845e^-5	0.866	INTRON tkv
2L	5248349	2L_5248349_SNP [dm3] 2L_5248349_SNP [dm6]	G	A	5.845e^-5	0.866	INTRON tkv
X	3153646	X_3153646_SNP [dm3] X_3259613_SNP [dm6]	G	C	6.267e^-5	0.866	INTRON dnc
3L	2921006	3L_2921006_SNP [dm3] 3L_2921006_SNP [dm6]	T	C	6.296e^-5	0.866	INTRON Shab
2R	8888926	2R_8888926_SNP [dm3] 2R_13001421_SNP [dm6]	G	A	6.439e^-5	0.866	SYNONYMOUS_CODING Su_z_2	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	8888932	2R_8888932_SNP [dm3] 2R_13001427_SNP [dm6]	G	A	6.439e^-5	0.866	SYNONYMOUS_CODING Su_z_2	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	8323937	2L_8323937_SNP [dm3] 2L_8323937_SNP [dm6]	A	G	6.607e^-5	0.866	INTRON CG7781
2R	18761962	2R_18761962_INS [dm3] 2R_22874439_INS [dm6]	G	TT	6.610e^-5	0.866	UPSTREAM PIP5K59B DOWNSTREAM CR45469 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl
2R	18761970	2R_18761970_SNP [dm3] 2R_22874447_SNP [dm6]	C	T	6.610e^-5	0.866	UPSTREAM PIP5K59B DOWNSTREAM CR45469 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl
2R	16121027	2R_16121027_SNP [dm3] 2R_20233522_SNP [dm6]	G	T	6.628e^-5	0.866	DOWNSTREAM tRNA:G3:56EFb INTRON CG11044
2R	16121033	2R_16121033_SNP [dm3] 2R_20233528_SNP [dm6]	C	T	6.628e^-5	0.866	DOWNSTREAM tRNA:G3:56EFb INTRON CG11044
2R	16121034	2R_16121034_SNP [dm3] 2R_20233529_SNP [dm6]	T	A	6.628e^-5	0.866	SPLICE_SITE_REGION CG11044 DOWNSTREAM tRNA:G3:56EFb INTRON CG11044
2R	16121036	2R_16121036_SNP [dm3] 2R_20233531_SNP [dm6]	C	T	6.628e^-5	0.866	SPLICE_SITE_REGION CG11044 DOWNSTREAM tRNA:G3:56EFb INTRON CG11044
3L	14084423	3L_14084423_SNP [dm3] 3L_14091323_SNP [dm6]	G	C	6.753e^-5	0.866	INTERGENIC
X	6455644	X_6455644_SNP [dm3] X_6561611_SNP [dm6]	G	C	6.848e^-5	0.866	INTRON CG34417	TF binding site mE1_TFBS_sens
3R	24514259	3R_24514259_SNP [dm3] 3R_28688537_SNP [dm6]	G	A	7.050e^-5	0.866	INTRON CG9990
3R	11511169	3R_11511169_SNP [dm3] 3R_15685447_SNP [dm6]	A	G	7.213e^-5	0.866	INTRON pxb	TF binding site BDTNP1_TFBS_hb mE1_TFBS_HSA mE1_TFBS_sens
2L	4219331	2L_4219331_SNP [dm3] 2L_4219331_SNP [dm6]	C	G	7.224e^-5	0.866	INTRON ft	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	6329796	2L_6329796_SNP [dm3] 2L_6329796_SNP [dm6]	T	G	7.689e^-5	0.866	INTRON PDZ-GEF	TF binding site mE1_TFBS_cad
2R	11911394	2R_11911394_SNP [dm3] 2R_16023889_SNP [dm6]	G	T	8.055e^-5	0.866	DOWNSTREAM casp INTRON CG8399
3R	10600659	3R_10600659_SNP [dm3] 3R_14774937_SNP [dm6]	T	A	8.177e^-5	0.866	INTRON jvl
3R	10600664	3R_10600664_SNP [dm3] 3R_14774942_SNP [dm6]	C	A	8.177e^-5	0.866	INTRON jvl
2R	11911343	2R_11911343_SNP [dm3] 2R_16023838_SNP [dm6]	A	G	8.260e^-5	0.866	SYNONYMOUS_CODING CG8399 DOWNSTREAM casp
3R	15676596	3R_15676596_SNP [dm3] 3R_19850874_SNP [dm6]	G	C	8.501e^-5	0.866	SYNONYMOUS_CODING CG4662
2L	4219131	2L_4219131_SNP [dm3] 2L_4219131_SNP [dm6]	C	T	8.526e^-5	0.866	INTRON ft	TF binding site mE1_TFBS_HSA
2L	4219151	2L_4219151_SNP [dm3] 2L_4219151_SNP [dm6]	G	A	8.526e^-5	0.866	INTRON ft	TF binding site mE1_TFBS_HSA
2L	4219158	2L_4219158_SNP [dm3] 2L_4219158_SNP [dm6]	T	C	8.526e^-5	0.866	INTRON ft	TF binding site mE1_TFBS_HSA
X	12441976	X_12441976_SNP [dm3] X_12547943_SNP [dm6]	C	A	8.588e^-5	0.866	UPSTREAM CG43921 INTRON CG43921	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3L	11868004	3L_11868004_SNP [dm3] 3L_11874904_SNP [dm6]	G	A	8.598e^-5	0.866	INTRON CG44837
3L	11868099	3L_11868099_SNP [dm3] 3L_11874999_SNP [dm6]	C	A	8.598e^-5	0.866	INTRON CG44837
2R	3868987	2R_3868987_SNP [dm3] 2R_7981482_SNP [dm6]	A	G	8.688e^-5	0.866	INTRON ACC	TF binding site mE1_TFBS_cad
2R	7070027	2R_7070027_SNP [dm3] 2R_11182522_SNP [dm6]	T	G	8.954e^-5	0.866	UPSTREAM shn INTRON shn	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
2R	7070036	2R_7070036_SNP [dm3] 2R_11182531_SNP [dm6]	G	C	8.954e^-5	0.866	UPSTREAM shn INTRON shn	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
3L	17744152	3L_17744152_SNP [dm3] 3L_17751052_SNP [dm6]	T	A	9.191e^-5	0.866	UPSTREAM Adgf-B DOWNSTREAM Adgf-A INTERGENIC
3L	17744158	3L_17744158_SNP [dm3] 3L_17751058_SNP [dm6]	G	C	9.191e^-5	0.866	UPSTREAM Adgf-B DOWNSTREAM Adgf-A INTERGENIC
3L	17744163	3L_17744163_SNP [dm3] 3L_17751063_SNP [dm6]	C	T	9.191e^-5	0.866	UPSTREAM Adgf-B DOWNSTREAM Adgf-A INTERGENIC
3L	17744164	3L_17744164_SNP [dm3] 3L_17751064_SNP [dm6]	C	T	9.191e^-5	0.866	UPSTREAM Adgf-B DOWNSTREAM Adgf-A INTERGENIC
3L	17744170	3L_17744170_SNP [dm3] 3L_17751070_SNP [dm6]	A	T	9.191e^-5	0.866	UPSTREAM Adgf-B DOWNSTREAM Adgf-A INTERGENIC
3L	17744173	3L_17744173_SNP [dm3] 3L_17751073_SNP [dm6]	A	G	9.191e^-5	0.866	UPSTREAM Adgf-B DOWNSTREAM Adgf-A INTERGENIC
3L	17744175	3L_17744175_SNP [dm3] 3L_17751075_SNP [dm6]	T	A	9.191e^-5	0.866	UPSTREAM Adgf-B DOWNSTREAM Adgf-A INTERGENIC
3L	17744179	3L_17744179_MNP [dm3] 3L_17751079_MNP [dm6]	GAA	TTC	9.191e^-5	0.866	UPSTREAM Adgf-B DOWNSTREAM Adgf-A INTERGENIC
3L	17744188	3L_17744188_SNP [dm3] 3L_17751088_SNP [dm6]	T	C	9.191e^-5	0.866	UPSTREAM Adgf-B DOWNSTREAM Adgf-A INTERGENIC
3L	17744189	3L_17744189_SNP [dm3] 3L_17751089_SNP [dm6]	A	T	9.191e^-5	0.866	UPSTREAM Adgf-B DOWNSTREAM Adgf-A INTERGENIC
2L	5248334	2L_5248334_SNP [dm3] 2L_5248334_SNP [dm6]	C	A	9.394e^-5	0.866	INTRON tkv
3R	16863149	3R_16863149_SNP [dm3] 3R_21037427_SNP [dm6]	A	T	9.635e^-5	0.866	INTRON Dhc93AB	TF binding site mE1_TFBS_cad
X	2331802	X_2331802_SNP [dm3] X_2437769_SNP [dm6]	T	C	9.781e^-5	0.866	INTERGENIC	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	17740227	3L_17740227_SNP [dm3] 3L_17747127_SNP [dm6]	G	A	1.005e^-4	0.866	UPSTREAM CG6034 INTRON Ccn
3L	17740673	3L_17740673_SNP [dm3] 3L_17747573_SNP [dm6]	C	T	1.005e^-4	0.866	UPSTREAM CG6034 INTRON Ccn
X	4302779	X_4302779_SNP [dm3] X_4408746_SNP [dm6]	A	G	1.024e^-4	0.866	INTRON CR32773
2L	4235634	2L_4235634_SNP [dm3] 2L_4235634_SNP [dm6]	T	C	1.031e^-4	0.866	INTERGENIC
3R	16018246	3R_16018246_INS [dm3] 3R_20192524_INS [dm6]	T	AC	1.031e^-4	0.866	INTERGENIC
3R	16018277	3R_16018277_SNP [dm3] 3R_20192555_SNP [dm6]	T	A	1.031e^-4	0.866	INTERGENIC
2L	7111776	2L_7111776_SNP [dm3] 2L_7111776_SNP [dm6]	C	A	1.039e^-4	0.866	INTRON Pvf3
X	13713305	X_13713305_SNP [dm3] X_13819272_SNP [dm6]	T	A	1.070e^-4	0.866	INTRON Clic
X	3012029	X_3012029_SNP [dm3] X_3117996_SNP [dm6]	C	T	1.071e^-4	0.866	INTRON kirre	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	15967419	3R_15967419_SNP [dm3] 3R_20141697_SNP [dm6]	C	A	1.098e^-4	0.866	INTERGENIC
2R	16693918	2R_16693918_SNP [dm3] 2R_20806413_SNP [dm6]	T	A	1.102e^-4	0.866	INTERGENIC
2L	14340967	2L_14340967_SNP [dm3] 2L_14340967_SNP [dm6]	C	A	1.128e^-4	0.866	DOWNSTREAM CG15286 INTRON CG33090
X	9228222	X_9228222_SNP [dm3] X_9334189_SNP [dm6]	G	T	1.142e^-4	0.866	INTRON CG34449
2R	6201222	2R_6201222_SNP [dm3] 2R_10313717_SNP [dm6]	G	T	1.172e^-4	0.866	UPSTREAM Ndg INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
2R	6201283	2R_6201283_SNP [dm3] 2R_10313778_SNP [dm6]	C	T	1.172e^-4	0.866	UPSTREAM Ndg INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
2R	5504251	2R_5504251_SNP [dm3] 2R_9616746_SNP [dm6]	T	C	1.232e^-4	0.866	INTRON Mmp2
3L	8472576	3L_8472576_SNP [dm3] 3L_8479476_SNP [dm6]	A	C	1.252e^-4	0.866	SYNONYMOUS_CODING CG43163	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo
2L	4451422	2L_4451422_SNP [dm3] 2L_4451422_SNP [dm6]	A	T	1.254e^-4	0.866	SYNONYMOUS_CODING CG15439	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_sens
3L	5164757	3L_5164757_SNP [dm3] 3L_5171657_SNP [dm6]	G	A	1.263e^-4	0.866	INTRON shep
3L	17934912	3L_17934912_SNP [dm3] 3L_17941812_SNP [dm6]	T	C	1.276e^-4	0.866	INTRON CG43174
2R	19902815	2R_19902815_SNP [dm3] 2R_24015292_SNP [dm6]	A	T	1.277e^-4	0.866	INTRON CG4324	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
X	13577007	X_13577007_SNP [dm3] X_13682974_SNP [dm6]	A	G	1.297e^-4	0.866	UTR_5_PRIME CG11158
3L	5164755	3L_5164755_SNP [dm3] 3L_5171655_SNP [dm6]	A	G	1.323e^-4	0.866	INTRON shep
3L	18648267	3L_18648267_INS [dm3] 3L_18655167_INS [dm6]	T	TT	1.324e^-4	0.866	INTRON MYPT-75D
2L	2259386	2L_2259386_SNP [dm3] 2L_2259386_SNP [dm6]	C	T	1.335e^-4	0.866	DOWNSTREAM CR44788 INTERGENIC
2L	2259404	2L_2259404_SNP [dm3] 2L_2259404_SNP [dm6]	T	C	1.335e^-4	0.866	EXON CR44788
2L	2259406	2L_2259406_SNP [dm3] 2L_2259406_SNP [dm6]	C	T	1.335e^-4	0.866	EXON CR44788
2L	2259407	2L_2259407_SNP [dm3] 2L_2259407_SNP [dm6]	T	C	1.335e^-4	0.866	EXON CR44788
2R	8891260	2R_8891260_SNP [dm3] 2R_13003755_SNP [dm6]	C	T	1.335e^-4	0.866	SYNONYMOUS_CODING Su_z_2	TF binding site mE1_TFBS_chinmo mE1_TFBS_sens
3L	12605689	3L_12605689_SNP [dm3] 3L_12612589_SNP [dm6]	C	G	1.335e^-4	0.866	INTRON caup
3L	12606083	3L_12606083_SNP [dm3] 3L_12612983_SNP [dm6]	C	T	1.335e^-4	0.866	INTRON caup	silencer mE1_HDAC_PRE
2L	13030083	2L_13030083_SNP [dm3] 2L_13030083_SNP [dm6]	T	C	1.340e^-4	0.866	SYNONYMOUS_CODING CG9932	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo

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By genomic position
Variant impact
Gene name

productivity3 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results