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=8.887e^-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
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1433 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	2105215	3L_2105215_SNP [dm3] 3L_2105215_SNP [dm6]	T	C	8.235e^-7	0.994	SYNONYMOUS_CODING sls	TF binding site BDTNP1_TFBS_sna mE1_TFBS_chinmo
3L	2105093	3L_2105093_SNP [dm3] 3L_2105093_SNP [dm6]	G	C	1.745e^-6	0.994	INTRON sls	TF binding site mE1_TFBS_chinmo
X	22047349	X_22047349_SNP [dm3] X_22645513_SNP [dm6]	T	C	2.649e^-6	0.994	INTERGENIC
3L	2105204	3L_2105204_SNP [dm3] 3L_2105204_SNP [dm6]	T	C	2.977e^-6	0.994	NON_SYNONYMOUS_CODING sls	TF binding site BDTNP1_TFBS_sna mE1_TFBS_chinmo
X	22047303	X_22047303_SNP [dm3] X_22645467_SNP [dm6]	T	A	3.901e^-6	0.994	INTERGENIC
3L	2105103	3L_2105103_SNP [dm3] 3L_2105103_SNP [dm6]	A	C	6.292e^-6	0.994	INTRON sls	TF binding site mE1_TFBS_chinmo
3R	15973841	3R_15973841_SNP [dm3] 3R_20148119_SNP [dm6]	A	T	6.511e^-6	0.994	INTERGENIC
3L	2105272	3L_2105272_SNP [dm3] 3L_2105272_SNP [dm6]	G	T	8.351e^-6	0.994	SYNONYMOUS_CODING sls	TF binding site BDTNP1_TFBS_sna mE1_TFBS_chinmo
2R	16579910	2R_16579910_SNP [dm3] 2R_20692405_SNP [dm6]	A	T	8.406e^-6	0.994	UPSTREAM CG13438 EXON CR44659
2R	16579911	2R_16579911_SNP [dm3] 2R_20692406_SNP [dm6]	T	C	8.406e^-6	0.994	UPSTREAM CG13438 EXON CR44659
2R	8625573	2R_8625573_DEL [dm3] 2R_12738068_DEL [dm6]	TAGCCATGCTT...	T	1.101e^-5	0.994	INTRON CG42663
2L	1999806	2L_1999806_SNP [dm3] 2L_1999806_SNP [dm6]	G	T	1.945e^-5	0.994	UPSTREAM CR43464 INTRON CG33543
2L	4022929	2L_4022929_SNP [dm3] 2L_4022929_SNP [dm6]	A	T	2.590e^-5	0.994	INTERGENIC	TF binding site BDTNP1_TFBS_da
3L	5182286	3L_5182286_SNP [dm3] 3L_5189186_SNP [dm6]	C	T	2.704e^-5	0.994	INTRON shep
3L	5182353	3L_5182353_SNP [dm3] 3L_5189253_SNP [dm6]	C	G	2.704e^-5	0.994	INTRON shep
3L	11527364	3L_11527364_SNP [dm3] 3L_11534264_SNP [dm6]	C	T	2.762e^-5	0.994	INTRON Mob2	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
2L	11506707	2L_11506707_SNP [dm3] 2L_11506707_SNP [dm6]	T	C	2.818e^-5	0.994	SYNONYMOUS_CODING spz4	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	2371970	2R_2371970_SNP [dm3] 2R_6484465_SNP [dm6]	G	T	2.959e^-5	0.994	INTERGENIC	transposable element FlyBase
X	13257039	X_13257039_SNP [dm3] X_13363006_SNP [dm6]	A	T	2.994e^-5	0.994	INTRON Syt12
2R	8625608	2R_8625608_SNP [dm3] 2R_12738103_SNP [dm6]	T	C	3.381e^-5	0.994	INTRON CG42663
2R	16488245	2R_16488245_SNP [dm3] 2R_20600740_SNP [dm6]	A	C	3.546e^-5	0.994	INTRON bl	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	16488246	2R_16488246_SNP [dm3] 2R_20600741_SNP [dm6]	G	C	3.546e^-5	0.994	INTRON bl	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	16488247	2R_16488247_INS [dm3] 2R_20600742_INS [dm6]	C	CA	3.546e^-5	0.994	INTRON bl	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	14142082	2L_14142082_SNP [dm3] 2L_14142082_SNP [dm6]	T	C	3.562e^-5	0.994	INTRON CG17341
2L	5266834	2L_5266834_SNP [dm3] 2L_5266834_SNP [dm6]	T	C	3.726e^-5	0.994	SYNONYMOUS_CODING Cyp4ac2 DOWNSTREAM Cyp4ac1 INTRON tkv
2L	13143997	2L_13143997_SNP [dm3] 2L_13143997_SNP [dm6]	T	A	3.759e^-5	0.994	UPSTREAM CG16978 INTERGENIC
2L	10346156	2L_10346156_SNP [dm3] 2L_10346156_SNP [dm6]	T	C	3.906e^-5	0.994	SYNONYMOUS_CODING CG5022
2L	13114940	2L_13114940_SNP [dm3] 2L_13114940_SNP [dm6]	G	A	4.039e^-5	0.994	INTERGENIC
2L	11344665	2L_11344665_SNP [dm3] 2L_11344665_SNP [dm6]	C	G	4.045e^-5	0.994	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Kr
3R	17087088	3R_17087088_SNP [dm3] 3R_21261366_SNP [dm6]	A	G	4.051e^-5	0.994	INTRON ETHR
3R	14188472	3R_14188472_SNP [dm3] 3R_18362750_SNP [dm6]	G	A	4.087e^-5	0.994	NON_SYNONYMOUS_CODING CG7669	TF binding site mE1_TFBS_cad
3R	11870743	3R_11870743_SNP [dm3] 3R_16045021_SNP [dm6]	G	A	4.107e^-5	0.994	SYNONYMOUS_CODING CG10407 DOWNSTREAM CG10264
X	21527077	X_21527077_SNP [dm3] X_21656050_SNP [dm6]	G	A	4.122e^-5	0.994	INTERGENIC	transposable element FlyBase
2L	5966209	2L_5966209_SNP [dm3] 2L_5966209_SNP [dm6]	T	G	4.170e^-5	0.994	SYNONYMOUS_CODING CG13992	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
X	7970720	X_7970720_SNP [dm3] X_8076687_SNP [dm6]	A	G	4.179e^-5	0.994	SYNONYMOUS_CODING CG1571	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2R	18571469	2R_18571469_SNP [dm3] 2R_22683964_SNP [dm6]	A	G	4.348e^-5	0.994	DOWNSTREAM ppa INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cnc
X	4636883	X_4636883_SNP [dm3] X_4742850_SNP [dm6]	A	G	4.398e^-5	0.994	INTERGENIC
2L	6855623	2L_6855623_SNP [dm3] 2L_6855623_SNP [dm6]	G	A	4.440e^-5	0.994	SYNONYMOUS_CODING l_2_k09022
3L	11473802	3L_11473802_SNP [dm3] 3L_11480702_SNP [dm6]	T	C	4.525e^-5	0.994	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2L	6787659	2L_6787659_SNP [dm3] 2L_6787659_SNP [dm6]	T	C	4.622e^-5	0.994	UPSTREAM nrv1 INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
2L	10346168	2L_10346168_SNP [dm3] 2L_10346168_SNP [dm6]	G	A	4.869e^-5	0.994	SYNONYMOUS_CODING CG5022
X	6448698	X_6448698_SNP [dm3] X_6554665_SNP [dm6]	C	T	5.118e^-5	0.994	SYNONYMOUS_CODING CG34417 INTRON CG34417	TF binding site mE1_TFBS_chinmo
2R	5822548	2R_5822548_SNP [dm3] 2R_9935043_SNP [dm6]	G	C	5.192e^-5	0.994	INTRON Mef2	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	4196823	2L_4196823_SNP [dm3] 2L_4196823_SNP [dm6]	G	T	5.195e^-5	0.994	INTRON CG3714	TF binding site mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sbb
3L	3633578	3L_3633578_SNP [dm3] 3L_3633578_SNP [dm6]	T	A	5.226e^-5	0.994	INTRON dar1	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
X	18636445	X_18636445_DEL [dm3] X_18742412_DEL [dm6]	CC	C	5.299e^-5	0.994	INTERGENIC
2R	8625628	2R_8625628_SNP [dm3] 2R_12738123_SNP [dm6]	G	A	5.588e^-5	0.994	INTRON CG42663
2R	18571606	2R_18571606_SNP [dm3] 2R_22684101_SNP [dm6]	G	A	5.663e^-5	0.994	DOWNSTREAM ppa INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	13120453	3L_13120453_SNP [dm3] 3L_13127353_SNP [dm6]	G	A	5.877e^-5	0.994	INTERGENIC
X	13482055	X_13482055_INS [dm3] X_13588022_INS [dm6]	T	TT	5.989e^-5	0.994	INTRON Tango13
X	22056550	X_22056550_SNP [dm3] X_22654714_SNP [dm6]	G	A	6.156e^-5	0.994	INTERGENIC
3R	13789150	3R_13789150_SNP [dm3] 3R_17963428_SNP [dm6]	G	T	6.388e^-5	0.994	INTRON cpo
X	6448651	X_6448651_SNP [dm3] X_6554618_SNP [dm6]	G	C	6.463e^-5	0.994	NON_SYNONYMOUS_CODING CG34417 INTRON CG34417	TF binding site mE1_TFBS_chinmo
3L	16987512	3L_16987512_SNP [dm3] 3L_16994412_SNP [dm6]	T	G	6.514e^-5	0.994	DOWNSTREAM CG3764 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_da
3L	16987692	3L_16987692_SNP [dm3] 3L_16994592_SNP [dm6]	G	A	6.514e^-5	0.994	DOWNSTREAM CG3764 & 1 other INTERGENIC
X	13482071	X_13482071_SNP [dm3] X_13588038_SNP [dm6]	A	G	6.619e^-5	0.994	INTRON Tango13
X	13482081	X_13482081_SNP [dm3] X_13588048_SNP [dm6]	C	G	6.619e^-5	0.994	INTRON Tango13
2R	13042332	2R_13042332_DEL [dm3] 2R_17154827_DEL [dm6]	TT	T	6.661e^-5	0.994	INTRON CG17290
3R	2704481	3R_2704481_SNP [dm3] 3R_6878759_SNP [dm6]	A	C	6.935e^-5	0.994	INTRON CR44931	regulatory region FlyBase REDfly_CRMs TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	7962865	X_7962865_MNP [dm3] X_8068832_MNP [dm6]	TCAA	GTTT	6.947e^-5	0.994	INTRON mys	TF binding site mE1_TFBS_cad
X	7962869	X_7962869_DEL [dm3] X_8068836_DEL [dm6]	ACGA	A	6.947e^-5	0.994	INTRON mys	TF binding site mE1_TFBS_cad
X	7962874	X_7962874_SNP [dm3] X_8068841_SNP [dm6]	A	C	6.947e^-5	0.994	INTRON mys	TF binding site mE1_TFBS_cad
2L	5265505	2L_5265505_SNP [dm3] 2L_5265505_SNP [dm6]	A	C	7.006e^-5	0.994	SYNONYMOUS_CODING Cyp4ac1 UPSTREAM Cyp4ac2 INTRON tkv	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	11870917	3R_11870917_SNP [dm3] 3R_16045195_SNP [dm6]	G	A	7.021e^-5	0.994	DOWNSTREAM CG10264 INTRON CG10407
2L	1242374	2L_1242374_SNP [dm3] 2L_1242374_SNP [dm6]	C	A	7.236e^-5	0.994	UTR_3_PRIME CG5397 DOWNSTREAM CG5397	TF binding site mE1_TFBS_chinmo
3R	7112774	3R_7112774_SNP [dm3] 3R_11287052_SNP [dm6]	T	C	7.579e^-5	0.994	INTRON CR31386
3L	19131521	3L_19131521_SNP [dm3] 3L_19138421_SNP [dm6]	C	T	7.603e^-5	0.994	INTRON CG14082
2L	11331143	2L_11331143_SNP [dm3] 2L_11331143_SNP [dm6]	T	C	7.651e^-5	0.994	DOWNSTREAM CR44584 INTERGENIC
2L	11331145	2L_11331145_SNP [dm3] 2L_11331145_SNP [dm6]	T	A	7.651e^-5	0.994	DOWNSTREAM CR44584 INTERGENIC
2L	4198308	2L_4198308_SNP [dm3] 2L_4198308_SNP [dm6]	A	G	7.684e^-5	0.994	UPSTREAM CG3714 DOWNSTREAM ft INTERGENIC	TF binding site BDTNP1_TFBS_dl
2R	16579815	2R_16579815_DEL [dm3] 2R_20692310_DEL [dm6]	TTCGCCCTGGGTTT...	T	7.775e^-5	0.994	UPSTREAM CG13438 EXON CR44659
2R	16579722	2R_16579722_SNP [dm3] 2R_20692217_SNP [dm6]	C	T	7.860e^-5	0.994	UPSTREAM CG13438 EXON CR44659
3R	11872094	3R_11872094_SNP [dm3] 3R_16046372_SNP [dm6]	C	T	7.988e^-5	0.994	UTR_3_PRIME ird5 UPSTREAM CG10407
3L	3150980	3L_3150980_SNP [dm3] 3L_3150980_SNP [dm6]	G	A	8.067e^-5	0.994	SYNONYMOUS_CODING BtbVII	TF binding site mE1_TFBS_chinmo
2L	8398469	2L_8398469_DEL [dm3] 2L_8398469_DEL [dm6]	GTTTTCGT	G	8.083e^-5	0.994	UPSTREAM CG13386 DOWNSTREAM CG13385 INTERGENIC
3R	25665920	3R_25665920_DEL [dm3] 3R_29840198_DEL [dm6]	CCTC	C	8.085e^-5	0.994	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	2783086	2L_2783086_SNP [dm3] 2L_2783086_SNP [dm6]	G	A	8.157e^-5	0.994	SYNONYMOUS_CODING Syt1 UTR_3_PRIME Syt1
2L	11331146	2L_11331146_SNP [dm3] 2L_11331146_SNP [dm6]	T	C	8.219e^-5	0.994	DOWNSTREAM CR44584 INTERGENIC
X	13988861	X_13988861_SNP [dm3] X_14094828_SNP [dm6]	C	A	8.349e^-5	0.994	INTERGENIC	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_inv
2R	13403447	2R_13403447_SNP [dm3] 2R_17515942_SNP [dm6]	G	A	8.393e^-5	0.994	NON_SYNONYMOUS_CODING CG4853
2L	4196788	2L_4196788_SNP [dm3] 2L_4196788_SNP [dm6]	G	T	8.557e^-5	0.994	UTR_5_PRIME CG3714 INTRON CG3714	TF binding site mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sbb
2R	16579808	2R_16579808_SNP [dm3] 2R_20692303_SNP [dm6]	T	C	8.566e^-5	0.994	UPSTREAM CG13438 EXON CR44659
2R	2372257	2R_2372257_SNP [dm3] 2R_6484752_SNP [dm6]	T	G	8.613e^-5	0.994	INTERGENIC	transposable element FlyBase
2L	5265511	2L_5265511_SNP [dm3] 2L_5265511_SNP [dm6]	A	G	8.617e^-5	0.994	SYNONYMOUS_CODING Cyp4ac1 UPSTREAM Cyp4ac2 INTRON tkv	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	17279197	3R_17279197_SNP [dm3] 3R_21453475_SNP [dm6]	T	C	8.647e^-5	0.994	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_prd mE1_TFBS_HSA
2R	8625501	2R_8625501_SNP [dm3] 2R_12737996_SNP [dm6]	A	C	8.665e^-5	0.994	INTRON CG42663
2R	7653085	2R_7653085_SNP [dm3] 2R_11765580_SNP [dm6]	T	C	8.667e^-5	0.994	INTRON ths
3L	7386578	3L_7386578_SNP [dm3] 3L_7393478_SNP [dm6]	C	A	8.705e^-5	0.994	INTRON CG8563
2R	13403231	2R_13403231_SNP [dm3] 2R_17515726_SNP [dm6]	C	A	8.716e^-5	0.994	NON_SYNONYMOUS_CODING CG4853
3R	16195775	3R_16195775_SNP [dm3] 3R_20370053_SNP [dm6]	T	C	8.754e^-5	0.994	INTERGENIC
3R	10172088	3R_10172088_SNP [dm3] 3R_14346366_SNP [dm6]	A	C	8.771e^-5	0.994	INTRON NK7.1	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	11303667	3R_11303667_SNP [dm3] 3R_15477945_SNP [dm6]	A	T	8.797e^-5	0.994	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_prd mE1_TFBS_HSA
3R	17087635	3R_17087635_SNP [dm3] 3R_21261913_SNP [dm6]	G	T	8.841e^-5	0.994	SYNONYMOUS_CODING ETHR INTRON ETHR	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	17087636	3R_17087636_SNP [dm3] 3R_21261914_SNP [dm6]	C	T	8.841e^-5	0.994	SYNONYMOUS_CODING ETHR INTRON ETHR	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	25441276	3R_25441276_SNP [dm3] 3R_29615554_SNP [dm6]	G	T	8.841e^-5	0.994	INTRON alph
3R	17259285	3R_17259285_SNP [dm3] 3R_21433563_SNP [dm6]	G	C	8.864e^-5	0.994	SYNONYMOUS_CODING lbl	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_Trl
2R	12617616	2R_12617616_DEL [dm3] 2R_16730111_DEL [dm6]	CCCTCGTCAAGTACGAC...	C	9.197e^-5	0.994	INTRON CG30463	TF binding site BDTNP1_TFBS_dl
2L	4198141	2L_4198141_SNP [dm3] 2L_4198141_SNP [dm6]	T	A	9.197e^-5	0.994	UPSTREAM CG3714 DOWNSTREAM ft INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
3L	18978979	3L_18978979_SNP [dm3] 3L_18985879_SNP [dm6]	A	T	9.604e^-5	0.994	DOWNSTREAM CG11619 & 1 other INTERGENIC
X	7962855	X_7962855_DEL [dm3] X_8068822_DEL [dm6]	AACC	A	9.611e^-5	0.994	INTRON mys	TF binding site mE1_TFBS_cad

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Missing results

By genomic position
Variant impact
Gene name

pc_CN_Hobo_HC phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results