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=7.164e^-7)
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_2L_t	0.02345
In_2R_NS	0.07297
In_3R_K	0.09167

Kruskal-Wallis test

Covariate	χ²	p-value
In_2L_t	10.0168	0.0067
In_3R_K	8.4465	0.0147
In_3R_Mo	7.3404	0.0255

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2041 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	13142019	2L_13142019_SNP [dm3] 2L_13142019_SNP [dm6]	C	T	8.419e^-8	0.158	DOWNSTREAM CG9928 INTERGENIC
2L	3327989	2L_3327989_SNP [dm3] 2L_3327989_SNP [dm6]	C	T	3.043e^-7	0.237	SYNONYMOUS_CODING CG33282
2L	3328061	2L_3328061_SNP [dm3] 2L_3328061_SNP [dm6]	T	C	4.732e^-7	0.237	INTRON CG33282
2L	13141397	2L_13141397_SNP [dm3] 2L_13141397_SNP [dm6]	A	G	5.295e^-7	0.237	INTERGENIC
2R	6729634	2R_6729634_SNP [dm3] 2R_10842129_SNP [dm6]	C	G	6.328e^-7	0.237	SYNONYMOUS_CODING CG30015	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_sens
2L	13890252	2L_13890252_SNP [dm3] 2L_13890252_SNP [dm6]	C	T	8.290e^-7	0.259	INTRON CenG1A
X	4563075	X_4563075_SNP [dm3] X_4669042_SNP [dm6]	A	T	1.104e^-6	0.266	SYNONYMOUS_CODING rap	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3L	15677603	3L_15677603_SNP [dm3] 3L_15684503_SNP [dm6]	A	G	1.134e^-6	0.266	INTRON pgant8
3L	4080922	3L_4080922_SNP [dm3] 3L_4080922_SNP [dm6]	C	T	1.672e^-6	0.348	INTRON Gad1
2L	13890280	2L_13890280_DEL [dm3] 2L_13890280_DEL [dm6]	TT	T	2.016e^-6	0.378	INTRON CenG1A
3L	18019671	3L_18019671_SNP [dm3] 3L_18026571_SNP [dm6]	T	C	2.799e^-6	0.477	INTRON Eip75B
3L	15677575	3L_15677575_SNP [dm3] 3L_15684475_SNP [dm6]	A	C	3.166e^-6	0.495	INTRON pgant8
2R	2923216	2R_2923216_SNP [dm3] 2R_7035711_SNP [dm6]	T	A	3.861e^-6	0.524	DOWNSTREAM Tsp42Eh INTRON Tsp42Ei
2L	10114160	2L_10114160_SNP [dm3] 2L_10114160_SNP [dm6]	C	T	4.604e^-6	0.524	INTRON CG44153 & 1 other
2L	1901064	2L_1901064_SNP [dm3] 2L_1901064_SNP [dm6]	G	T	4.846e^-6	0.524	INTRON CG7337
3L	15677579	3L_15677579_SNP [dm3] 3L_15684479_SNP [dm6]	A	C	5.019e^-6	0.524	INTRON pgant8
2R	18099434	2R_18099434_SNP [dm3] 2R_22211929_SNP [dm6]	C	T	5.095e^-6	0.524	SYNONYMOUS_CODING CG11291 UPSTREAM ari-2	TF binding site mE1_TFBS_sens
3R	20258883	3R_20258883_INS [dm3] 3R_24433161_INS [dm6]	G	GGCGTGG	5.308e^-6	0.524	INTRON nAChRalpha1
3L	19158935	3L_19158935_SNP [dm3] 3L_19165835_SNP [dm6]	T	C	6.012e^-6	0.524	INTRON fz2	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad
2R	18102102	2R_18102102_SNP [dm3] 2R_22214597_SNP [dm6]	G	A	6.101e^-6	0.524	INTRON ari-2	TF binding site BDTNP1_TFBS_dl
3R	3272711	3R_3272711_SNP [dm3] 3R_7446989_SNP [dm6]	T	C	6.147e^-6	0.524	INTERGENIC
X	14799320	X_14799320_SNP [dm3] X_14905287_SNP [dm6]	T	C	6.152e^-6	0.524	INTRON Flo2 & 1 other	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	9073108	2R_9073108_INS [dm3] 2R_13185603_INS [dm6]	T	TCT	6.788e^-6	0.554	UTR_3_PRIME Kdm4B UPSTREAM CG17724 INTRON CG17724 & 2 others	TF binding site mE1_TFBS_cad
3L	5329534	3L_5329534_INS [dm3] 3L_5336434_INS [dm6]	A	AA	7.719e^-6	0.59	INTERGENIC
X	10860319	X_10860319_SNP [dm3] X_10966286_SNP [dm6]	G	A	7.864e^-6	0.59	SYNONYMOUS_CODING C901
2L	13142031	2L_13142031_SNP [dm3] 2L_13142031_SNP [dm6]	C	T	8.211e^-6	0.592	DOWNSTREAM CG9928 INTERGENIC
X	10860396	X_10860396_SNP [dm3] X_10966363_SNP [dm6]	T	A	8.602e^-6	0.598	INTRON C901
2R	6729922	2R_6729922_SNP [dm3] 2R_10842417_SNP [dm6]	A	T	9.768e^-6	0.653	SYNONYMOUS_CODING CG30015	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	24452306	3R_24452306_SNP [dm3] 3R_28626584_SNP [dm6]	C	A	1.067e^-5	0.653	INTRON CG10011
2L	13142029	2L_13142029_SNP [dm3] 2L_13142029_SNP [dm6]	T	C	1.095e^-5	0.653	DOWNSTREAM CG9928 INTERGENIC
2R	6730144	2R_6730144_SNP [dm3] 2R_10842639_SNP [dm6]	G	A	1.125e^-5	0.653	SYNONYMOUS_CODING CG30015	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	11683420	2L_11683420_SNP [dm3] 2L_11683420_SNP [dm6]	T	G	1.232e^-5	0.653	INTERGENIC
3L	15677545	3L_15677545_SNP [dm3] 3L_15684445_SNP [dm6]	G	C	1.234e^-5	0.653	UPSTREAM CG7579 INTRON pgant8
2R	18100190	2R_18100190_SNP [dm3] 2R_22212685_SNP [dm6]	T	G	1.270e^-5	0.653	UTR_3_PRIME CG11291 UPSTREAM ari-2	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_D mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_Trl mE1_TFBS_Ubx
3L	15677606	3L_15677606_SNP [dm3] 3L_15684506_SNP [dm6]	G	A	1.356e^-5	0.653	INTRON pgant8
2R	7255299	2R_7255299_SNP [dm3] 2R_11367794_SNP [dm6]	A	G	1.376e^-5	0.653	UPSTREAM CG13204 INTRON CG13204	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
2L	3491236	2L_3491236_SNP [dm3] 2L_3491236_SNP [dm6]	A	T	1.456e^-5	0.653	UPSTREAM CG15414 INTERGENIC
2R	8913891	2R_8913891_SNP [dm3] 2R_13026386_SNP [dm6]	A	C	1.471e^-5	0.653	INTERGENIC
2R	8913868	2R_8913868_SNP [dm3] 2R_13026363_SNP [dm6]	C	G	1.483e^-5	0.653	INTERGENIC
3R	21726417	3R_21726417_SNP [dm3] 3R_25900695_SNP [dm6]	A	G	1.490e^-5	0.653	SYNONYMOUS_CODING CG31091 DOWNSTREAM MCO3
2L	3491286	2L_3491286_SNP [dm3] 2L_3491286_SNP [dm6]	G	A	1.506e^-5	0.653	UPSTREAM CG15414 INTERGENIC
3L	5939364	3L_5939364_SNP [dm3] 3L_5946264_SNP [dm6]	C	T	1.511e^-5	0.653	INTRON CG33993	TF binding site BDTNP1_TFBS_twi
2L	1433376	2L_1433376_INS [dm3] 2L_1433376_INS [dm6]	T	TCTAATTATTAAATCTAATT...	1.526e^-5	0.653	DOWNSTREAM snRNA:U3:22A INTERGENIC
2L	3487249	2L_3487249_SNP [dm3] 2L_3487249_SNP [dm6]	G	A	1.532e^-5	0.653	INTRON CG15414
2R	6868004	2R_6868004_SNP [dm3] 2R_10980499_SNP [dm6]	C	T	1.633e^-5	0.681	UTR_3_PRIME luna
3L	19162017	3L_19162017_SNP [dm3] 3L_19168917_SNP [dm6]	G	A	1.728e^-5	0.704	INTRON fz2	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3R	18788304	3R_18788304_SNP [dm3] 3R_22962582_SNP [dm6]	G	A	1.774e^-5	0.704	DOWNSTREAM klg INTERGENIC
2R	9264654	2R_9264654_SNP [dm3] 2R_13377149_SNP [dm6]	C	T	1.906e^-5	0.704	SYNONYMOUS_CODING CG10814	TF binding site mE1_TFBS_chinmo
3R	25273949	3R_25273949_SNP [dm3] 3R_29448227_SNP [dm6]	G	C	1.949e^-5	0.704	INTRON Ptp99A
2R	18092484	2R_18092484_SNP [dm3] 2R_22204979_SNP [dm6]	G	A	1.954e^-5	0.704	SYNONYMOUS_CODING CG3292
2R	15839028	2R_15839028_SNP [dm3] 2R_19951523_SNP [dm6]	C	T	1.969e^-5	0.704	INTRON CG10822
X	12359745	X_12359745_SNP [dm3] X_12465712_SNP [dm6]	C	T	1.986e^-5	0.704	INTRON CG42258
2L	19203342	2L_19203342_SNP [dm3] 2L_19203342_SNP [dm6]	A	C	2.065e^-5	0.704	INTRON drl	regulatory region REDfly_CRMs
2R	9052709	2R_9052709_SNP [dm3] 2R_13165204_SNP [dm6]	T	A	2.112e^-5	0.704	INTRON GLaz
3R	21004616	3R_21004616_SNP [dm3] 3R_25178894_SNP [dm6]	T	C	2.138e^-5	0.704	INTRON lobo	TF binding site BDTNP1_TFBS_twi
2R	4735893	2R_4735893_SNP [dm3] 2R_8848388_SNP [dm6]	T	C	2.147e^-5	0.704	INTRON sns	TF binding site mE1_TFBS_cad
3R	22081566	3R_22081566_SNP [dm3] 3R_26255844_SNP [dm6]	C	A	2.175e^-5	0.704	DOWNSTREAM Ald INTRON Ald	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_bcd
X	12359853	X_12359853_INS [dm3] X_12465820_INS [dm6]	T	TT	2.220e^-5	0.704	INTRON CG42258
3L	2488536	3L_2488536_SNP [dm3] 3L_2488536_SNP [dm6]	C	T	2.233e^-5	0.704	UPSTREAM CG1146 INTRON CG45186	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	19202627	2L_19202627_SNP [dm3] 2L_19202627_SNP [dm6]	C	T	2.251e^-5	0.704	INTRON drl	regulatory region REDfly_CRMs TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	2822648	2R_2822648_SNP [dm3] 2R_6935143_SNP [dm6]	G	A	2.424e^-5	0.708	INTRON mim	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2L	19209375	2L_19209375_SNP [dm3] 2L_19209375_SNP [dm6]	T	C	2.485e^-5	0.708	DOWNSTREAM drl INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	1200754	3L_1200754_INS [dm3] 3L_1200754_INS [dm6]	C	CAGTC	2.510e^-5	0.708	UPSTREAM mwh INTERGENIC
2R	18098835	2R_18098835_SNP [dm3] 2R_22211330_SNP [dm6]	A	C	2.640e^-5	0.708	UPSTREAM CG11291 & 1 other INTERGENIC
X	16518166	X_16518166_SNP [dm3] X_16624133_SNP [dm6]	C	T	2.660e^-5	0.708	DOWNSTREAM Rok INTRON Rok
3L	12036932	3L_12036932_SNP [dm3] 3L_12043832_SNP [dm6]	C	T	2.719e^-5	0.708	SYNONYMOUS_CODING CG6793 UPSTREAM CG43638 INTRON rols
2L	2944680	2L_2944680_SNP [dm3] 2L_2944680_SNP [dm6]	C	A	2.737e^-5	0.708	INTRON lilli	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad
2L	3326832	2L_3326832_SNP [dm3] 2L_3326832_SNP [dm6]	G	A	2.810e^-5	0.708	DOWNSTREAM CG33281 INTERGENIC
2R	18092508	2R_18092508_SNP [dm3] 2R_22205003_SNP [dm6]	T	G	2.885e^-5	0.708	SPLICE_SITE_REGION CG3292 SYNONYMOUS_CODING CG3292
2L	8552696	2L_8552696_SNP [dm3] 2L_8552696_SNP [dm6]	A	T	2.965e^-5	0.708	INTRON Sema-1a
2R	2830978	2R_2830978_SNP [dm3] 2R_6943473_SNP [dm6]	T	A	3.046e^-5	0.708	INTRON mim & 1 other
3R	12811759	3R_12811759_SNP [dm3] 3R_16986037_SNP [dm6]	C	T	3.262e^-5	0.708	INTRON CG18622
2L	6127330	2L_6127330_SNP [dm3] 2L_6127330_SNP [dm6]	C	A	3.264e^-5	0.708	NON_SYNONYMOUS_CODING WDR79 DOWNSTREAM CG42730 & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
2L	1433226	2L_1433226_SNP [dm3] 2L_1433226_SNP [dm6]	A	G	3.277e^-5	0.708	DOWNSTREAM snRNA:U3:22A INTERGENIC
2L	1433233	2L_1433233_SNP [dm3] 2L_1433233_SNP [dm6]	G	A	3.296e^-5	0.708	DOWNSTREAM snRNA:U3:22A INTERGENIC
2R	6719764	2R_6719764_SNP [dm3] 2R_10832259_SNP [dm6]	C	T	3.302e^-5	0.708	INTRON CG12344	TF binding site mE1_TFBS_inv
2R	6107604	2R_6107604_SNP [dm3] 2R_10220099_SNP [dm6]	C	T	3.368e^-5	0.708	INTRON Hr46 & 1 other	enhancer mE1_CBP_Enhancers TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Trl
2R	18101723	2R_18101723_SNP [dm3] 2R_22214218_SNP [dm6]	T	C	3.400e^-5	0.708	INTRON ari-2	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
2L	19211488	2L_19211488_INS [dm3] 2L_19211488_INS [dm6]	A	AA	3.412e^-5	0.708	INTERGENIC
2R	18101253	2R_18101253_SNP [dm3] 2R_22213748_SNP [dm6]	A	G	3.428e^-5	0.708	INTRON ari-2	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_sens mE1_TFBS_Trl
3R	27306163	3R_27306163_SNP [dm3] 3R_31480441_SNP [dm6]	C	T	3.465e^-5	0.708	INTERGENIC
2R	18096443	2R_18096443_SNP [dm3] 2R_22208938_SNP [dm6]	G	T	3.530e^-5	0.708	UTR_3_PRIME CG3264 UPSTREAM CG3290
X	10874357	X_10874357_SNP [dm3] X_10980324_SNP [dm6]	A	G	3.617e^-5	0.708	INTRON CG42339
3R	13555073	3R_13555073_SNP [dm3] 3R_17729351_SNP [dm6]	A	G	3.632e^-5	0.708	SYNONYMOUS_CODING Lgr1
2L	3028336	2L_3028336_SNP [dm3] 2L_3028336_SNP [dm6]	G	A	3.634e^-5	0.708	UPSTREAM CG17219 INTRON CG3605	TF binding site BDTNP1_TFBS_dl mE1_TFBS_sens
X	10860418	X_10860418_DEL [dm3] X_10966385_DEL [dm6]	AAA	A	3.691e^-5	0.708	INTRON C901
2R	18101176	2R_18101176_SNP [dm3] 2R_22213671_SNP [dm6]	C	T	3.794e^-5	0.708	DOWNSTREAM CG11291 INTRON ari-2	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_sens mE1_TFBS_Trl
2R	18101263	2R_18101263_SNP [dm3] 2R_22213758_SNP [dm6]	T	C	3.794e^-5	0.708	INTRON ari-2	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_sens mE1_TFBS_Trl
2R	4836972	2R_4836972_SNP [dm3] 2R_8949467_SNP [dm6]	G	A	3.946e^-5	0.708	DOWNSTREAM CG8229 INTRON CG8229 & 1 other
2R	18100250	2R_18100250_SNP [dm3] 2R_22212745_SNP [dm6]	A	G	3.948e^-5	0.708	UPSTREAM ari-2 DOWNSTREAM CG11291 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_D mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_Trl mE1_TFBS_Ubx
X	14803137	X_14803137_INS [dm3] X_14909104_INS [dm6]	C	CAC	3.997e^-5	0.708	UTR_5_PRIME CG9509 UPSTREAM CG9509 DOWNSTREAM CG14406 INTRON Flo2	regulatory region REDfly_CRMs TF binding site mE1_TFBS_cad
3L	5933257	3L_5933257_SNP [dm3] 3L_5940157_SNP [dm6]	G	A	4.011e^-5	0.708	INTRON CG33993
X	12215558	X_12215558_SNP [dm3] X_12321525_SNP [dm6]	T	C	4.036e^-5	0.708	INTRON Ten-a	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	22079945	3R_22079945_SNP [dm3] 3R_26254223_SNP [dm6]	A	G	4.047e^-5	0.708	UTR_3_PRIME Ald DOWNSTREAM Ald	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_ttk mE1_TFBS_zfh1
2R	4941580	2R_4941580_SNP [dm3] 2R_9054075_SNP [dm6]	T	C	4.061e^-5	0.708	INTRON CG13743
3L	14907908	3L_14907908_SNP [dm3] 3L_14914808_SNP [dm6]	G	T	4.080e^-5	0.708	INTRON DCX-EMAP
3R	18721529	3R_18721529_SNP [dm3] 3R_22895807_SNP [dm6]	G	C	4.082e^-5	0.708	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	4835856	3L_4835856_SNP [dm3] 3L_4835856_SNP [dm6]	T	A	4.218e^-5	0.708	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	4835861	3L_4835861_SNP [dm3] 3L_4835861_SNP [dm6]	C	G	4.218e^-5	0.708	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	7460137	2L_7460137_SNP [dm3] 2L_7460137_SNP [dm6]	C	T	4.258e^-5	0.708	SYNONYMOUS_CODING Gr28b INTRON Gr28b	TF binding site mE1_TFBS_HSA mE1_TFBS_sens

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By genomic position
Variant impact
Gene name

Starvation Resistance phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results