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=6.996e^-3)
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

2047 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
3R	23663574	3R_23663574_SNP [dm3] 3R_27837852_SNP [dm6]	C	T	2.802e^-6	0.888	INTRON CG34353
2R	20321436	2R_20321436_SNP [dm3] 2R_24433913_SNP [dm6]	C	A	3.522e^-6	0.888	INTERGENIC
3R	3022243	3R_3022243_SNP [dm3] 3R_7196521_SNP [dm6]	T	C	3.700e^-6	0.888	INTRON lap
2R	13081927	2R_13081927_SNP [dm3] 2R_17194422_SNP [dm6]	T	C	4.240e^-6	0.888	UPSTREAM CG10950 INTERGENIC
3L	5273161	3L_5273161_SNP [dm3] 3L_5280061_SNP [dm6]	G	A	5.238e^-6	0.888	INTERGENIC
3L	5273132	3L_5273132_DEL [dm3] 3L_5280032_DEL [dm6]	TGCC	CTT	6.599e^-6	0.888	INTERGENIC
3L	1234139	3L_1234139_SNP [dm3] 3L_1234139_SNP [dm6]	C	T	7.304e^-6	0.888	UTR_5_PRIME CG33966 DOWNSTREAM CG33965
X	4863995	X_4863995_SNP [dm3] X_4969962_SNP [dm6]	A	C	7.672e^-6	0.888	INTRON CR44833	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
X	4762956	X_4762956_SNP [dm3] X_4868923_SNP [dm6]	A	C	8.938e^-6	0.888	INTRON CG42594
3L	2219101	3L_2219101_SNP [dm3] 3L_2219101_SNP [dm6]	G	A	9.788e^-6	0.888	INTERGENIC
3R	26037678	3R_26037678_SNP [dm3] 3R_30211956_SNP [dm6]	T	A	1.009e^-5	0.888	UPSTREAM CecA2 & 1 other DOWNSTREAM CecA1 & 1 other INTERGENIC
X	9462758	X_9462758_SNP [dm3] X_9568725_SNP [dm6]	C	T	1.097e^-5	0.888	SYNONYMOUS_CODING Cubn	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	14884001	3R_14884001_SNP [dm3] 3R_19058279_SNP [dm6]	T	A	1.150e^-5	0.888	INTRON cdi	TF binding site BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_chinmo mE1_TFBS_HSA
X	9421083	X_9421083_SNP [dm3] X_9527050_SNP [dm6]	G	A	1.153e^-5	0.888	INTRON CG32700
3L	12750782	3L_12750782_SNP [dm3] 3L_12757682_SNP [dm6]	T	G	1.155e^-5	0.888	SYNONYMOUS_CODING CG32113
3R	21087888	3R_21087888_SNP [dm3] 3R_25262166_SNP [dm6]	A	C	1.392e^-5	0.888	UPSTREAM CG11858 INTRON CG10425	TF binding site mE1_TFBS_sens
3L	4349773	3L_4349773_INS [dm3] 3L_4349773_INS [dm6]	T	TT	1.407e^-5	0.888	INTRON Cip4
3L	12751782	3L_12751782_SNP [dm3] 3L_12758682_SNP [dm6]	C	A	1.542e^-5	0.888	SYNONYMOUS_CODING CG32113	TF binding site mE1_TFBS_inv
3R	969947	3R_969947_SNP [dm3] 3R_5144225_SNP [dm6]	T	C	1.584e^-5	0.888	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	8761961	3L_8761961_SNP [dm3] 3L_8768861_SNP [dm6]	T	C	1.661e^-5	0.888	INTRON Fhos
2L	18475359	2L_18475359_SNP [dm3] 2L_18475359_SNP [dm6]	T	G	1.693e^-5	0.888	NON_SYNONYMOUS_CODING CG10283	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad mE1_TFBS_HSA
2L	12330220	2L_12330220_SNP [dm3] 2L_12330220_SNP [dm6]	C	T	1.702e^-5	0.888	INTERGENIC
3L	7450279	3L_7450279_SNP [dm3] 3L_7457179_SNP [dm6]	G	C	1.777e^-5	0.888	SYNONYMOUS_CODING ppk26
3R	17491965	3R_17491965_SNP [dm3] 3R_21666243_SNP [dm6]	A	C	1.799e^-5	0.888	DOWNSTREAM DNApol-alpha180 INTRON CG15497	TF binding site BDTNP1_TFBS_sna mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	22143785	3R_22143785_SNP [dm3] 3R_26318063_SNP [dm6]	G	A	1.842e^-5	0.888	UPSTREAM CG33970 INTERGENIC
X	10329667	X_10329667_SNP [dm3] X_10435634_SNP [dm6]	G	C	1.868e^-5	0.888	INTRON CG32683
3R	26047464	3R_26047464_SNP [dm3] 3R_30221742_SNP [dm6]	A	G	2.204e^-5	0.888	INTERGENIC	TF binding site BDTNP1_TFBS_twi
X	12772228	X_12772228_SNP [dm3] X_12878195_SNP [dm6]	T	C	2.234e^-5	0.888	INTRON Pde9
3L	4387877	3L_4387877_SNP [dm3] 3L_4387877_SNP [dm6]	A	T	2.239e^-5	0.888	INTRON slow
X	4998044	X_4998044_SNP [dm3] X_5104011_SNP [dm6]	T	G	2.254e^-5	0.888	INTRON rg & 1 other
3R	19925178	3R_19925178_SNP [dm3] 3R_24099456_SNP [dm6]	C	A	2.318e^-5	0.888	INTRON 4EHP
3L	8816893	3L_8816893_INS [dm3] 3L_8823793_INS [dm6]	A	AA	2.381e^-5	0.888	INTERGENIC	TF binding site mE1_TFBS_cad
X	19000975	X_19000975_INS [dm3] X_19106942_INS [dm6]	A	ACAA	2.452e^-5	0.888	INTERGENIC	TF binding site BDTNP1_TFBS_dl
X	4375086	X_4375086_SNP [dm3] X_4481053_SNP [dm6]	T	C	2.455e^-5	0.888	INTRON CR32773 & 1 other
3L	7093952	3L_7093952_SNP [dm3] 3L_7100852_SNP [dm6]	C	T	2.526e^-5	0.888	INTRON form3
3L	7094193	3L_7094193_SNP [dm3] 3L_7101093_SNP [dm6]	A	C	2.526e^-5	0.888	INTRON form3
3L	961004	3L_961004_SNP [dm3] 3L_961004_SNP [dm6]	G	C	2.535e^-5	0.888	INTRON Glut1
2R	12127762	2R_12127762_SNP [dm3] 2R_16240257_SNP [dm6]	C	A	2.565e^-5	0.888	NON_SYNONYMOUS_CODING krimp DOWNSTREAM CG15708	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	18980078	3R_18980078_SNP [dm3] 3R_23154356_SNP [dm6]	A	G	2.635e^-5	0.888	SYNONYMOUS_CODING unk	TF binding site mE1_TFBS_sens
X	8749872	X_8749872_SNP [dm3] X_8855839_SNP [dm6]	T	A	2.652e^-5	0.888	INTRON CG12075
3R	22143770	3R_22143770_SNP [dm3] 3R_26318048_SNP [dm6]	G	A	2.669e^-5	0.888	UPSTREAM CG33970 INTERGENIC
2L	4815917	2L_4815917_SNP [dm3] 2L_4815917_SNP [dm6]	C	T	2.680e^-5	0.888	SPLICE_SITE_REGION CG3225 UTR_3_PRIME CG3225 DOWNSTREAM CG15629
X	8359031	X_8359031_SNP [dm3] X_8464998_SNP [dm6]	A	G	2.772e^-5	0.888	UPSTREAM Sptr DOWNSTREAM CG33223 INTERGENIC
3R	5121647	3R_5121647_DEL [dm3] 3R_9295925_DEL [dm6]	GAATGTTTATGG...	G	2.798e^-5	0.888	INTRON CG8861
3L	14548660	3L_14548660_SNP [dm3] 3L_14555560_SNP [dm6]	C	T	2.807e^-5	0.888	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_zfh1
2R	5513131	2R_5513131_SNP [dm3] 2R_9625626_SNP [dm6]	G	T	2.833e^-5	0.888	INTRON Mmp2
3L	14176905	3L_14176905_INS [dm3] 3L_14183805_INS [dm6]	C	CTAC	2.878e^-5	0.888	INTERGENIC	TF binding site mE1_TFBS_cad
3R	8863894	3R_8863894_SNP [dm3] 3R_13038172_SNP [dm6]	G	T	2.936e^-5	0.888	UPSTREAM CG11668 DOWNSTREAM ry INTERGENIC
3L	12751574	3L_12751574_SNP [dm3] 3L_12758474_SNP [dm6]	A	C	2.948e^-5	0.888	INTRON CG32113	TF binding site mE1_TFBS_inv
3R	15629738	3R_15629738_SNP [dm3] 3R_19804016_SNP [dm6]	G	A	3.083e^-5	0.888	INTRON bnl	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	18923927	2R_18923927_SNP [dm3] 2R_23036404_SNP [dm6]	A	T	3.145e^-5	0.888	INTRON twi & 1 other	TF binding site mE1_TFBS_inv
3R	7933106	3R_7933106_SNP [dm3] 3R_12107384_SNP [dm6]	C	T	3.255e^-5	0.888	NON_SYNONYMOUS_CODING dpr17	TF binding site BDTNP1_TFBS_sna
2L	19616845	2L_19616845_SNP [dm3] 2L_19616845_SNP [dm6]	T	G	3.455e^-5	0.888	INTRON Lar
X	12772229	X_12772229_SNP [dm3] X_12878196_SNP [dm6]	G	A	3.503e^-5	0.888	INTRON Pde9
X	5185806	X_5185806_SNP [dm3] X_5291773_SNP [dm6]	G	T	3.568e^-5	0.888	INTERGENIC
3R	15684720	3R_15684720_SNP [dm3] 3R_19858998_SNP [dm6]	G	A	3.637e^-5	0.888	INTRON Ire1	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA
X	19000910	X_19000910_DEL [dm3] X_19106877_DEL [dm6]	CGAACGAGAGAGATGTGTTT...	C	3.647e^-5	0.888	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	15629744	3R_15629744_SNP [dm3] 3R_19804022_SNP [dm6]	C	G	3.689e^-5	0.888	INTRON bnl	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
X	10329663	X_10329663_SNP [dm3] X_10435630_SNP [dm6]	A	G	3.774e^-5	0.888	INTRON CG32683
X	17758219	X_17758219_SNP [dm3] X_17864186_SNP [dm6]	C	G	3.788e^-5	0.888	NON_SYNONYMOUS_CODING mnb	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
X	7553535	X_7553535_SNP [dm3] X_7659502_SNP [dm6]	A	T	3.835e^-5	0.888	INTRON ct	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
3R	22415571	3R_22415571_SNP [dm3] 3R_26589849_SNP [dm6]	T	C	3.850e^-5	0.888	INTRON scrib
2R	13882739	2R_13882739_SNP [dm3] 2R_17995234_SNP [dm6]	G	C	3.918e^-5	0.888	INTRON dpr13
3L	18368375	3L_18368375_SNP [dm3] 3L_18375275_SNP [dm6]	G	T	3.978e^-5	0.888	INTERGENIC	TF binding site mE1_TFBS_HSA
2L	12330222	2L_12330222_SNP [dm3] 2L_12330222_SNP [dm6]	G	T	4.028e^-5	0.888	INTERGENIC
3R	2506572	3R_2506572_DEL [dm3] 3R_6680850_DEL [dm6]	CAG	C	4.036e^-5	0.888	INTERGENIC	regulatory region FlyBase REDfly_CRMs transposable element FlyBase
3R	19925179	3R_19925179_SNP [dm3] 3R_24099457_SNP [dm6]	C	T	4.099e^-5	0.888	INTRON 4EHP
X	7553517	X_7553517_SNP [dm3] X_7659484_SNP [dm6]	T	A	4.184e^-5	0.888	INTRON ct	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
3L	7092878	3L_7092878_SNP [dm3] 3L_7099778_SNP [dm6]	T	A	4.187e^-5	0.888	INTRON form3	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
X	12722117	X_12722117_SNP [dm3] X_12828084_SNP [dm6]	A	G	4.266e^-5	0.888	INTRON Pde9
3L	12752187	3L_12752187_SNP [dm3] 3L_12759087_SNP [dm6]	A	C	4.267e^-5	0.888	INTRON CG32113
2L	16537741	2L_16537741_SNP [dm3] 2L_16537741_SNP [dm6]	A	T	4.302e^-5	0.888	INTERGENIC
2R	17869427	2R_17869427_SNP [dm3] 2R_21981922_SNP [dm6]	A	G	4.304e^-5	0.888	DOWNSTREAM Gr58a INTERGENIC
3R	970259	3R_970259_SNP [dm3] 3R_5144537_SNP [dm6]	A	T	4.324e^-5	0.888	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	970357	3R_970357_DEL [dm3] 3R_5144635_DEL [dm6]	CCTATTTGTCCTGC...	C	4.417e^-5	0.888	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
X	4999440	X_4999440_SNP [dm3] X_5105407_SNP [dm6]	T	G	4.528e^-5	0.888	INTRON rg & 1 other
3L	4076380	3L_4076380_SNP [dm3] 3L_4076380_SNP [dm6]	T	A	4.624e^-5	0.888	INTRON Gad1
3L	7518431	3L_7518431_SNP [dm3] 3L_7525331_SNP [dm6]	G	A	4.637e^-5	0.888	NON_SYNONYMOUS_CODING ltl
2L	19939831	2L_19939831_SNP [dm3] 2L_19939831_SNP [dm6]	G	C	4.668e^-5	0.888	INTRON sick	TF binding site BDTNP1_TFBS_da mE1_TFBS_sens
3R	22143658	3R_22143658_SNP [dm3] 3R_26317936_SNP [dm6]	T	A	4.755e^-5	0.888	UPSTREAM CG33970 INTERGENIC
3L	5329534	3L_5329534_INS [dm3] 3L_5336434_INS [dm6]	A	AA	4.759e^-5	0.888	INTERGENIC
3R	21088098	3R_21088098_SNP [dm3] 3R_25262376_SNP [dm6]	A	G	4.765e^-5	0.888	NON_SYNONYMOUS_CODING CG10425 UPSTREAM CG11858 DOWNSTREAM Aats-gln
2L	4493017	2L_4493017_SNP [dm3] 2L_4493017_SNP [dm6]	T	G	4.885e^-5	0.888	SYNONYMOUS_CODING dp INTRON dp	TF binding site mE1_TFBS_sens
2L	4493167	2L_4493167_SNP [dm3] 2L_4493167_SNP [dm6]	T	A	4.885e^-5	0.888	SYNONYMOUS_CODING dp INTRON dp
X	4375089	X_4375089_SNP [dm3] X_4481056_SNP [dm6]	A	C	4.907e^-5	0.888	INTRON CR32773 & 1 other
3L	7450372	3L_7450372_SNP [dm3] 3L_7457272_SNP [dm6]	T	C	4.934e^-5	0.888	SYNONYMOUS_CODING ppk26
3R	11239224	3R_11239224_SNP [dm3] 3R_15413502_SNP [dm6]	A	G	5.032e^-5	0.888	NON_SYNONYMOUS_CODING Atx2	TF binding site BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_chinmo
X	13441615	X_13441615_SNP [dm3] X_13547582_SNP [dm6]	C	A	5.068e^-5	0.888	INTERGENIC
3L	18368273	3L_18368273_SNP [dm3] 3L_18375173_SNP [dm6]	G	T	5.076e^-5	0.888	INTERGENIC	TF binding site mE1_TFBS_HSA
X	2685439	X_2685439_SNP [dm3] X_2791406_SNP [dm6]	T	A	5.206e^-5	0.888	SPLICE_SITE_REGION w UPSTREAM CG32795 INTRON kirre & 1 other	regulatory region REDfly_CRMs TF binding site mE1_TFBS_cad mE1_TFBS_HSA
X	6805087	X_6805087_SNP [dm3] X_6911054_SNP [dm6]	A	T	5.528e^-5	0.888	INTRON CG14431
3R	15618069	3R_15618069_SNP [dm3] 3R_19792347_SNP [dm6]	T	G	5.531e^-5	0.888	INTERGENIC
3L	667983	3L_667983_SNP [dm3] 3L_667983_SNP [dm6]	C	T	5.538e^-5	0.888	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	12049367	3L_12049367_SNP [dm3] 3L_12056267_SNP [dm6]	A	G	5.543e^-5	0.888	UTR_5_PRIME rols INTRON rols	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3R	974858	3R_974858_SNP [dm3] 3R_5149136_SNP [dm6]	A	T	5.562e^-5	0.888	INTERGENIC
X	19000866	X_19000866_SNP [dm3] X_19106833_SNP [dm6]	G	A	5.653e^-5	0.888	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	5333197	3L_5333197_SNP [dm3] 3L_5340097_SNP [dm6]	G	A	5.706e^-5	0.888	INTERGENIC
X	9462862	X_9462862_SNP [dm3] X_9568829_SNP [dm6]	C	G	5.757e^-5	0.888	NON_SYNONYMOUS_CODING Cubn	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
X	4762934	X_4762934_SNP [dm3] X_4868901_SNP [dm6]	A	T	5.758e^-5	0.888	INTRON CG42594
3R	980363	3R_980363_SNP [dm3] 3R_5154641_SNP [dm6]	C	T	5.769e^-5	0.888	INTRON dpr16

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By genomic position
Variant impact
Gene name

Sc2_CT phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results