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=1.013e^-5)
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

2328 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	17937594	3L_17937594_SNP [dm3] 3L_17944494_SNP [dm6]	T	C	2.161e^-7	0.246	INTRON CG43174
3L	11122657	3L_11122657_SNP [dm3] 3L_11129557_SNP [dm6]	A	G	2.712e^-7	0.246	UTR_5_PRIME CG42575
2L	9152379	2L_9152379_SNP [dm3] 2L_9152379_SNP [dm6]	A	G	7.080e^-7	0.271	INTRON CG32982
3R	21794488	3R_21794488_DEL [dm3] 3R_25968766_DEL [dm6]	GG	G	8.057e^-7	0.271	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3R	21794368	3R_21794368_INS [dm3] 3R_25968646_INS [dm6]	T	TT	1.046e^-6	0.271	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3L	4659310	3L_4659310_SNP [dm3] 3L_4659310_SNP [dm6]	G	A	1.406e^-6	0.271	INTRON axo
3L	4659296	3L_4659296_SNP [dm3] 3L_4659296_SNP [dm6]	T	C	1.413e^-6	0.271	INTRON axo
3L	4659302	3L_4659302_SNP [dm3] 3L_4659302_SNP [dm6]	A	G	1.413e^-6	0.271	INTRON axo
3L	4659304	3L_4659304_SNP [dm3] 3L_4659304_SNP [dm6]	A	T	1.413e^-6	0.271	INTRON axo
3L	5430349	3L_5430349_INS [dm3] 3L_5437249_INS [dm6]	T	TT	1.492e^-6	0.271	INTRON CG34391
2R	14346359	2R_14346359_SNP [dm3] 2R_18458854_SNP [dm6]	A	C	1.679e^-6	0.277	DOWNSTREAM CG30116 INTRON CG30116
3R	21794477	3R_21794477_SNP [dm3] 3R_25968755_SNP [dm6]	C	T	2.381e^-6	0.361	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3L	4659254	3L_4659254_SNP [dm3] 3L_4659254_SNP [dm6]	A	T	3.152e^-6	0.408	INTRON axo
2L	3985015	2L_3985015_SNP [dm3] 2L_3985015_SNP [dm6]	C	A	3.893e^-6	0.408	INTRON fred
3L	11124419	3L_11124419_SNP [dm3] 3L_11131319_SNP [dm6]	G	T	3.955e^-6	0.408	UTR_3_PRIME nol DOWNSTREAM CG32074 INTRON CG42575
3L	11124420	3L_11124420_SNP [dm3] 3L_11131320_SNP [dm6]	G	A	3.955e^-6	0.408	UTR_3_PRIME nol DOWNSTREAM CG32074 INTRON CG42575
2R	18942398	2R_18942398_SNP [dm3] 2R_23054875_SNP [dm6]	G	A	4.032e^-6	0.408	UPSTREAM CG44252 INTERGENIC
3L	4659280	3L_4659280_SNP [dm3] 3L_4659280_SNP [dm6]	A	G	4.329e^-6	0.408	INTRON axo
3L	4659283	3L_4659283_SNP [dm3] 3L_4659283_SNP [dm6]	A	C	4.329e^-6	0.408	INTRON axo
3L	4659205	3L_4659205_SNP [dm3] 3L_4659205_SNP [dm6]	G	T	5.004e^-6	0.408	INTRON axo
3L	4659225	3L_4659225_SNP [dm3] 3L_4659225_SNP [dm6]	G	C	5.004e^-6	0.408	INTRON axo
3L	4659235	3L_4659235_SNP [dm3] 3L_4659235_SNP [dm6]	T	C	5.004e^-6	0.408	INTRON axo
3L	11125617	3L_11125617_SNP [dm3] 3L_11132517_SNP [dm6]	A	G	5.335e^-6	0.408	UPSTREAM CG32074 INTRON CG42575
3L	4659210	3L_4659210_SNP [dm3] 3L_4659210_SNP [dm6]	G	T	5.392e^-6	0.408	INTRON axo
2R	16960128	2R_16960128_SNP [dm3] 2R_21072623_SNP [dm6]	A	G	6.087e^-6	0.426	DOWNSTREAM CR44704 INTRON CG10527	TF binding site mE1_TFBS_Trl
3L	4659206	3L_4659206_SNP [dm3] 3L_4659206_SNP [dm6]	G	T	6.104e^-6	0.426	INTRON axo
3L	12129782	3L_12129782_SNP [dm3] 3L_12136682_SNP [dm6]	C	T	6.688e^-6	0.45	UTR_5_PRIME CG5645 UPSTREAM Atg12 DOWNSTREAM l_3_neo18	TF binding site mE1_TFBS_cad
3L	4659222	3L_4659222_SNP [dm3] 3L_4659222_SNP [dm6]	T	G	7.553e^-6	0.473	INTRON axo
2L	9147938	2L_9147938_SNP [dm3] 2L_9147938_SNP [dm6]	T	G	7.554e^-6	0.473	INTRON CG32982	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad
3R	4296467	3R_4296467_SNP [dm3] 3R_8470745_SNP [dm6]	G	A	8.018e^-6	0.486	INTRON CG45263	TF binding site BDTNP1_TFBS_dl
2R	9656866	2R_9656866_SNP [dm3] 2R_13769361_SNP [dm6]	A	G	8.887e^-6	0.521	UPSTREAM Cpr50Ca INTERGENIC
3R	22563163	3R_22563163_SNP [dm3] 3R_26737441_SNP [dm6]	T	C	9.498e^-6	0.525	UPSTREAM CG14247 INTERGENIC
3R	4325628	3R_4325628_SNP [dm3] 3R_8499906_SNP [dm6]	T	C	9.804e^-6	0.525	INTERGENIC
3L	12978525	3L_12978525_SNP [dm3] 3L_12985425_SNP [dm6]	C	T	9.823e^-6	0.525	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_zfh1
2R	16959829	2R_16959829_SNP [dm3] 2R_21072324_SNP [dm6]	T	G	1.143e^-5	0.593	DOWNSTREAM CR44704 INTRON CG10527	TF binding site mE1_TFBS_Trl
2L	12491349	2L_12491349_SNP [dm3] 2L_12491349_SNP [dm6]	A	T	1.217e^-5	0.593	INTRON bun
3L	13060245	3L_13060245_SNP [dm3] 3L_13067145_SNP [dm6]	C	T	1.239e^-5	0.593	INTERGENIC
3R	8400796	3R_8400796_SNP [dm3] 3R_12575074_SNP [dm6]	A	G	1.241e^-5	0.593	INTRON Octbeta2R
3L	11112660	3L_11112660_DEL [dm3] 3L_11119560_DEL [dm6]	GA	G	1.288e^-5	0.6	UPSTREAM fd68A INTRON fd68A	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl mE1_TFBS_zfh1
3L	7188049	3L_7188049_SNP [dm3] 3L_7194949_SNP [dm6]	A	G	1.334e^-5	0.606	INTERGENIC
3R	4253096	3R_4253096_SNP [dm3] 3R_8427374_SNP [dm6]	G	T	1.392e^-5	0.612	INTRON CG45263
3L	11120080	3L_11120080_SNP [dm3] 3L_11126980_SNP [dm6]	T	A	1.415e^-5	0.612	INTRON CG42575	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1
3L	1843145	3L_1843145_SNP [dm3] 3L_1843145_SNP [dm6]	C	T	1.544e^-5	0.652	INTERGENIC
3L	12018890	3L_12018890_SNP [dm3] 3L_12025790_SNP [dm6]	T	A	1.627e^-5	0.672	INTRON rols
2R	17810642	2R_17810642_INS [dm3] 2R_21923137_INS [dm6]	G	GG	1.681e^-5	0.679	INTRON Fili
3L	11120002	3L_11120002_SNP [dm3] 3L_11126902_SNP [dm6]	C	G	1.924e^-5	0.725	INTRON CG42575	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_cad
3L	11120016	3L_11120016_SNP [dm3] 3L_11126916_SNP [dm6]	G	A	1.924e^-5	0.725	INTRON CG42575	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1
3L	11120078	3L_11120078_SNP [dm3] 3L_11126978_SNP [dm6]	C	G	1.924e^-5	0.725	INTRON CG42575	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1
3L	9291467	3L_9291467_SNP [dm3] 3L_9298367_SNP [dm6]	A	T	1.956e^-5	0.725	INTERGENIC
3L	11122095	3L_11122095_SNP [dm3] 3L_11128995_SNP [dm6]	T	A	2.014e^-5	0.732	UTR_5_PRIME CG42575 UPSTREAM CG42575
3R	4099775	3R_4099775_SNP [dm3] 3R_8274053_SNP [dm6]	A	C	2.133e^-5	0.74	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_slp1
2L	6809268	2L_6809268_SNP [dm3] 2L_6809268_SNP [dm6]	T	C	2.176e^-5	0.74	INTERGENIC
3L	14095880	3L_14095880_SNP [dm3] 3L_14102780_SNP [dm6]	A	C	2.353e^-5	0.74	DOWNSTREAM Sox21a INTERGENIC
3L	16868190	3L_16868190_SNP [dm3] 3L_16875090_SNP [dm6]	T	A	2.409e^-5	0.74	INTRON Lmpt
3L	21968433	3L_21968433_SNP [dm3] 3L_21975333_SNP [dm6]	A	G	2.560e^-5	0.74	INTRON CG7470
2L	19952504	2L_19952504_SNP [dm3] 2L_19952504_SNP [dm6]	G	A	2.656e^-5	0.74	INTRON sick	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA
2L	12491435	2L_12491435_SNP [dm3] 2L_12491435_SNP [dm6]	A	T	2.697e^-5	0.74	INTRON bun
3L	13935632	3L_13935632_SNP [dm3] 3L_13942532_SNP [dm6]	C	T	2.713e^-5	0.74	INTRON CG32137	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna mE1_TFBS_HSA
3R	17222535	3R_17222535_SNP [dm3] 3R_21396813_SNP [dm6]	G	A	2.796e^-5	0.74	DOWNSTREAM CG6475 INTERGENIC	regulatory region REDfly_CRMs
2L	9147765	2L_9147765_SNP [dm3] 2L_9147765_SNP [dm6]	C	T	2.866e^-5	0.74	INTRON CG32982	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad
X	8151464	X_8151464_SNP [dm3] X_8257431_SNP [dm6]	G	T	2.867e^-5	0.74	INTRON CG1632
2R	17752132	2R_17752132_SNP [dm3] 2R_21864627_SNP [dm6]	T	C	2.899e^-5	0.74	DOWNSTREAM comr INTERGENIC
2R	17752140	2R_17752140_SNP [dm3] 2R_21864635_SNP [dm6]	C	T	2.899e^-5	0.74	DOWNSTREAM comr INTERGENIC
3L	17938749	3L_17938749_SNP [dm3] 3L_17945649_SNP [dm6]	G	A	2.997e^-5	0.74	UTR_5_PRIME CG43174
2R	15183577	2R_15183577_SNP [dm3] 2R_19296072_SNP [dm6]	G	C	3.023e^-5	0.74	INTRON Tab2	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
3R	8396319	3R_8396319_SNP [dm3] 3R_12570597_SNP [dm6]	G	A	3.093e^-5	0.74	INTRON Octbeta2R
2R	12667091	2R_12667091_SNP [dm3] 2R_16779586_SNP [dm6]	C	T	3.107e^-5	0.74	UPSTREAM resilin DOWNSTREAM Vkor INTERGENIC	TF binding site mE1_TFBS_cad
3L	11050564	3L_11050564_SNP [dm3] 3L_11057464_SNP [dm6]	A	G	3.139e^-5	0.74	INTRON CG7888
3L	1853270	3L_1853270_SNP [dm3] 3L_1853270_SNP [dm6]	C	T	3.139e^-5	0.74	INTRON CG13936
2R	12139285	2R_12139285_SNP [dm3] 2R_16251780_SNP [dm6]	C	T	3.159e^-5	0.74	INTRON CngA
3R	9663863	3R_9663863_SNP [dm3] 3R_13838141_SNP [dm6]	G	C	3.187e^-5	0.74	UPSTREAM Nsf2 DOWNSTREAM CG31495 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_Ubx
2L	12491401	2L_12491401_SNP [dm3] 2L_12491401_SNP [dm6]	G	A	3.199e^-5	0.74	INTRON bun
3R	26240869	3R_26240869_SNP [dm3] 3R_30415147_SNP [dm6]	T	C	3.284e^-5	0.74	INTERGENIC
2R	12542676	2R_12542676_SNP [dm3] 2R_16655171_SNP [dm6]	G	A	3.287e^-5	0.74	UPSTREAM Nach DOWNSTREAM Picot INTERGENIC
3R	15301280	3R_15301280_SNP [dm3] 3R_19475558_SNP [dm6]	G	C	3.456e^-5	0.74	INTRON Dys	TF binding site mE1_TFBS_inv
2R	16959828	2R_16959828_SNP [dm3] 2R_21072323_SNP [dm6]	C	G	3.456e^-5	0.74	DOWNSTREAM CR44704 INTRON CG10527	TF binding site mE1_TFBS_Trl
3L	10113014	3L_10113014_SNP [dm3] 3L_10119914_SNP [dm6]	C	A	3.489e^-5	0.74	INTRON dpr6
3R	6797474	3R_6797474_SNP [dm3] 3R_10971752_SNP [dm6]	C	T	3.490e^-5	0.74	UPSTREAM CG34114 INTERGENIC
3L	5430378	3L_5430378_SNP [dm3] 3L_5437278_SNP [dm6]	A	T	3.556e^-5	0.74	INTRON CG34391
3R	5575562	3R_5575562_SNP [dm3] 3R_9749840_SNP [dm6]	C	T	3.567e^-5	0.74	SYNONYMOUS_CODING PpD3
2R	17334235	2R_17334235_SNP [dm3] 2R_21446730_SNP [dm6]	T	C	3.686e^-5	0.74	INTRON Sdc
2R	16097859	2R_16097859_SNP [dm3] 2R_20210354_SNP [dm6]	C	T	3.710e^-5	0.74	INTERGENIC	TF binding site mE1_TFBS_inv
3L	8447007	3L_8447007_SNP [dm3] 3L_8453907_SNP [dm6]	T	C	3.742e^-5	0.74	INTRON Gug	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad
3L	4483604	3L_4483604_SNP [dm3] 3L_4483604_SNP [dm6]	T	C	3.831e^-5	0.74	SYNONYMOUS_CODING CG11350
2L	16658646	2L_16658646_SNP [dm3] 2L_16658646_SNP [dm6]	A	G	3.832e^-5	0.74	SYNONYMOUS_CODING CG42389	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	17937972	3L_17937972_SNP [dm3] 3L_17944872_SNP [dm6]	G	C	3.843e^-5	0.74	INTRON CG43174
3R	8372968	3R_8372968_SNP [dm3] 3R_12547246_SNP [dm6]	G	T	3.871e^-5	0.74	INTRON Octbeta3R
2R	12542618	2R_12542618_SNP [dm3] 2R_16655113_SNP [dm6]	G	T	4.100e^-5	0.74	UPSTREAM Nach DOWNSTREAM Picot INTERGENIC
2R	17158227	2R_17158227_SNP [dm3] 2R_21270722_SNP [dm6]	C	T	4.142e^-5	0.74	INTRON Rgk3
2R	19341961	2R_19341961_SNP [dm3] 2R_23454438_SNP [dm6]	T	C	4.214e^-5	0.74	INTRON CG43795
2L	2120921	2L_2120921_SNP [dm3] 2L_2120921_SNP [dm6]	G	C	4.221e^-5	0.74	INTERGENIC
3L	6840566	3L_6840566_SNP [dm3] 3L_6847466_SNP [dm6]	A	C	4.281e^-5	0.74	INTERGENIC	TF binding site mE1_TFBS_inv
3R	6735148	3R_6735148_SNP [dm3] 3R_10909426_SNP [dm6]	T	C	4.284e^-5	0.74	INTERGENIC
2R	2619287	2R_2619287_SNP [dm3] 2R_6731782_SNP [dm6]	G	T	4.333e^-5	0.74	INTRON l_2_01289
3L	11126371	3L_11126371_SNP [dm3] 3L_11133271_SNP [dm6]	G	T	4.336e^-5	0.74	NON_SYNONYMOUS_CODING CG42575 UPSTREAM CG32074	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3L	11119051	3L_11119051_SNP [dm3] 3L_11125951_SNP [dm6]	C	T	4.340e^-5	0.74	INTRON CG42575	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_cad
3L	7097325	3L_7097325_SNP [dm3] 3L_7104225_SNP [dm6]	A	G	4.485e^-5	0.74	INTRON form3
2R	16097956	2R_16097956_SNP [dm3] 2R_20210451_SNP [dm6]	T	C	4.549e^-5	0.74	INTERGENIC	TF binding site mE1_TFBS_inv
3L	11112363	3L_11112363_SNP [dm3] 3L_11119263_SNP [dm6]	G	A	4.572e^-5	0.74	UTR_5_PRIME fd68A UPSTREAM fd68A INTRON fd68A	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_Trl
3R	21794341	3R_21794341_SNP [dm3] 3R_25968619_SNP [dm6]	T	G	4.622e^-5	0.74	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb

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Missing results

By genomic position
Variant impact
Gene name

pc_FPKP_PElem_SS phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results