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=5.324e^-25)
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

Covariate	p-value	Significance
In_3R_K	1.238e-07

Kruskal-Wallis test

Covariate	χ²	p-value
wolba	3.1805	0.0745
In_2L_t	10.3001	0.0058
In_3R_K	29.6606	3.6248e-07

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1753 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
2L	1478024	2L_1478024_SNP [dm3] 2L_1478024_SNP [dm6]	A	G	2.403e^-7	0.236	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl
2L	1477782	2L_1477782_DEL [dm3] 2L_1477782_DEL [dm6]	ACTTGTATTTTAATGCAAA...	A	2.519e^-7	0.236	INTERGENIC
2L	1477870	2L_1477870_SNP [dm3] 2L_1477870_SNP [dm6]	A	G	5.868e^-7	0.268	INTERGENIC
2L	1477876	2L_1477876_SNP [dm3] 2L_1477876_SNP [dm6]	C	G	7.065e^-7	0.268	INTERGENIC
2L	1477748	2L_1477748_SNP [dm3] 2L_1477748_SNP [dm6]	A	C	7.132e^-7	0.268	INTERGENIC
2L	1477770	2L_1477770_SNP [dm3] 2L_1477770_SNP [dm6]	C	G	1.204e^-6	0.376	INTERGENIC
2L	21166539	2L_21166539_SNP [dm3] 2L_21166539_SNP [dm6]	G	T	1.850e^-6	0.441	NON_SYNONYMOUS_CODING CG43346 UTR_3_PRIME CG43345 DOWNSTREAM CG9246	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
2L	21157970	2L_21157970_SNP [dm3] 2L_21157970_SNP [dm6]	C	T	1.882e^-6	0.441	SYNONYMOUS_CODING CG9249 UPSTREAM CG9248 DOWNSTREAM Mpp6	TF binding site mE1_TFBS_sens
2L	21112848	2L_21112848_SNP [dm3] 2L_21112848_SNP [dm6]	A	T	3.588e^-6	0.748	INTRON Nhe2
3L	7452459	3L_7452459_SNP [dm3] 3L_7459359_SNP [dm6]	C	T	5.412e^-6	0.866	DOWNSTREAM ppk26 INTERGENIC
3R	14388987	3R_14388987_SNP [dm3] 3R_18563265_SNP [dm6]	C	T	5.437e^-6	0.866	DOWNSTREAM CG43210 & 1 other INTERGENIC
2L	21111347	2L_21111347_SNP [dm3] 2L_21111347_SNP [dm6]	T	C	6.404e^-6	0.866	INTRON Nhe2
2L	14265547	2L_14265547_SNP [dm3] 2L_14265547_SNP [dm6]	A	G	7.760e^-6	0.866	INTRON wb	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Kr
2L	1477230	2L_1477230_SNP [dm3] 2L_1477230_SNP [dm6]	A	T	7.877e^-6	0.866	INTERGENIC	TF binding site mE1_TFBS_sens
3R	18246679	3R_18246679_SNP [dm3] 3R_22420957_SNP [dm6]	G	A	8.198e^-6	0.866	UTR_5_PRIME Nop56 UPSTREAM mats	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	1076496	2R_1076496_SNP [dm3] 2R_5188991_SNP [dm6]	G	T	8.374e^-6	0.866	INTRON Nipped-A
2R	19251220	2R_19251220_SNP [dm3] 2R_23363697_SNP [dm6]	G	T	8.430e^-6	0.866	NON_SYNONYMOUS_CODING vir	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	21076984	2L_21076984_DEL [dm3] 2L_21076984_DEL [dm6]	AA	A	8.768e^-6	0.866	INTRON tadr
2L	21077069	2L_21077069_DEL [dm3] 2L_21077069_DEL [dm6]	TTTGCGC	GATTA	8.768e^-6	0.866	INTRON tadr
3R	14388983	3R_14388983_SNP [dm3] 3R_18563261_SNP [dm6]	T	A	9.797e^-6	0.872	INTERGENIC
3L	1825298	3L_1825298_SNP [dm3] 3L_1825298_SNP [dm6]	T	C	1.015e^-5	0.872	INTRON Cpr62Ba
X	1889459	X_1889459_SNP [dm3] X_1995426_SNP [dm6]	A	G	1.155e^-5	0.872	INTRON Hr4	TF binding site BDTNP1_TFBS_dl
X	13606673	X_13606673_SNP [dm3] X_13712640_SNP [dm6]	G	T	1.191e^-5	0.872	SYNONYMOUS_CODING NnaD INTRON CG9940
3R	14388986	3R_14388986_SNP [dm3] 3R_18563264_SNP [dm6]	G	T	1.205e^-5	0.872	DOWNSTREAM CG43210 & 1 other INTERGENIC
2L	21076144	2L_21076144_SNP [dm3] 2L_21076144_SNP [dm6]	C	T	1.245e^-5	0.872	INTRON tadr
2L	14265526	2L_14265526_SNP [dm3] 2L_14265526_SNP [dm6]	A	C	1.332e^-5	0.872	INTRON wb	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Kr
3L	7119481	3L_7119481_SNP [dm3] 3L_7126381_SNP [dm6]	A	C	1.368e^-5	0.872	SYNONYMOUS_CODING BBS1 UPSTREAM msl-3	TF binding site BDTNP1_TFBS_dl mE1_TFBS_chinmo mE1_TFBS_HSA
2L	21149705	2L_21149705_SNP [dm3] 2L_21149705_SNP [dm6]	C	T	1.384e^-5	0.872	INTERGENIC	transposable element FlyBase
2L	21108159	2L_21108159_SNP [dm3] 2L_21108159_SNP [dm6]	C	T	1.387e^-5	0.872	UTR_5_PRIME Nhe2 UPSTREAM CR44056 INTRON Nhe2	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
2L	21086296	2L_21086296_SNP [dm3] 2L_21086296_SNP [dm6]	G	A	1.424e^-5	0.872	NON_SYNONYMOUS_CODING CG33509 DOWNSTREAM ppk13
3L	16975630	3L_16975630_SNP [dm3] 3L_16982530_SNP [dm6]	T	A	1.441e^-5	0.872	NON_SYNONYMOUS_CODING Exn	TF binding site mE1_TFBS_cad
3L	5706169	3L_5706169_SNP [dm3] 3L_5713069_SNP [dm6]	C	A	1.516e^-5	0.888	UPSTREAM CG44521 INTRON sif
2R	6923942	2R_6923942_SNP [dm3] 2R_11036437_SNP [dm6]	A	T	1.656e^-5	0.915	INTRON luna
2L	21163362	2L_21163362_SNP [dm3] 2L_21163362_SNP [dm6]	T	G	1.756e^-5	0.915	UPSTREAM CG9246 & 1 other DOWNSTREAM CR44910 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	14670959	3R_14670959_SNP [dm3] 3R_18845237_SNP [dm6]	G	T	1.758e^-5	0.915	INTRON CG18208
2L	21155005	2L_21155005_SNP [dm3] 2L_21155005_SNP [dm6]	T	C	1.799e^-5	0.915	INTRON E2f2	TF binding site BDTNP1_TFBS_dl mE1_TFBS_sens
X	5922882	X_5922882_SNP [dm3] X_6028849_SNP [dm6]	T	G	1.805e^-5	0.915	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	12634410	3L_12634410_SNP [dm3] 3L_12641310_SNP [dm6]	T	C	1.976e^-5	0.969	INTRON CR32111	TF binding site mE1_TFBS_HSA
2R	12092069	2R_12092069_SNP [dm3] 2R_16204564_SNP [dm6]	C	G	2.052e^-5	0.969	SYNONYMOUS_CODING mrj
X	19760686	X_19760686_DEL [dm3] X_19866653_DEL [dm6]	TT	T	2.108e^-5	0.969	INTRON Hers	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl mE1_TFBS_zfh1
2R	19237734	2R_19237734_SNP [dm3] 2R_23350211_SNP [dm6]	A	G	2.118e^-5	0.969	INTERGENIC	TF binding site mE1_TFBS_chinmo
3R	21257788	3R_21257788_SNP [dm3] 3R_25432066_SNP [dm6]	A	G	2.299e^-5	0.988	INTRON Fur1
2L	21153908	2L_21153908_SNP [dm3] 2L_21153908_SNP [dm6]	C	T	2.301e^-5	0.988	DOWNSTREAM E2f2 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_disco mE1_TFBS_GATAe mE1_TFBS_hkb mE1_TFBS_HSA
2R	19246030	2R_19246030_SNP [dm3] 2R_23358507_SNP [dm6]	T	A	2.348e^-5	0.988	UTR_3_PRIME CG9875 UPSTREAM CG3500 & 2 others DOWNSTREAM CG9875 EXON CR44168
2R	9042232	2R_9042232_SNP [dm3] 2R_13154727_SNP [dm6]	T	C	2.376e^-5	0.988	SYNONYMOUS_CODING TppII
2L	21118004	2L_21118004_SNP [dm3] 2L_21118004_SNP [dm6]	C	T	2.559e^-5	0.988	SYNONYMOUS_CODING Nhe2
2L	21091215	2L_21091215_SNP [dm3] 2L_21091215_SNP [dm6]	C	T	2.604e^-5	0.988	UPSTREAM CG14397 DOWNSTREAM CG9259 INTERGENIC
3R	7286950	3R_7286950_SNP [dm3] 3R_11461228_SNP [dm6]	A	T	2.671e^-5	0.988	UPSTREAM PGRP-LB INTRON CG17230
X	7987952	X_7987952_SNP [dm3] X_8093919_SNP [dm6]	T	C	2.830e^-5	0.988	UTR_5_PRIME Ubc-E2H DOWNSTREAM CG2258	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_bab1 mE1_TFBS_D mE1_TFBS_hkb mE1_TFBS_HSA
3R	21265064	3R_21265064_SNP [dm3] 3R_25439342_SNP [dm6]	A	G	2.881e^-5	0.988	INTRON Fur1
2L	21153999	2L_21153999_SNP [dm3] 2L_21153999_SNP [dm6]	T	C	2.948e^-5	0.988	DOWNSTREAM E2f2 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_disco mE1_TFBS_GATAe mE1_TFBS_h mE1_TFBS_hkb mE1_TFBS_HSA
2L	526385	2L_526385_SNP [dm3] 2L_526385_SNP [dm6]	G	A	3.006e^-5	0.988	INTRON ush	regulatory region REDfly_CRMs TF binding site mE1_TFBS_Kr
2L	21056327	2L_21056327_SNP [dm3] 2L_21056327_SNP [dm6]	A	G	3.049e^-5	0.988	NON_SYNONYMOUS_CODING Itgbetanu
3L	13105636	3L_13105636_SNP [dm3] 3L_13112536_SNP [dm6]	T	G	3.197e^-5	0.988	INTERGENIC
2L	11491598	2L_11491598_DEL [dm3] 2L_11491598_DEL [dm6]	AA	A	3.202e^-5	0.988	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA
2R	18289049	2R_18289049_SNP [dm3] 2R_22401544_SNP [dm6]	C	T	3.207e^-5	0.988	INTRON babos	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2L	18754520	2L_18754520_SNP [dm3] 2L_18754520_SNP [dm6]	G	A	3.246e^-5	0.988	INTERGENIC
2L	2935970	2L_2935970_SNP [dm3] 2L_2935970_SNP [dm6]	G	T	3.251e^-5	0.988	INTRON lilli
3L	13105641	3L_13105641_SNP [dm3] 3L_13112541_SNP [dm6]	A	T	3.275e^-5	0.988	INTERGENIC
3R	18150474	3R_18150474_DEL [dm3] 3R_22324752_DEL [dm6]	AACAGCA	A	3.348e^-5	0.988	UPSTREAM CG34377 INTERGENIC
3L	5706094	3L_5706094_SNP [dm3] 3L_5712994_SNP [dm6]	G	A	3.368e^-5	0.988	UPSTREAM CG44521 INTRON sif
2L	1605945	2L_1605945_SNP [dm3] 2L_1605945_SNP [dm6]	G	C	3.502e^-5	0.988	INTRON CG31935 & 1 other
2L	21105431	2L_21105431_SNP [dm3] 2L_21105431_SNP [dm6]	C	A	3.512e^-5	0.988	INTRON Nhe2	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
3L	7379276	3L_7379276_SNP [dm3] 3L_7386176_SNP [dm6]	A	G	3.513e^-5	0.988	SYNONYMOUS_CODING CG8564 DOWNSTREAM smid	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2L	21100369	2L_21100369_SNP [dm3] 2L_21100369_SNP [dm6]	T	C	3.569e^-5	0.988	SYNONYMOUS_CODING CG12050
X	7987732	X_7987732_SNP [dm3] X_8093699_SNP [dm6]	A	G	3.632e^-5	0.988	DOWNSTREAM CG2258 INTRON Ubc-E2H	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_Trl
2L	14265677	2L_14265677_SNP [dm3] 2L_14265677_SNP [dm6]	A	G	3.715e^-5	0.988	INTRON wb	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Kr
3R	9733360	3R_9733360_SNP [dm3] 3R_13907638_SNP [dm6]	G	A	3.770e^-5	0.988	INTERGENIC
2L	1477367	2L_1477367_SNP [dm3] 2L_1477367_SNP [dm6]	G	A	3.857e^-5	0.988	INTERGENIC
3R	14671269	3R_14671269_SNP [dm3] 3R_18845547_SNP [dm6]	A	C	3.871e^-5	0.988	INTRON CG18208
X	6453447	X_6453447_SNP [dm3] X_6559414_SNP [dm6]	G	A	3.937e^-5	0.988	NON_SYNONYMOUS_CODING CG34417 INTRON CG34417	TF binding site mE1_TFBS_inv
3R	12938684	3R_12938684_SNP [dm3] 3R_17112962_SNP [dm6]	T	A	4.075e^-5	0.988	INTRON cher	TF binding site mE1_TFBS_cnc mE1_TFBS_D mE1_TFBS_HSA
2L	11225802	2L_11225802_SNP [dm3] 2L_11225802_SNP [dm6]	G	A	4.160e^-5	0.988	UTR_5_PRIME ab	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_sens
3L	1079442	3L_1079442_INS [dm3] 3L_1079442_INS [dm6]	T	TT	4.162e^-5	0.988	INTRON bab1
2R	6923904	2R_6923904_SNP [dm3] 2R_11036399_SNP [dm6]	A	G	4.170e^-5	0.988	INTRON luna
3L	13105642	3L_13105642_SNP [dm3] 3L_13112542_SNP [dm6]	C	A	4.197e^-5	0.988	INTERGENIC
3R	12039781	3R_12039781_SNP [dm3] 3R_16214059_SNP [dm6]	G	T	4.292e^-5	0.988	UPSTREAM CR45641 DOWNSTREAM CR45642 INTERGENIC
2L	15225825	2L_15225825_SNP [dm3] 2L_15225825_SNP [dm6]	T	G	4.303e^-5	0.988	INTERGENIC
X	5923064	X_5923064_SNP [dm3] X_6029031_SNP [dm6]	A	G	4.308e^-5	0.988	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	9043535	2R_9043535_SNP [dm3] 2R_13156030_SNP [dm6]	G	T	4.368e^-5	0.988	INTRON TppII
2L	21075772	2L_21075772_SNP [dm3] 2L_21075772_SNP [dm6]	A	G	4.388e^-5	0.988	INTRON tadr
3L	5706325	3L_5706325_SNP [dm3] 3L_5713225_SNP [dm6]	A	T	4.411e^-5	0.988	UPSTREAM CG44521 INTRON sif
X	6453704	X_6453704_SNP [dm3] X_6559671_SNP [dm6]	C	G	4.535e^-5	0.988	SYNONYMOUS_CODING CG34417 INTRON CG34417	TF binding site mE1_TFBS_inv
3L	2659303	3L_2659303_SNP [dm3] 3L_2659303_SNP [dm6]	T	A	4.547e^-5	0.988	UPSTREAM CG33233 INTRON Fife	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	23184649	3R_23184649_SNP [dm3] 3R_27358927_SNP [dm6]	G	A	4.590e^-5	0.988	UPSTREAM CG42534 INTRON CG42534
2R	10727562	2R_10727562_SNP [dm3] 2R_14840057_SNP [dm6]	G	C	4.612e^-5	0.988	INTERGENIC
2L	21088889	2L_21088889_SNP [dm3] 2L_21088889_SNP [dm6]	C	T	4.647e^-5	0.988	UPSTREAM CG9259 & 1 other INTERGENIC
2L	11472637	2L_11472637_SNP [dm3] 2L_11472637_SNP [dm6]	C	G	4.689e^-5	0.988	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	10516565	3L_10516565_SNP [dm3] 3L_10523465_SNP [dm6]	C	A	4.880e^-5	0.988	INTRON A2bp1
3L	11309245	3L_11309245_SNP [dm3] 3L_11316145_SNP [dm6]	C	T	4.995e^-5	0.988	EXON CR44361	TF binding site BDTNP1_TFBS_twi
X	6280430	X_6280430_SNP [dm3] X_6386397_SNP [dm6]	C	T	5.041e^-5	0.988	INTERGENIC
3R	9218362	3R_9218362_SNP [dm3] 3R_13392640_SNP [dm6]	G	C	5.126e^-5	0.988	INTRON CCHa2
2L	21146222	2L_21146222_SNP [dm3] 2L_21146222_SNP [dm6]	A	G	5.173e^-5	0.988	NON_SYNONYMOUS_CODING del	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	21166674	2L_21166674_SNP [dm3] 2L_21166674_SNP [dm6]	G	C	5.173e^-5	0.988	UTR_5_PRIME CG43346 UTR_3_PRIME CG43345 UPSTREAM CG43346 DOWNSTREAM CG9246	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
2L	12951597	2L_12951597_SNP [dm3] 2L_12951597_SNP [dm6]	C	A	5.210e^-5	0.988	INTERGENIC
2L	14693633	2L_14693633_SNP [dm3] 2L_14693633_SNP [dm6]	G	A	5.227e^-5	0.988	INTERGENIC
2R	1076441	2R_1076441_SNP [dm3] 2R_5188936_SNP [dm6]	T	C	5.234e^-5	0.988	INTRON Nipped-A
3L	11039110	3L_11039110_SNP [dm3] 3L_11046010_SNP [dm6]	A	G	5.291e^-5	0.988	INTRON CG43693	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Trl
X	13619821	X_13619821_SNP [dm3] X_13725788_SNP [dm6]	T	C	5.317e^-5	0.988	SYNONYMOUS_CODING mus101	TF binding site BDTNP1_TFBS_prd mE1_TFBS_chinmo mE1_TFBS_HSA
2R	5945995	2R_5945995_SNP [dm3] 2R_10058490_SNP [dm6]	T	C	5.319e^-5	0.988	INTRON magu

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Missing results

By genomic position
Variant impact
Gene name

Cuticul_5_C27_1 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results