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=9.024e^-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_3R_K	0.02547

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_3R_K	7.5097	0.0234

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1885 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
3R	20706594	3R_20706594_SNP [dm3] 3R_24880872_SNP [dm6]	C	T	9.746e^-7	0.969	SYNONYMOUS_CODING CG11089 DOWNSTREAM CG31121	TF binding site mE1_TFBS_cad
3R	17970244	3R_17970244_SNP [dm3] 3R_22144522_SNP [dm6]	G	A	1.259e^-6	0.969	INTRON SKIP
3L	22925422	3L_22925422_SNP [dm3] 3L_22932322_SNP [dm6]	G	T	2.291e^-6	0.969	INTERGENIC
2L	11431434	2L_11431434_SNP [dm3] 2L_11431434_SNP [dm6]	C	T	2.921e^-6	0.969	INTERGENIC
3R	11303457	3R_11303457_SNP [dm3] 3R_15477735_SNP [dm6]	A	T	3.911e^-6	0.969	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	20706588	3R_20706588_SNP [dm3] 3R_24880866_SNP [dm6]	G	A	4.662e^-6	0.969	SYNONYMOUS_CODING CG11089 DOWNSTREAM CG31121	TF binding site mE1_TFBS_cad
2R	5829099	2R_5829099_SNP [dm3] 2R_9941594_SNP [dm6]	C	T	5.048e^-6	0.969	INTRON Mef2	regulatory region REDfly_CRMs TF binding site mE1_TFBS_Trl
2R	5829077	2R_5829077_INS [dm3] 2R_9941572_INS [dm6]	A	AGA	5.835e^-6	0.969	INTRON Mef2	regulatory region REDfly_CRMs TF binding site mE1_TFBS_Trl
3L	12309107	3L_12309107_SNP [dm3] 3L_12316007_SNP [dm6]	A	C	5.958e^-6	0.969	INTERGENIC
3R	12105207	3R_12105207_SNP [dm3] 3R_16279485_SNP [dm6]	G	A	6.335e^-6	0.969	INTRON gish	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_z mE1_TFBS_disco mE1_TFBS_Trl
3R	17970232	3R_17970232_SNP [dm3] 3R_22144510_SNP [dm6]	A	T	6.834e^-6	0.969	INTRON SKIP
2R	15488863	2R_15488863_SNP [dm3] 2R_19601358_SNP [dm6]	A	T	8.160e^-6	0.969	INTRON sm
3R	18085901	3R_18085901_SNP [dm3] 3R_22260179_SNP [dm6]	T	C	8.843e^-6	0.969	INTRON SKIP
3L	18201532	3L_18201532_SNP [dm3] 3L_18208432_SNP [dm6]	C	A	9.252e^-6	0.969	INTERGENIC
3R	20706601	3R_20706601_SNP [dm3] 3R_24880879_SNP [dm6]	T	C	1.043e^-5	0.969	SYNONYMOUS_CODING CG11089 DOWNSTREAM CG31121	TF binding site mE1_TFBS_cad
X	17961371	X_17961371_SNP [dm3] X_18067338_SNP [dm6]	A	T	1.127e^-5	0.969	SPLICE_SITE_REGION Dhc16F INTRON Dhc16F
2R	12308878	2R_12308878_SNP [dm3] 2R_16421373_SNP [dm6]	G	A	1.364e^-5	0.969	INTRON Sema-2b
3R	9714127	3R_9714127_SNP [dm3] 3R_13888405_SNP [dm6]	C	T	1.377e^-5	0.969	INTERGENIC	TF binding site BDTNP1_TFBS_twi
3L	15246936	3L_15246936_SNP [dm3] 3L_15253836_SNP [dm6]	A	G	1.486e^-5	0.969	INTERGENIC	TF binding site BDTNP1_TFBS_dl
X	5091444	X_5091444_SNP [dm3] X_5197411_SNP [dm6]	T	C	1.553e^-5	0.969	INTRON rg & 1 other
3L	10009328	3L_10009328_SNP [dm3] 3L_10016228_SNP [dm6]	C	T	1.573e^-5	0.969	INTRON dpr6
3L	9732908	3L_9732908_SNP [dm3] 3L_9739808_SNP [dm6]	G	A	1.658e^-5	0.969	UPSTREAM CG42268 INTRON CG42268	TF binding site mE1_TFBS_cad
3L	7382102	3L_7382102_SNP [dm3] 3L_7389002_SNP [dm6]	T	C	1.663e^-5	0.969	INTERGENIC
3R	16857467	3R_16857467_SNP [dm3] 3R_21031745_SNP [dm6]	G	A	1.703e^-5	0.969	SPLICE_SITE_REGION Dhc93AB INTRON Dhc93AB
3L	15246939	3L_15246939_SNP [dm3] 3L_15253839_SNP [dm6]	C	T	1.765e^-5	0.969	INTERGENIC	TF binding site BDTNP1_TFBS_dl
3L	8552804	3L_8552804_SNP [dm3] 3L_8559704_SNP [dm6]	T	A	1.850e^-5	0.969	UPSTREAM rhea INTRON rhea	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2L	15285324	2L_15285324_SNP [dm3] 2L_15285324_SNP [dm6]	G	A	1.977e^-5	0.969	NON_SYNONYMOUS_CODING CG15263
3L	8552786	3L_8552786_DEL [dm3] 3L_8559686_DEL [dm6]	AAGTTTTTGTTTGGTGA...	T	2.028e^-5	0.969	UPSTREAM rhea INTRON rhea	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2L	11623798	2L_11623798_SNP [dm3] 2L_11623798_SNP [dm6]	T	G	2.189e^-5	0.969	SYNONYMOUS_CODING kek2	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	10177649	2L_10177649_DEL [dm3] 2L_10177649_DEL [dm6]	TT	T	2.346e^-5	0.969	INTRON CG44153
3L	10825312	3L_10825312_SNP [dm3] 3L_10832212_SNP [dm6]	T	C	2.478e^-5	0.969	INTERGENIC
2R	19628144	2R_19628144_SNP [dm3] 2R_23740621_SNP [dm6]	C	G	2.512e^-5	0.969	INTRON egl
3L	3859487	3L_3859487_SNP [dm3] 3L_3859487_SNP [dm6]	A	G	2.646e^-5	0.969	INTRON Awh	TF binding site mE1_TFBS_cad
2R	17028143	2R_17028143_SNP [dm3] 2R_21140638_SNP [dm6]	A	G	2.791e^-5	0.969	UPSTREAM Magi INTRON Magi	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna mE1_TFBS_HSA mE1_TFBS_sens
3R	20706579	3R_20706579_SNP [dm3] 3R_24880857_SNP [dm6]	A	G	2.801e^-5	0.969	SYNONYMOUS_CODING CG11089 DOWNSTREAM CG31121	TF binding site mE1_TFBS_cad
2L	9932917	2L_9932917_SNP [dm3] 2L_9932917_SNP [dm6]	T	C	2.861e^-5	0.969	SYNONYMOUS_CODING Cpr30F	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2L	11507215	2L_11507215_SNP [dm3] 2L_11507215_SNP [dm6]	A	C	2.879e^-5	0.969	NON_SYNONYMOUS_CODING spz4	TF binding site mE1_TFBS_cad
2L	7680333	2L_7680333_DEL [dm3] 2L_7680333_DEL [dm6]	ATCTATATA	A	2.890e^-5	0.969	INTRON Myo28B1
3R	24598995	3R_24598995_SNP [dm3] 3R_28773273_SNP [dm6]	A	G	2.996e^-5	0.969	INTERGENIC
3R	9604613	3R_9604613_DEL [dm3] 3R_13778891_DEL [dm6]	AGCATAACCCTAA...	A	3.142e^-5	0.969	UTR_3_PRIME CG9297 UPSTREAM CG9288 & 1 other	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
2L	11507729	2L_11507729_SNP [dm3] 2L_11507729_SNP [dm6]	A	G	3.206e^-5	0.969	SYNONYMOUS_CODING spz4 DOWNSTREAM CG6509	TF binding site mE1_TFBS_cad
2R	5829107	2R_5829107_SNP [dm3] 2R_9941602_SNP [dm6]	T	A	3.235e^-5	0.969	INTRON Mef2	regulatory region REDfly_CRMs TF binding site mE1_TFBS_Trl
3R	12102774	3R_12102774_SNP [dm3] 3R_16277052_SNP [dm6]	T	C	3.239e^-5	0.969	INTRON gish	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	15488872	2R_15488872_SNP [dm3] 2R_19601367_SNP [dm6]	C	T	3.243e^-5	0.969	INTRON sm
2R	15488868	2R_15488868_SNP [dm3] 2R_19601363_SNP [dm6]	T	A	3.421e^-5	0.969	INTRON sm
3R	10134223	3R_10134223_SNP [dm3] 3R_14308501_SNP [dm6]	T	G	3.433e^-5	0.969	UTR_5_PRIME su_Hw_ UPSTREAM RpII15 INTRON su_Hw_	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_Ubx
2L	11508124	2L_11508124_SNP [dm3] 2L_11508124_SNP [dm6]	T	A	3.582e^-5	0.969	UTR_3_PRIME spz4 DOWNSTREAM CG6509
2R	5829526	2R_5829526_SNP [dm3] 2R_9942021_SNP [dm6]	C	A	3.616e^-5	0.969	INTRON Mef2	regulatory region REDfly_CRMs TF binding site mE1_TFBS_Trl
3L	10718344	3L_10718344_SNP [dm3] 3L_10725244_SNP [dm6]	T	A	3.685e^-5	0.969	INTERGENIC
2L	18867476	2L_18867476_SNP [dm3] 2L_18867476_SNP [dm6]	A	T	3.856e^-5	0.969	UPSTREAM mir-4946 INTRON tup	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	1637781	2R_1637781_SNP [dm3] 2R_5750276_SNP [dm6]	G	T	3.931e^-5	0.969	INTERGENIC
X	16017447	X_16017447_SNP [dm3] X_16123414_SNP [dm6]	T	C	3.950e^-5	0.969	INTRON disco-r
2R	7029701	2R_7029701_SNP [dm3] 2R_11142196_SNP [dm6]	T	C	4.062e^-5	0.969	INTRON CG13229
3R	10130552	3R_10130552_SNP [dm3] 3R_14304830_SNP [dm6]	A	G	4.093e^-5	0.969	NON_SYNONYMOUS_CODING su_Hw_ DOWNSTREAM CG3259
3R	6053184	3R_6053184_SNP [dm3] 3R_10227462_SNP [dm6]	T	A	4.321e^-5	0.969	INTRON CG42795	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	15848537	3L_15848537_SNP [dm3] 3L_15855437_SNP [dm6]	T	G	4.321e^-5	0.969	INTRON pHCl
X	13932160	X_13932160_SNP [dm3] X_14038127_SNP [dm6]	A	G	4.401e^-5	0.969	INTERGENIC	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	6539202	2R_6539202_SNP [dm3] 2R_10651697_SNP [dm6]	T	G	4.422e^-5	0.969	INTERGENIC
3L	7109350	3L_7109350_SNP [dm3] 3L_7116250_SNP [dm6]	T	A	4.465e^-5	0.969	INTRON form3
3R	19382958	3R_19382958_SNP [dm3] 3R_23557236_SNP [dm6]	G	A	4.498e^-5	0.969	UPSTREAM beat-IV & 1 other INTERGENIC
2R	16818215	2R_16818215_SNP [dm3] 2R_20930710_SNP [dm6]	T	C	4.514e^-5	0.969	INTRON Rx
2R	5830088	2R_5830088_SNP [dm3] 2R_9942583_SNP [dm6]	T	A	4.553e^-5	0.969	INTRON Mef2	TF binding site BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_zfh1
2R	6649894	2R_6649894_SNP [dm3] 2R_10762389_SNP [dm6]	G	A	4.575e^-5	0.969	DOWNSTREAM CR43605 INTRON CG33144
3R	20368884	3R_20368884_SNP [dm3] 3R_24543162_SNP [dm6]	C	G	4.608e^-5	0.969	INTRON CG5789
2R	19358354	2R_19358354_SNP [dm3] 2R_23470831_SNP [dm6]	G	A	4.638e^-5	0.969	SYNONYMOUS_CODING Or59b INTRON CG43795
3R	12104366	3R_12104366_SNP [dm3] 3R_16278644_SNP [dm6]	T	C	4.641e^-5	0.969	INTRON gish	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
2R	6539339	2R_6539339_SNP [dm3] 2R_10651834_SNP [dm6]	C	A	4.687e^-5	0.969	INTERGENIC
2L	6734745	2L_6734745_SNP [dm3] 2L_6734745_SNP [dm6]	C	T	4.746e^-5	0.969	SYNONYMOUS_CODING TTLL3B	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3R	15826494	3R_15826494_DEL [dm3] 3R_20000772_DEL [dm6]	GAAACAGATCTTAATGCTAG...	G	4.792e^-5	0.969	INTRON Hs6st	TF binding site BDTNP1_TFBS_twi
3L	17815277	3L_17815277_SNP [dm3] 3L_17822177_SNP [dm6]	T	G	4.805e^-5	0.969	NON_SYNONYMOUS_CODING Ir75c
X	17962133	X_17962133_SNP [dm3] X_18068100_SNP [dm6]	T	A	4.857e^-5	0.969	SYNONYMOUS_CODING Dhc16F
3L	3532165	3L_3532165_SNP [dm3] 3L_3532165_SNP [dm6]	T	C	4.885e^-5	0.969	INTRON Eip63E
2R	19608279	2R_19608279_SNP [dm3] 2R_23720756_SNP [dm6]	G	A	4.952e^-5	0.969	UPSTREAM CG18128 INTRON Sesn EXON CR45325
X	14434973	X_14434973_SNP [dm3] X_14540940_SNP [dm6]	A	G	4.952e^-5	0.969	EXON CR45521
3R	12626076	3R_12626076_SNP [dm3] 3R_16800354_SNP [dm6]	A	G	4.979e^-5	0.969	UPSTREAM CR45750 & 1 other INTERGENIC	enhancer mE1_CBP_Enhancers
2R	5829932	2R_5829932_SNP [dm3] 2R_9942427_SNP [dm6]	A	T	4.991e^-5	0.969	INTRON Mef2	TF binding site BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_zfh1
3R	20368664	3R_20368664_SNP [dm3] 3R_24542942_SNP [dm6]	C	T	5.114e^-5	0.969	INTRON CG5789
3R	12722585	3R_12722585_SNP [dm3] 3R_16896863_SNP [dm6]	T	C	5.118e^-5	0.969	UPSTREAM iab-8 INTRON iab-8 & 1 other	TF binding site mE1_TFBS_cad
3L	12219209	3L_12219209_SNP [dm3] 3L_12226109_SNP [dm6]	C	A	5.204e^-5	0.969	INTRON app
3R	20706724	3R_20706724_SNP [dm3] 3R_24881002_SNP [dm6]	C	G	5.297e^-5	0.969	SYNONYMOUS_CODING CG11089 DOWNSTREAM CG31121	TF binding site mE1_TFBS_cad
2R	13119399	2R_13119399_SNP [dm3] 2R_17231894_SNP [dm6]	T	C	5.315e^-5	0.969	INTRON mbl
3L	15246948	3L_15246948_SNP [dm3] 3L_15253848_SNP [dm6]	C	G	5.355e^-5	0.969	INTERGENIC	TF binding site BDTNP1_TFBS_dl
3L	10718334	3L_10718334_SNP [dm3] 3L_10725234_SNP [dm6]	C	A	5.495e^-5	0.969	INTERGENIC
2R	5847821	2R_5847821_SNP [dm3] 2R_9960316_SNP [dm6]	G	C	5.624e^-5	0.969	UPSTREAM CG15863 INTRON Pal1	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3R	10302088	3R_10302088_SNP [dm3] 3R_14476366_SNP [dm6]	C	T	5.693e^-5	0.969	INTRON cv-c
2R	10006736	2R_10006736_SNP [dm3] 2R_14119231_SNP [dm6]	C	T	5.724e^-5	0.969	INTRON Prosap
2L	5284689	2L_5284689_SNP [dm3] 2L_5284689_SNP [dm6]	C	T	5.795e^-5	0.969	INTERGENIC	TF binding site mE1_TFBS_cad
3R	12722542	3R_12722542_SNP [dm3] 3R_16896820_SNP [dm6]	C	A	5.807e^-5	0.969	UPSTREAM iab-8 INTRON iab-8 & 1 other	TF binding site mE1_TFBS_cad
2R	4753063	2R_4753063_DEL [dm3] 2R_8865558_DEL [dm6]	GTTATTCG	G	5.852e^-5	0.969	INTRON RyR	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	16983394	3L_16983394_SNP [dm3] 3L_16990294_SNP [dm6]	C	A	5.890e^-5	0.969	INTRON Exn
X	17961375	X_17961375_SNP [dm3] X_18067342_SNP [dm6]	C	T	5.893e^-5	0.969	SPLICE_SITE_REGION Dhc16F INTRON Dhc16F
3R	12132123	3R_12132123_SNP [dm3] 3R_16306401_SNP [dm6]	T	C	6.035e^-5	0.969	SYNONYMOUS_CODING Zip89B	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3L	22965695	3L_22965695_SNP [dm3] 3L_22972595_SNP [dm6]	G	C	6.087e^-5	0.969	INTERGENIC
3L	2147547	3L_2147547_SNP [dm3] 3L_2147547_SNP [dm6]	T	A	6.088e^-5	0.969	INTRON zormin
2R	15488814	2R_15488814_SNP [dm3] 2R_19601309_SNP [dm6]	G	A	6.095e^-5	0.969	INTRON sm
3L	3532136	3L_3532136_SNP [dm3] 3L_3532136_SNP [dm6]	G	A	6.288e^-5	0.969	INTRON Eip63E
3R	10130549	3R_10130549_SNP [dm3] 3R_14304827_SNP [dm6]	C	A	6.350e^-5	0.969	NON_SYNONYMOUS_CODING su_Hw_ DOWNSTREAM CG3259
3L	16154344	3L_16154344_SNP [dm3] 3L_16161244_SNP [dm6]	C	T	6.406e^-5	0.969	INTRON CG5151
3R	10132151	3R_10132151_SNP [dm3] 3R_14306429_SNP [dm6]	T	A	6.425e^-5	0.969	SYNONYMOUS_CODING su_Hw_
3R	12104367	3R_12104367_SNP [dm3] 3R_16278645_SNP [dm6]	C	T	6.554e^-5	0.969	INTRON gish	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl

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By genomic position
Variant impact
Gene name

mn_MortalityInd phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results