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=1.228e^-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

Covariate	χ²	p-value	Significance
In_2R_NS	5.4801	0.0646

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2958 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	13344168	2L_13344168_SNP [dm3] 2L_13344168_SNP [dm6]	T	C	7.572e^-8	0.082	INTERGENIC
2L	11469389	2L_11469389_SNP [dm3] 2L_11469389_SNP [dm6]	A	G	8.755e^-8	0.082	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA
X	6639918	X_6639918_SNP [dm3] X_6745885_SNP [dm6]	T	C	4.677e^-7	0.233	DOWNSTREAM CR44964 EXON CR44895
2R	10233603	2R_10233603_SNP [dm3] 2R_14346098_SNP [dm6]	T	C	4.967e^-7	0.233	INTRON Shroom
3L	3781681	3L_3781681_SNP [dm3] 3L_3781681_SNP [dm6]	C	A	6.826e^-7	0.256	INTRON CG32264	TF binding site BDTNP1_TFBS_twi
2R	10054874	2R_10054874_SNP [dm3] 2R_14167369_SNP [dm6]	G	A	9.098e^-7	0.271	DOWNSTREAM CG8323 INTRON CG18327
X	11342198	X_11342198_DEL [dm3] X_11448165_DEL [dm6]	TTT	C	1.043e^-6	0.271	INTRON Evi5
3R	25850533	3R_25850533_SNP [dm3] 3R_30024811_SNP [dm6]	T	A	1.295e^-6	0.271	INTRON Axn
3R	25850278	3R_25850278_SNP [dm3] 3R_30024556_SNP [dm6]	A	C	1.300e^-6	0.271	UTR_5_PRIME Axn
2R	13717575	2R_13717575_SNP [dm3] 2R_17830070_SNP [dm6]	G	A	1.444e^-6	0.271	INTRON grh	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_bcd mE1_TFBS_HSA
2R	16221749	2R_16221749_SNP [dm3] 2R_20334244_SNP [dm6]	A	G	1.813e^-6	0.306	INTERGENIC
X	17780001	X_17780001_INS [dm3] X_17885968_INS [dm6]	T	TGTTCAGCGCACCTTAGAAT...	2.601e^-6	0.306	DOWNSTREAM CG12985 INTRON mnb	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
2R	18426231	2R_18426231_SNP [dm3] 2R_22538726_SNP [dm6]	A	C	2.704e^-6	0.306	INTRON px
3R	7144180	3R_7144180_SNP [dm3] 3R_11318458_SNP [dm6]	A	G	2.719e^-6	0.306	INTERGENIC	TF binding site BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_chinmo mE1_TFBS_HSA
2R	2517539	2R_2517539_SNP [dm3] 2R_6630034_SNP [dm6]	T	G	2.878e^-6	0.306	INTRON Vha16-1	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
X	16668561	X_16668561_SNP [dm3] X_16774528_SNP [dm6]	A	T	3.123e^-6	0.306	INTRON if	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3L	5520403	3L_5520403_DEL [dm3] 3L_5527303_DEL [dm6]	TAT	A	3.173e^-6	0.306	INTRON Lkr
X	14849169	X_14849169_SNP [dm3] X_14955136_SNP [dm6]	A	G	3.214e^-6	0.306	UPSTREAM eag & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_sens
2R	10420411	2R_10420411_SNP [dm3] 2R_14532906_SNP [dm6]	A	G	3.437e^-6	0.306	INTRON ttv
3R	15762952	3R_15762952_SNP [dm3] 3R_19937230_SNP [dm6]	G	C	3.458e^-6	0.306	INTRON Hs6st	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3L	5520397	3L_5520397_DEL [dm3] 3L_5527297_DEL [dm6]	CGG	C	3.521e^-6	0.306	INTRON Lkr
3L	5520423	3L_5520423_SNP [dm3] 3L_5527323_SNP [dm6]	T	A	3.588e^-6	0.306	INTRON Lkr
3L	11909012	3L_11909012_SNP [dm3] 3L_11915912_SNP [dm6]	T	A	4.334e^-6	0.353	INTRON CG44837
X	11342481	X_11342481_SNP [dm3] X_11448448_SNP [dm6]	A	T	5.248e^-6	0.365	INTRON Evi5
2R	1386529	2R_1386529_SNP [dm3] 2R_5499024_SNP [dm6]	T	A	5.325e^-6	0.365	INTRON CG30438
2L	15277889	2L_15277889_SNP [dm3] 2L_15277889_SNP [dm6]	C	T	5.469e^-6	0.365	INTRON CR43682
3R	15762853	3R_15762853_SNP [dm3] 3R_19937131_SNP [dm6]	T	C	5.746e^-6	0.365	INTRON Hs6st	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3R	1446355	3R_1446355_DEL [dm3] 3R_5620633_DEL [dm6]	GTAG	G	5.917e^-6	0.365	INTRON Spec2
2L	1881001	2L_1881001_SNP [dm3] 2L_1881001_SNP [dm6]	G	T	6.160e^-6	0.365	UPSTREAM CG31663 INTRON CG31663
2L	6066980	2L_6066980_SNP [dm3] 2L_6066980_SNP [dm6]	T	A	6.523e^-6	0.365	NON_SYNONYMOUS_CODING CG9147 DOWNSTREAM CG9150	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3L	1151800	3L_1151800_DEL [dm3] 3L_1151800_DEL [dm6]	AACAGATTTTCA...	A	6.561e^-6	0.365	INTRON bab2
3L	909746	3L_909746_SNP [dm3] 3L_909746_SNP [dm6]	C	T	6.735e^-6	0.365	NON_SYNONYMOUS_CODING nerfin-1	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_chinmo mE1_TFBS_HSA
3L	11747369	3L_11747369_SNP [dm3] 3L_11754269_SNP [dm6]	A	C	6.951e^-6	0.365	INTRON CG6024
2L	6067095	2L_6067095_SNP [dm3] 2L_6067095_SNP [dm6]	C	G	7.023e^-6	0.365	SYNONYMOUS_CODING CG9147 DOWNSTREAM CG9150	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens
2L	18366653	2L_18366653_SNP [dm3] 2L_18366653_SNP [dm6]	C	T	7.200e^-6	0.365	INTRON Fas3
3R	15762788	3R_15762788_SNP [dm3] 3R_19937066_SNP [dm6]	T	C	7.340e^-6	0.365	INTRON Hs6st	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
2R	16221819	2R_16221819_SNP [dm3] 2R_20334314_SNP [dm6]	G	A	7.406e^-6	0.365	INTERGENIC
3R	15758893	3R_15758893_SNP [dm3] 3R_19933171_SNP [dm6]	C	A	7.483e^-6	0.365	SYNONYMOUS_CODING mira INTRON Hs6st	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3L	3784944	3L_3784944_SNP [dm3] 3L_3784944_SNP [dm6]	C	A	7.972e^-6	0.365	INTRON CG32264	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad
3L	11909135	3L_11909135_SNP [dm3] 3L_11916035_SNP [dm6]	T	A	9.015e^-6	0.365	INTRON CG44837
3L	3781686	3L_3781686_SNP [dm3] 3L_3781686_SNP [dm6]	C	T	9.046e^-6	0.365	INTRON CG32264	TF binding site BDTNP1_TFBS_twi
3R	15758742	3R_15758742_SNP [dm3] 3R_19933020_SNP [dm6]	A	G	9.069e^-6	0.365	SYNONYMOUS_CODING mira INTRON Hs6st	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Mad mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2R	18006014	2R_18006014_SNP [dm3] 2R_22118509_SNP [dm6]	C	T	9.342e^-6	0.365	INTRON Vrp1	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	11914483	3L_11914483_SNP [dm3] 3L_11921383_SNP [dm6]	C	A	9.379e^-6	0.365	UPSTREAM CG11588 INTRON CG44837
3L	10685065	3L_10685065_SNP [dm3] 3L_10691965_SNP [dm6]	A	G	9.391e^-6	0.365	UTR_3_PRIME CG11811 DOWNSTREAM CG33493
3L	10133831	3L_10133831_SNP [dm3] 3L_10140731_SNP [dm6]	C	T	9.418e^-6	0.365	INTERGENIC	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	15762150	3R_15762150_SNP [dm3] 3R_19936428_SNP [dm6]	G	C	9.447e^-6	0.365	INTRON Hs6st	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	11908998	3L_11908998_SNP [dm3] 3L_11915898_SNP [dm6]	T	C	9.745e^-6	0.365	INTRON CG44837
3R	26649581	3R_26649581_SNP [dm3] 3R_30823859_SNP [dm6]	A	T	1.009e^-5	0.365	INTRON cindr
3L	11909129	3L_11909129_SNP [dm3] 3L_11916029_SNP [dm6]	A	T	1.034e^-5	0.365	INTRON CG44837
3R	18555526	3R_18555526_SNP [dm3] 3R_22729804_SNP [dm6]	A	T	1.044e^-5	0.365	INTRON CG45049	TF binding site mE1_TFBS_sens
X	6640013	X_6640013_SNP [dm3] X_6745980_SNP [dm6]	C	T	1.044e^-5	0.365	DOWNSTREAM CR44964 EXON CR44895
3L	8541498	3L_8541498_SNP [dm3] 3L_8548398_SNP [dm6]	T	A	1.087e^-5	0.365	INTRON rhea	TF binding site mE1_TFBS_inv
X	11327080	X_11327080_SNP [dm3] X_11433047_SNP [dm6]	T	C	1.096e^-5	0.365	UTR_3_PRIME Evi5
3L	7247634	3L_7247634_SNP [dm3] 3L_7254534_SNP [dm6]	C	T	1.111e^-5	0.365	INTRON CG14830
3R	18555520	3R_18555520_SNP [dm3] 3R_22729798_SNP [dm6]	A	G	1.142e^-5	0.365	INTRON CG45049	TF binding site mE1_TFBS_sens
2L	11469466	2L_11469466_SNP [dm3] 2L_11469466_SNP [dm6]	G	T	1.142e^-5	0.365	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	11469479	2L_11469479_SNP [dm3] 2L_11469479_SNP [dm6]	A	G	1.142e^-5	0.365	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
3L	1099251	3L_1099251_SNP [dm3] 3L_1099251_SNP [dm6]	T	C	1.171e^-5	0.365	SYNONYMOUS_CODING bab1	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_D mE1_TFBS_Trl
3R	1446393	3R_1446393_SNP [dm3] 3R_5620671_SNP [dm6]	C	A	1.196e^-5	0.365	INTRON Spec2
3R	15763029	3R_15763029_SNP [dm3] 3R_19937307_SNP [dm6]	T	G	1.218e^-5	0.365	SYNONYMOUS_CODING Hs6st
3R	25855618	3R_25855618_SNP [dm3] 3R_30029896_SNP [dm6]	G	T	1.228e^-5	0.365	INTRON Axn	TF binding site BDTNP1_TFBS_dl
2L	4596267	2L_4596267_SNP [dm3] 2L_4596267_SNP [dm6]	A	G	1.232e^-5	0.365	INTRON dp
X	17781522	X_17781522_SNP [dm3] X_17887489_SNP [dm6]	G	A	1.253e^-5	0.365	UPSTREAM CG6788 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_Trl mE1_TFBS_Ubx
X	7892316	X_7892316_SNP [dm3] X_7998283_SNP [dm6]	A	C	1.265e^-5	0.365	UPSTREAM Tbh INTRON Tbh
3R	18863614	3R_18863614_SNP [dm3] 3R_23037892_SNP [dm6]	A	T	1.283e^-5	0.365	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	3816723	3L_3816723_SNP [dm3] 3L_3816723_SNP [dm6]	G	A	1.314e^-5	0.368	SYNONYMOUS_CODING Scsalpha UPSTREAM CR45034 & 1 other
3L	8541510	3L_8541510_SNP [dm3] 3L_8548410_SNP [dm6]	T	A	1.346e^-5	0.369	INTRON rhea	TF binding site mE1_TFBS_inv
2L	16601419	2L_16601419_SNP [dm3] 2L_16601419_SNP [dm6]	T	C	1.359e^-5	0.369	UPSTREAM CG42389 INTRON CG42389	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
3L	5269966	3L_5269966_SNP [dm3] 3L_5276866_SNP [dm6]	A	T	1.386e^-5	0.369	INTRON shep	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
2L	11097106	2L_11097106_SNP [dm3] 2L_11097106_SNP [dm6]	A	G	1.398e^-5	0.369	SYNONYMOUS_CODING Ge-1
X	6610574	X_6610574_SNP [dm3] X_6716541_SNP [dm6]	A	G	1.431e^-5	0.373	SYNONYMOUS_CODING CG14441	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
X	3898543	X_3898543_SNP [dm3] X_4004510_SNP [dm6]	A	C	1.463e^-5	0.374	INTERGENIC
2L	15278014	2L_15278014_SNP [dm3] 2L_15278014_SNP [dm6]	C	G	1.476e^-5	0.374	INTRON CR43682
2R	12127251	2R_12127251_SNP [dm3] 2R_16239746_SNP [dm6]	T	G	1.533e^-5	0.383	NON_SYNONYMOUS_CODING krimp	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	16782522	3R_16782522_SNP [dm3] 3R_20956800_SNP [dm6]	T	G	1.618e^-5	0.384	UPSTREAM Atpalpha INTRON Atpalpha	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3L	4121032	3L_4121032_SNP [dm3] 3L_4121032_SNP [dm6]	C	T	1.639e^-5	0.384	INTRON Chd64
3L	3773882	3L_3773882_SNP [dm3] 3L_3773882_SNP [dm6]	G	T	1.646e^-5	0.384	INTRON CG32264
2R	14346376	2R_14346376_SNP [dm3] 2R_18458871_SNP [dm6]	T	A	1.656e^-5	0.384	DOWNSTREAM CG30116 INTRON CG30116
3R	7129194	3R_7129194_SNP [dm3] 3R_11303472_SNP [dm6]	G	A	1.658e^-5	0.384	INTRON CR31386	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
2L	11097017	2L_11097017_SNP [dm3] 2L_11097017_SNP [dm6]	A	T	1.701e^-5	0.384	INTRON Ge-1	TF binding site mE1_TFBS_HSA
3R	15382117	3R_15382117_SNP [dm3] 3R_19556395_SNP [dm6]	C	T	1.731e^-5	0.384	INTRON Dys
2L	12979562	2L_12979562_SNP [dm3] 2L_12979562_SNP [dm6]	C	T	1.755e^-5	0.384	SYNONYMOUS_CODING Vha68-3 DOWNSTREAM Vha68-2
3R	20171805	3R_20171805_SNP [dm3] 3R_24346083_SNP [dm6]	A	T	1.766e^-5	0.384	UTR_3_PRIME CG5746
3L	11916430	3L_11916430_SNP [dm3] 3L_11923330_SNP [dm6]	G	C	1.767e^-5	0.384	SYNONYMOUS_CODING CG5718 DOWNSTREAM CG11588 INTRON CG44837	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2R	19117745	2R_19117745_SNP [dm3] 2R_23230222_SNP [dm6]	G	T	1.780e^-5	0.384	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2R	12127227	2R_12127227_SNP [dm3] 2R_16239722_SNP [dm6]	T	C	1.785e^-5	0.384	SYNONYMOUS_CODING krimp	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	11213150	2R_11213150_SNP [dm3] 2R_15325645_SNP [dm6]	G	A	1.815e^-5	0.384	UTR_3_PRIME CG8157 DOWNSTREAM Arf51F & 1 other	TF binding site BDTNP1_TFBS_dl
2L	18277860	2L_18277860_SNP [dm3] 2L_18277860_SNP [dm6]	G	C	1.844e^-5	0.384	DOWNSTREAM CR44902 INTERGENIC
3L	11745663	3L_11745663_SNP [dm3] 3L_11752563_SNP [dm6]	T	A	1.848e^-5	0.384	DOWNSTREAM Gr68a INTRON CG6024
2R	16221820	2R_16221820_SNP [dm3] 2R_20334315_SNP [dm6]	T	C	1.888e^-5	0.384	INTERGENIC
2R	14611802	2R_14611802_SNP [dm3] 2R_18724297_SNP [dm6]	T	G	1.900e^-5	0.384	INTRON Hs3st-A
X	10142245	X_10142245_SNP [dm3] X_10248212_SNP [dm6]	A	T	1.904e^-5	0.384	INTRON Hk	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	4361176	2L_4361176_SNP [dm3] 2L_4361176_SNP [dm6]	T	G	1.962e^-5	0.384	UPSTREAM Traf4 INTERGENIC	TF binding site mE1_TFBS_chinmo
3R	15762792	3R_15762792_SNP [dm3] 3R_19937070_SNP [dm6]	A	G	1.993e^-5	0.384	INTRON Hs6st	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3L	6563738	3L_6563738_SNP [dm3] 3L_6570638_SNP [dm6]	C	T	2.029e^-5	0.384	INTRON CG18769 & 1 other
3L	11715129	3L_11715129_SNP [dm3] 3L_11722029_SNP [dm6]	A	G	2.037e^-5	0.384	SYNONYMOUS_CODING Bmcp	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	4121075	3L_4121075_SNP [dm3] 3L_4121075_SNP [dm6]	G	A	2.055e^-5	0.384	INTRON Chd64
3R	11288781	3R_11288781_SNP [dm3] 3R_15463059_SNP [dm6]	G	C	2.056e^-5	0.384	NON_SYNONYMOUS_CODING AdamTS-A INTRON AdamTS-A
3R	23306658	3R_23306658_SNP [dm3] 3R_27480936_SNP [dm6]	A	G	2.079e^-5	0.384	UTR_3_PRIME Cyp6a18 DOWNSTREAM Cyp6a18

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By genomic position
Variant impact
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mn_Viability_Lead phenotype

Phenotype distribution and association to known covariates

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GWAS results