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=1.269e^-14)
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

2653 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	2004922	3L_2004922_INS [dm3] 3L_2004922_INS [dm6]	T	TGGTGTGT	3.681e^-7	0.297	DOWNSTREAM CG42841 INTRON CG42841
3L	1999043	3L_1999043_SNP [dm3] 3L_1999043_SNP [dm6]	G	A	4.344e^-7	0.297	INTERGENIC
3L	1999145	3L_1999145_SNP [dm3] 3L_1999145_SNP [dm6]	G	A	4.952e^-7	0.297	INTERGENIC
3L	1999062	3L_1999062_SNP [dm3] 3L_1999062_SNP [dm6]	T	C	6.521e^-7	0.297	INTERGENIC
3L	1997949	3L_1997949_SNP [dm3] 3L_1997949_SNP [dm6]	G	C	7.920e^-7	0.297	INTERGENIC
3L	2003168	3L_2003168_SNP [dm3] 3L_2003168_SNP [dm6]	C	A	1.350e^-6	0.297	UTR_3_PRIME CG42841
X	16430681	X_16430681_SNP [dm3] X_16536648_SNP [dm6]	T	A	1.497e^-6	0.297	INTERGENIC
3L	2004455	3L_2004455_DEL [dm3] 3L_2004455_DEL [dm6]	TCG	A	1.822e^-6	0.297	DOWNSTREAM CG42841 INTRON CG42841
3R	25398180	3R_25398180_SNP [dm3] 3R_29572458_SNP [dm6]	A	G	1.984e^-6	0.297	INTERGENIC	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_Trl
3R	25398178	3R_25398178_SNP [dm3] 3R_29572456_SNP [dm6]	A	G	1.999e^-6	0.297	INTERGENIC	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_Trl
3L	1996667	3L_1996667_SNP [dm3] 3L_1996667_SNP [dm6]	A	G	2.041e^-6	0.297	INTERGENIC
2R	17204081	2R_17204081_SNP [dm3] 2R_21316576_SNP [dm6]	G	A	2.386e^-6	0.297	SYNONYMOUS_CODING CG9485	TF binding site mE1_TFBS_cad mE1_TFBS_sens
X	11349981	X_11349981_SNP [dm3] X_11455948_SNP [dm6]	C	A	2.449e^-6	0.297	NON_SYNONYMOUS_CODING HP5	TF binding site mE1_TFBS_sens
3L	9355412	3L_9355412_SNP [dm3] 3L_9362312_SNP [dm6]	C	T	2.539e^-6	0.297	SYNONYMOUS_CODING CG34456 DOWNSTREAM Klp67A & 1 other
3L	5992565	3L_5992565_SNP [dm3] 3L_5999465_SNP [dm6]	C	A	2.702e^-6	0.297	INTRON PVRAP
3L	1999192	3L_1999192_SNP [dm3] 3L_1999192_SNP [dm6]	G	A	2.734e^-6	0.297	INTERGENIC
2L	10834243	2L_10834243_SNP [dm3] 2L_10834243_SNP [dm6]	C	T	2.869e^-6	0.297	INTRON Nos
3R	19088328	3R_19088328_SNP [dm3] 3R_23262606_SNP [dm6]	G	A	2.992e^-6	0.297	UTR_3_PRIME orb
3L	2004753	3L_2004753_SNP [dm3] 3L_2004753_SNP [dm6]	G	A	3.145e^-6	0.297	DOWNSTREAM CG42841 INTRON CG42841
3L	2005293	3L_2005293_SNP [dm3] 3L_2005293_SNP [dm6]	A	G	3.302e^-6	0.297	UTR_3_PRIME CG42841
3L	5273681	3L_5273681_SNP [dm3] 3L_5280581_SNP [dm6]	G	C	3.623e^-6	0.297	INTERGENIC
3L	1997819	3L_1997819_SNP [dm3] 3L_1997819_SNP [dm6]	A	G	3.757e^-6	0.297	INTERGENIC
3L	6001607	3L_6001607_SNP [dm3] 3L_6008507_SNP [dm6]	T	C	3.772e^-6	0.297	DOWNSTREAM alphaKap4 INTRON PVRAP
3L	2000949	3L_2000949_SNP [dm3] 3L_2000949_SNP [dm6]	C	T	3.850e^-6	0.297	INTERGENIC
3R	25398136	3R_25398136_DEL [dm3] 3R_29572414_DEL [dm6]	TT	T	4.099e^-6	0.297	INTERGENIC	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_Trl
3L	5197134	3L_5197134_SNP [dm3] 3L_5204034_SNP [dm6]	C	G	4.248e^-6	0.297	INTRON shep
2R	17204093	2R_17204093_SNP [dm3] 2R_21316588_SNP [dm6]	A	C	4.375e^-6	0.297	SYNONYMOUS_CODING CG9485	TF binding site mE1_TFBS_cad mE1_TFBS_sens
3L	2004308	3L_2004308_SNP [dm3] 3L_2004308_SNP [dm6]	G	C	4.431e^-6	0.297	DOWNSTREAM CG42841 INTRON CG42841
3R	19200773	3R_19200773_SNP [dm3] 3R_23375051_SNP [dm6]	C	T	5.439e^-6	0.337	DOWNSTREAM CG42828 & 1 other INTERGENIC
3L	1996694	3L_1996694_SNP [dm3] 3L_1996694_SNP [dm6]	T	C	5.512e^-6	0.337	INTERGENIC
3R	25398191	3R_25398191_SNP [dm3] 3R_29572469_SNP [dm6]	G	A	5.944e^-6	0.337	INTERGENIC	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_Trl
3L	2004298	3L_2004298_SNP [dm3] 3L_2004298_SNP [dm6]	T	A	6.194e^-6	0.337	DOWNSTREAM CG42841 INTRON CG42841
3L	1273290	3L_1273290_SNP [dm3] 3L_1273290_SNP [dm6]	A	T	6.319e^-6	0.337	INTRON CG9134
2L	10834245	2L_10834245_SNP [dm3] 2L_10834245_SNP [dm6]	G	A	6.608e^-6	0.337	INTRON Nos
3L	1996691	3L_1996691_SNP [dm3] 3L_1996691_SNP [dm6]	G	C	6.781e^-6	0.337	INTERGENIC
3L	10236960	3L_10236960_SNP [dm3] 3L_10243860_SNP [dm6]	A	T	6.948e^-6	0.337	UPSTREAM CR44541 INTRON Or67c
2L	21065272	2L_21065272_SNP [dm3] 2L_21065272_SNP [dm6]	A	G	7.082e^-6	0.337	INTRON CG9265
3L	2835271	3L_2835271_SNP [dm3] 3L_2835271_SNP [dm6]	T	A	7.114e^-6	0.337	INTRON CG43444
3L	1996662	3L_1996662_SNP [dm3] 3L_1996662_SNP [dm6]	A	G	7.428e^-6	0.337	INTERGENIC
2L	20942131	2L_20942131_SNP [dm3] 2L_20942131_SNP [dm6]	G	A	7.439e^-6	0.337	INTERGENIC
3L	20876225	3L_20876225_INS [dm3] 3L_20883125_INS [dm6]	T	TAAATTATATTAATTAAATA...	7.749e^-6	0.337	INTRON CG32432
3L	5197517	3L_5197517_SNP [dm3] 3L_5204417_SNP [dm6]	C	A	7.900e^-6	0.337	INTRON shep
3R	14437375	3R_14437375_SNP [dm3] 3R_18611653_SNP [dm6]	T	A	7.990e^-6	0.337	INTRON qin & 1 other
3R	18644615	3R_18644615_SNP [dm3] 3R_22818893_SNP [dm6]	G	A	8.088e^-6	0.337	INTERGENIC
X	18859778	X_18859778_SNP [dm3] X_18965745_SNP [dm6]	C	G	8.092e^-6	0.337	INTRON CG43759
3L	1996616	3L_1996616_SNP [dm3] 3L_1996616_SNP [dm6]	C	G	8.503e^-6	0.347	INTERGENIC
3L	6777779	3L_6777779_SNP [dm3] 3L_6784679_SNP [dm6]	C	G	9.119e^-6	0.364	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Kr
3R	14437361	3R_14437361_SNP [dm3] 3R_18611639_SNP [dm6]	T	A	9.837e^-6	0.379	INTRON qin & 1 other
3L	2002534	3L_2002534_SNP [dm3] 3L_2002534_SNP [dm6]	T	A	9.932e^-6	0.379	DOWNSTREAM CG42841 INTERGENIC
3R	14841118	3R_14841118_SNP [dm3] 3R_19015396_SNP [dm6]	T	C	1.010e^-5	0.379	INTRON gukh	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Trl
2R	3902264	2R_3902264_SNP [dm3] 2R_8014759_SNP [dm6]	T	C	1.076e^-5	0.391	UPSTREAM mir-4981 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_bab1
3L	2001536	3L_2001536_SNP [dm3] 3L_2001536_SNP [dm6]	G	T	1.085e^-5	0.391	INTERGENIC
3L	2835279	3L_2835279_SNP [dm3] 3L_2835279_SNP [dm6]	A	T	1.151e^-5	0.407	INTRON CG43444
3L	2002301	3L_2002301_SNP [dm3] 3L_2002301_SNP [dm6]	C	G	1.178e^-5	0.409	DOWNSTREAM CG42841 INTERGENIC
3L	2002183	3L_2002183_DEL [dm3] 3L_2002183_DEL [dm6]	TA	T	1.214e^-5	0.414	DOWNSTREAM CG42841 INTERGENIC
3L	2002214	3L_2002214_SNP [dm3] 3L_2002214_SNP [dm6]	C	T	1.313e^-5	0.44	DOWNSTREAM CG42841 INTERGENIC
3L	1997206	3L_1997206_SNP [dm3] 3L_1997206_SNP [dm6]	T	C	1.341e^-5	0.441	INTERGENIC
2L	21065275	2L_21065275_SNP [dm3] 2L_21065275_SNP [dm6]	C	T	1.384e^-5	0.445	INTRON CG9265
X	3986496	X_3986496_SNP [dm3] X_4092463_SNP [dm6]	C	A	1.410e^-5	0.445	DOWNSTREAM CG43689 INTERGENIC
3L	3439380	3L_3439380_SNP [dm3] 3L_3439380_SNP [dm6]	C	A	1.423e^-5	0.445	INTRON eIF5B	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl
3L	3439389	3L_3439389_SNP [dm3] 3L_3439389_SNP [dm6]	C	T	1.468e^-5	0.451	INTRON eIF5B	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl
3L	2004628	3L_2004628_SNP [dm3] 3L_2004628_SNP [dm6]	A	G	1.512e^-5	0.454	DOWNSTREAM CG42841 INTRON CG42841
2L	9523873	2L_9523873_SNP [dm3] 2L_9523873_SNP [dm6]	G	A	1.532e^-5	0.454	INTRON Oatp30B	TF binding site mE1_TFBS_inv mE1_TFBS_Trl
3R	25463438	3R_25463438_SNP [dm3] 3R_29637716_SNP [dm6]	A	G	1.603e^-5	0.454	INTRON Dop1R2
2L	7898211	2L_7898211_SNP [dm3] 2L_7898211_SNP [dm6]	C	A	1.620e^-5	0.454	INTRON Snoo
3R	14837826	3R_14837826_DEL [dm3] 3R_19012104_DEL [dm6]	TT	T	1.628e^-5	0.454	INTRON gukh	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv
3R	22067020	3R_22067020_SNP [dm3] 3R_26241298_SNP [dm6]	C	G	1.630e^-5	0.454	INTRON CR42745
3R	14437372	3R_14437372_SNP [dm3] 3R_18611650_SNP [dm6]	A	T	1.645e^-5	0.454	INTRON qin & 1 other
X	8937158	X_8937158_SNP [dm3] X_9043125_SNP [dm6]	T	G	1.678e^-5	0.454	INTRON CR43836 & 1 other	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
3L	1997139	3L_1997139_SNP [dm3] 3L_1997139_SNP [dm6]	T	C	1.720e^-5	0.454	INTERGENIC
3R	19034837	3R_19034837_SNP [dm3] 3R_23209115_SNP [dm6]	A	T	1.735e^-5	0.454	INTRON cnc
3R	23382864	3R_23382864_DEL [dm3] 3R_27557142_DEL [dm6]	AGA	A	1.761e^-5	0.454	INTRON Klp98A	TF binding site BDTNP1_TFBS_z
X	8937161	X_8937161_SNP [dm3] X_9043128_SNP [dm6]	G	A	1.788e^-5	0.454	INTRON CR43836 & 1 other	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
3R	13924655	3R_13924655_SNP [dm3] 3R_18098933_SNP [dm6]	T	C	1.794e^-5	0.454	INTRON sr
3R	16534452	3R_16534452_SNP [dm3] 3R_20708730_SNP [dm6]	A	T	1.817e^-5	0.454	INTRON Oamb
2L	1140456	2L_1140456_SNP [dm3] 2L_1140456_SNP [dm6]	C	T	1.854e^-5	0.458	UTR_3_PRIME CG4577
3L	5944919	3L_5944919_SNP [dm3] 3L_5951819_SNP [dm6]	G	A	1.901e^-5	0.463	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad
3R	20264189	3R_20264189_SNP [dm3] 3R_24438467_SNP [dm6]	A	T	2.018e^-5	0.485	INTRON nAChRalpha1
2R	11788652	2R_11788652_SNP [dm3] 2R_15901147_SNP [dm6]	G	T	2.100e^-5	0.492	INTRON sli	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	14790095	2L_14790095_DEL [dm3] 2L_14790095_DEL [dm6]	ATCTCCCACTGGGATGCGAA...	A	2.140e^-5	0.492	INTERGENIC
3L	9934181	3L_9934181_SNP [dm3] 3L_9941081_SNP [dm6]	G	A	2.177e^-5	0.492	INTRON CG34356	TF binding site BDTNP1_TFBS_hb
3L	2001857	3L_2001857_SNP [dm3] 3L_2001857_SNP [dm6]	G	C	2.185e^-5	0.492	INTERGENIC
3L	1997143	3L_1997143_SNP [dm3] 3L_1997143_SNP [dm6]	A	T	2.192e^-5	0.492	INTERGENIC
3L	2003258	3L_2003258_SNP [dm3] 3L_2003258_SNP [dm6]	C	A	2.229e^-5	0.492	UTR_3_PRIME CG42841
3R	26068476	3R_26068476_SNP [dm3] 3R_30242754_SNP [dm6]	C	T	2.229e^-5	0.492	SYNONYMOUS_CODING CG9737
3R	7877765	3R_7877765_SNP [dm3] 3R_12052043_SNP [dm6]	A	T	2.334e^-5	0.509	INTERGENIC
3R	13964446	3R_13964446_SNP [dm3] 3R_18138724_SNP [dm6]	A	G	2.461e^-5	0.53	INTERGENIC
2L	2623839	2L_2623839_SNP [dm3] 2L_2623839_SNP [dm6]	A	G	2.539e^-5	0.541	INTERGENIC
2R	9420329	2R_9420329_SNP [dm3] 2R_13532824_SNP [dm6]	A	G	2.613e^-5	0.551	UTR_5_PRIME Vmat INTRON Vmat	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
3L	10237066	3L_10237066_SNP [dm3] 3L_10243966_SNP [dm6]	C	G	2.671e^-5	0.551	NON_SYNONYMOUS_CODING Or67c UPSTREAM CR44541
2R	14191675	2R_14191675_SNP [dm3] 2R_18304170_SNP [dm6]	A	T	2.702e^-5	0.551	UPSTREAM CG14505 INTRON sbb	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Kr
3L	3928101	3L_3928101_SNP [dm3] 3L_3928101_SNP [dm6]	G	A	2.744e^-5	0.551	INTRON Eip63F-1
2R	9385622	2R_9385622_SNP [dm3] 2R_13498117_SNP [dm6]	T	A	2.764e^-5	0.551	INTRON drk
3L	1996345	3L_1996345_SNP [dm3] 3L_1996345_SNP [dm6]	C	T	2.779e^-5	0.551	INTERGENIC
3R	25220787	3R_25220787_SNP [dm3] 3R_29395065_SNP [dm6]	C	G	2.790e^-5	0.551	INTRON Ptp99A
3R	26024512	3R_26024512_SNP [dm3] 3R_30198790_SNP [dm6]	A	C	2.844e^-5	0.556	NON_SYNONYMOUS_CODING CG9743	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	2000000	3L_2000000_SNP [dm3] 3L_2000000_SNP [dm6]	G	C	2.948e^-5	0.562	INTERGENIC
3R	20989003	3R_20989003_SNP [dm3] 3R_25163281_SNP [dm6]	T	C	2.982e^-5	0.562	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	18947292	3L_18947292_SNP [dm3] 3L_18954192_SNP [dm6]	A	C	2.995e^-5	0.562	INTRON CG6836
3R	13685496	3R_13685496_SNP [dm3] 3R_17859774_SNP [dm6]	C	A	2.995e^-5	0.562	INTRON tinc

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By genomic position
Variant impact
Gene name

Mitochon_Depth_Cov phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results