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=4.810e^-1)
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

612 significant hits at p-value < 0.001.

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
2R	9716167	2R_9716167_SNP [dm3] 2R_13828662_SNP [dm6]	A	T	1.660e^-5	0.614	UPSTREAM CG6329 INTRON CG6329	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	4197944	3L_4197944_SNP [dm3] 3L_4197944_SNP [dm6]	A	G	4.991e^-5	0.614	SYNONYMOUS_CODING CG43367	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	4197972	3L_4197972_SNP [dm3] 3L_4197972_SNP [dm6]	C	T	4.991e^-5	0.614	SYNONYMOUS_CODING CG43367	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	4197998	3L_4197998_SNP [dm3] 3L_4197998_SNP [dm6]	T	C	4.991e^-5	0.614	SYNONYMOUS_CODING CG43367	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	4197941	3L_4197941_SNP [dm3] 3L_4197941_SNP [dm6]	G	C	5.518e^-5	0.614	SYNONYMOUS_CODING CG43367	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	2586614	2L_2586614_SNP [dm3] 2L_2586614_SNP [dm6]	G	A	6.036e^-5	0.614	INTERGENIC
2L	2586636	2L_2586636_SNP [dm3] 2L_2586636_SNP [dm6]	G	A	6.036e^-5	0.614	INTERGENIC
2R	17782579	2R_17782579_SNP [dm3] 2R_21895074_SNP [dm6]	C	A	6.871e^-5	0.614	INTRON Fili
2R	17782568	2R_17782568_SNP [dm3] 2R_21895063_SNP [dm6]	G	A	8.606e^-5	0.614	INTRON Fili
2R	17782577	2R_17782577_INS [dm3] 2R_21895072_INS [dm6]	A	AT	8.606e^-5	0.614	INTRON Fili
2R	17782580	2R_17782580_SNP [dm3] 2R_21895075_SNP [dm6]	T	A	8.606e^-5	0.614	INTRON Fili
3L	18979056	3L_18979056_SNP [dm3] 3L_18985956_SNP [dm6]	A	G	9.073e^-5	0.614	UTR_3_PRIME CG11619 DOWNSTREAM CG14075
3L	11141452	3L_11141452_SNP [dm3] 3L_11148352_SNP [dm6]	G	T	1.115e^-4	0.614	INTRON CG32082
X	5575305	X_5575305_SNP [dm3] X_5681272_SNP [dm6]	G	A	1.266e^-4	0.614	SYNONYMOUS_CODING Gr5a EXON CR44958	TF binding site mE1_TFBS_cad
2L	661616	2L_661616_SNP [dm3] 2L_661616_SNP [dm6]	T	C	1.310e^-4	0.614	INTRON ds	TF binding site mE1_TFBS_HSA
2R	10957937	2R_10957937_SNP [dm3] 2R_15070432_SNP [dm6]	G	A	1.310e^-4	0.614	INTERGENIC
3L	12277711	3L_12277711_SNP [dm3] 3L_12284611_SNP [dm6]	C	T	1.478e^-4	0.614	INTERGENIC
3L	18690962	3L_18690962_SNP [dm3] 3L_18697862_SNP [dm6]	G	A	1.621e^-4	0.614	SYNONYMOUS_CODING Dic4
3L	19448008	3L_19448008_SNP [dm3] 3L_19454908_SNP [dm6]	C	T	1.621e^-4	0.614	EXON CR45434	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
3L	19449033	3L_19449033_SNP [dm3] 3L_19455933_SNP [dm6]	A	C	1.621e^-4	0.614	DOWNSTREAM CR45434 INTERGENIC
2R	17960542	2R_17960542_SNP [dm3] 2R_22073037_SNP [dm6]	A	G	1.659e^-4	0.614	SYNONYMOUS_CODING CG11474 DOWNSTREAM CG2921
2R	17006815	2R_17006815_SNP [dm3] 2R_21119310_SNP [dm6]	G	A	1.762e^-4	0.614	SYNONYMOUS_CODING CG9394 INTRON ktub	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
X	2412883	X_2412883_SNP [dm3] X_2518850_SNP [dm6]	T	A	1.762e^-4	0.614	UPSTREAM trol INTRON trol	TF binding site mE1_TFBS_HSA
X	2412910	X_2412910_DEL [dm3] X_2518877_DEL [dm6]	CTTGACTTT	A	1.762e^-4	0.614	UPSTREAM trol INTRON trol	TF binding site mE1_TFBS_HSA
3L	14389630	3L_14389630_SNP [dm3] 3L_14396530_SNP [dm6]	T	C	1.779e^-4	0.614	INTERGENIC
3L	9826640	3L_9826640_SNP [dm3] 3L_9833540_SNP [dm6]	G	A	1.779e^-4	0.614	UTR_3_PRIME CG43897 DOWNSTREAM I-2
2R	10717893	2R_10717893_SNP [dm3] 2R_14830388_SNP [dm6]	G	A	1.900e^-4	0.614	INTERGENIC
X	12813660	X_12813660_SNP [dm3] X_12919627_SNP [dm6]	A	G	1.924e^-4	0.614	UTR_5_PRIME fne
3R	19264202	3R_19264202_SNP [dm3] 3R_23438480_SNP [dm6]	G	A	1.955e^-4	0.614	INTRON CG4374	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	21390934	3R_21390934_SNP [dm3] 3R_25565212_SNP [dm6]	T	C	1.955e^-4	0.614	INTRON msi
3R	21412677	3R_21412677_SNP [dm3] 3R_25586955_SNP [dm6]	C	T	1.955e^-4	0.614	INTRON msi	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
3R	21412852	3R_21412852_SNP [dm3] 3R_25587130_SNP [dm6]	C	T	1.955e^-4	0.614	INTRON msi	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl
3R	25434920	3R_25434920_DEL [dm3] 3R_29609198_DEL [dm6]	TGCTACACG	A	1.955e^-4	0.614	DOWNSTREAM Diedel2 INTRON alph
3R	5469839	3R_5469839_SNP [dm3] 3R_9644117_SNP [dm6]	G	A	1.955e^-4	0.614	DOWNSTREAM Fst INTRON Dh44	TF binding site BDTNP1_TFBS_twi
X	5607100	X_5607100_SNP [dm3] X_5713067_SNP [dm6]	A	G	1.998e^-4	0.614	INTRON CG33080
3L	18576720	3L_18576720_SNP [dm3] 3L_18583620_SNP [dm6]	G	T	2.251e^-4	0.614	EXON CR45435
3R	21412650	3R_21412650_DEL [dm3] 3R_25586928_DEL [dm6]	CCC	C	2.294e^-4	0.614	INTRON msi	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
X	19092385	X_19092385_SNP [dm3] X_19198352_SNP [dm6]	T	C	2.412e^-4	0.614	SYNONYMOUS_CODING CG7990 UTR_3_PRIME CG7990 DOWNSTREAM CG7990	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
X	19092677	X_19092677_SNP [dm3] X_19198644_SNP [dm6]	C	T	2.412e^-4	0.614	SYNONYMOUS_CODING CG7990 UTR_3_PRIME CG7990 DOWNSTREAM CG7990
2R	16359733	2R_16359733_SNP [dm3] 2R_20472228_SNP [dm6]	T	C	2.423e^-4	0.614	SYNONYMOUS_CODING CG12484
X	7086346	X_7086346_INS [dm3] X_7192313_INS [dm6]	T	TCTT	2.463e^-4	0.614	INTRON CG9650 & 1 other	TF binding site mE1_TFBS_HSA mE1_TFBS_jumu mE1_TFBS_sbb
X	21299200	X_21299200_SNP [dm3] X_21428173_SNP [dm6]	G	A	2.536e^-4	0.614	DOWNSTREAM CG10918 INTRON CG42343
2L	2559957	2L_2559957_SNP [dm3] 2L_2559957_SNP [dm6]	C	T	2.548e^-4	0.614	INTERGENIC
X	22203256	X_22203256_DEL [dm3] X_22801420_DEL [dm6]	ATA	A	2.551e^-4	0.614	INTERGENIC
2R	14661124	2R_14661124_SNP [dm3] 2R_18773619_SNP [dm6]	T	A	2.569e^-4	0.614	INTRON Mctp
2R	14714371	2R_14714371_SNP [dm3] 2R_18826866_SNP [dm6]	T	C	2.647e^-4	0.614	INTRON CG15097
3L	7739405	3L_7739405_SNP [dm3] 3L_7746305_SNP [dm6]	G	T	2.647e^-4	0.614	INTRON CG32373
3L	20161441	3L_20161441_SNP [dm3] 3L_20168341_SNP [dm6]	C	A	2.672e^-4	0.614	INTRON CG42674
3R	25783926	3R_25783926_SNP [dm3] 3R_29958204_SNP [dm6]	C	G	2.672e^-4	0.614	INTRON TkR99D
3R	6984638	3R_6984638_SNP [dm3] 3R_11158916_SNP [dm6]	G	T	2.672e^-4	0.614	SYNONYMOUS_CODING Ugt86Da
3R	6993089	3R_6993089_SNP [dm3] 3R_11167367_SNP [dm6]	A	G	2.672e^-4	0.614	SYNONYMOUS_CODING Ugt86De
2R	18246676	2R_18246676_SNP [dm3] 2R_22359171_SNP [dm6]	T	A	2.743e^-4	0.614	INTRON Liprin-gamma
3R	13815491	3R_13815491_SNP [dm3] 3R_17989769_SNP [dm6]	T	C	2.802e^-4	0.614	INTRON cpo	TF binding site mE1_TFBS_inv
2R	3526560	2R_3526560_SNP [dm3] 2R_7639055_SNP [dm6]	A	G	2.899e^-4	0.614	UPSTREAM CG43340 INTRON CG43340	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2R	4328760	2R_4328760_SNP [dm3] 2R_8441255_SNP [dm6]	C	T	2.903e^-4	0.614	UPSTREAM Cyp4ad1 INTRON Cyp4ad1
2R	4328790	2R_4328790_SNP [dm3] 2R_8441285_SNP [dm6]	T	A	2.903e^-4	0.614	UPSTREAM Cyp4ad1 INTRON Cyp4ad1
2R	4328809	2R_4328809_SNP [dm3] 2R_8441304_SNP [dm6]	T	A	2.903e^-4	0.614	UPSTREAM Cyp4ad1 INTRON Cyp4ad1
3L	10817845	3L_10817845_INS [dm3] 3L_10824745_INS [dm6]	T	TGTAC	2.945e^-4	0.614	UPSTREAM CR45246 INTERGENIC
3L	14220777	3L_14220777_SNP [dm3] 3L_14227677_SNP [dm6]	G	A	2.973e^-4	0.614	INTRON nuf	TF binding site BDTNP1_TFBS_sna
3L	14221515	3L_14221515_SNP [dm3] 3L_14228415_SNP [dm6]	T	C	2.973e^-4	0.614	UPSTREAM nuf INTRON nuf	TF binding site BDTNP1_TFBS_sna
3L	18248294	3L_18248294_SNP [dm3] 3L_18255194_SNP [dm6]	T	C	2.973e^-4	0.614	INTERGENIC
3L	18248299	3L_18248299_SNP [dm3] 3L_18255199_SNP [dm6]	G	T	2.973e^-4	0.614	INTERGENIC
3L	18248331	3L_18248331_INS [dm3] 3L_18255231_INS [dm6]	T	AA	2.973e^-4	0.614	INTERGENIC
3L	3800669	3L_3800669_SNP [dm3] 3L_3800669_SNP [dm6]	G	T	2.973e^-4	0.614	UTR_5_PRIME CG32264 INTRON CG32264	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
3L	3800672	3L_3800672_SNP [dm3] 3L_3800672_SNP [dm6]	G	C	2.973e^-4	0.614	UTR_5_PRIME CG32264 INTRON CG32264	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
3L	7739318	3L_7739318_SNP [dm3] 3L_7746218_SNP [dm6]	C	A	2.973e^-4	0.614	INTRON CG32373
X	9978521	X_9978521_SNP [dm3] X_10084488_SNP [dm6]	A	G	3.001e^-4	0.614	SYNONYMOUS_CODING CG2972 DOWNSTREAM CG2974	TF binding site mE1_TFBS_cad
X	2412906	X_2412906_SNP [dm3] X_2518873_SNP [dm6]	C	T	3.034e^-4	0.614	UPSTREAM trol INTRON trol	TF binding site mE1_TFBS_HSA
X	21297342	X_21297342_SNP [dm3] X_21426315_SNP [dm6]	G	C	3.100e^-4	0.614	INTRON CG42343
X	21299141	X_21299141_SNP [dm3] X_21428114_SNP [dm6]	G	A	3.100e^-4	0.614	DOWNSTREAM CG10918 INTRON CG42343
X	21299159	X_21299159_SNP [dm3] X_21428132_SNP [dm6]	T	C	3.100e^-4	0.614	DOWNSTREAM CG10918 INTRON CG42343
2R	10957975	2R_10957975_SNP [dm3] 2R_15070470_SNP [dm6]	C	G	3.135e^-4	0.614	INTERGENIC
X	8671738	X_8671738_INS [dm3] X_8777705_INS [dm6]	T	TGGT	3.135e^-4	0.614	INTRON Lim1	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi
3L	2888428	3L_2888428_SNP [dm3] 3L_2888428_SNP [dm6]	T	C	3.191e^-4	0.614	INTRON spz5	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	19447853	3L_19447853_SNP [dm3] 3L_19454753_SNP [dm6]	A	G	3.225e^-4	0.614	UPSTREAM CR45434 INTERGENIC	TF binding site mE1_TFBS_inv
2R	7542334	2R_7542334_SNP [dm3] 2R_11654829_SNP [dm6]	G	C	3.338e^-4	0.614	UPSTREAM CG13198 INTRON Roc2
3L	14757005	3L_14757005_SNP [dm3] 3L_14763905_SNP [dm6]	C	T	3.342e^-4	0.614	UTR_5_PRIME CG9384	TF binding site mE1_TFBS_cad
3L	18978979	3L_18978979_SNP [dm3] 3L_18985879_SNP [dm6]	A	T	3.349e^-4	0.614	DOWNSTREAM CG11619 & 1 other INTERGENIC
3L	19447725	3L_19447725_SNP [dm3] 3L_19454625_SNP [dm6]	G	T	3.368e^-4	0.614	UPSTREAM CR45434 INTERGENIC	TF binding site mE1_TFBS_inv
X	10775097	X_10775097_SNP [dm3] X_10881064_SNP [dm6]	T	C	3.368e^-4	0.614	INTRON Ork1
3L	3507295	3L_3507295_SNP [dm3] 3L_3507295_SNP [dm6]	C	T	3.517e^-4	0.614	INTRON CG42324	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3R	13768719	3R_13768719_SNP [dm3] 3R_17942997_SNP [dm6]	G	A	3.527e^-4	0.614	INTRON cpo	TF binding site BDTNP1_TFBS_dl mE1_TFBS_chinmo mE1_TFBS_sens mE1_TFBS_Trl
2L	16940033	2L_16940033_SNP [dm3] 2L_16940033_SNP [dm6]	C	G	3.606e^-4	0.614	INTERGENIC
3R	15738438	3R_15738438_SNP [dm3] 3R_19912716_SNP [dm6]	C	T	3.628e^-4	0.614	SYNONYMOUS_CODING RhoGAP92B	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3R	6996631	3R_6996631_SNP [dm3] 3R_11170909_SNP [dm6]	G	C	3.628e^-4	0.614	UTR_3_PRIME Ugt35a UPSTREAM Ugt35b
3R	6997257	3R_6997257_SNP [dm3] 3R_11171535_SNP [dm6]	C	T	3.628e^-4	0.614	SYNONYMOUS_CODING Ugt35a
3L	16543479	3L_16543479_SNP [dm3] 3L_16550379_SNP [dm6]	C	T	3.636e^-4	0.614	INTERGENIC
3L	13920332	3L_13920332_SNP [dm3] 3L_13927232_SNP [dm6]	C	T	3.724e^-4	0.614	SYNONYMOUS_CODING CG8833
2R	10717596	2R_10717596_SNP [dm3] 2R_14830091_SNP [dm6]	T	C	3.765e^-4	0.614	INTERGENIC
2R	10999516	2R_10999516_SNP [dm3] 2R_15112011_SNP [dm6]	G	A	3.765e^-4	0.614	INTERGENIC
2R	10999541	2R_10999541_SNP [dm3] 2R_15112036_SNP [dm6]	G	T	3.765e^-4	0.614	INTERGENIC
3L	13930506	3L_13930506_SNP [dm3] 3L_13937406_SNP [dm6]	A	G	3.804e^-4	0.614	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	19535135	3L_19535135_SNP [dm3] 3L_19542035_SNP [dm6]	C	A	3.836e^-4	0.614	NON_SYNONYMOUS_CODING CG9279	TF binding site mE1_TFBS_cad
3L	826301	3L_826301_SNP [dm3] 3L_826301_SNP [dm6]	A	G	3.836e^-4	0.614	DOWNSTREAM CG13900 & 2 others INTERGENIC
2L	13942553	2L_13942553_SNP [dm3] 2L_13942553_SNP [dm6]	T	G	3.841e^-4	0.614	INTRON Ance-3
2R	9965059	2R_9965059_SNP [dm3] 2R_14077554_SNP [dm6]	T	C	3.873e^-4	0.614	INTRON Prosap
2L	7536368	2L_7536368_SNP [dm3] 2L_7536368_SNP [dm6]	G	T	3.874e^-4	0.614	SYNONYMOUS_CODING RapGAP1	TF binding site mE1_TFBS_cad
2L	7536371	2L_7536371_SNP [dm3] 2L_7536371_SNP [dm6]	T	G	3.874e^-4	0.614	SYNONYMOUS_CODING RapGAP1	TF binding site mE1_TFBS_cad
X	22339660	X_22339660_SNP [dm3] X_22937824_SNP [dm6]	A	G	3.907e^-4	0.614	INTERGENIC
3R	26039612	3R_26039612_SNP [dm3] 3R_30213890_SNP [dm6]	C	T	3.997e^-4	0.614	UPSTREAM CecB DOWNSTREAM Cec2 INTERGENIC

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Phenotype distribution and association to known covariates

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GWAS results