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=4.940e^-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

Covariate	p-value	Significance
In_2R_NS	0.006375
In_3R_Mo	0.049842

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2R_NS	6.6726	0.0356
In_3R_Mo	6.3349	0.0421

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1785 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
2R	9146182	2R_9146182_SNP [dm3] 2R_13258677_SNP [dm6]	G	A	2.455e^-6	0.867	DOWNSTREAM CG10799 INTERGENIC
3R	26527712	3R_26527712_SNP [dm3] 3R_30701990_SNP [dm6]	G	T	2.727e^-6	0.867	INTERGENIC	TF binding site mE1_TFBS_inv
2R	9146231	2R_9146231_SNP [dm3] 2R_13258726_SNP [dm6]	G	A	2.887e^-6	0.867	DOWNSTREAM CG10799 INTERGENIC
2R	9146238	2R_9146238_SNP [dm3] 2R_13258733_SNP [dm6]	A	G	2.887e^-6	0.867	DOWNSTREAM CG10799 INTERGENIC
X	21324090	X_21324090_SNP [dm3] X_21453063_SNP [dm6]	G	C	3.563e^-6	0.867	INTRON CG42343
2R	9048840	2R_9048840_SNP [dm3] 2R_13161335_SNP [dm6]	T	C	3.572e^-6	0.867	INTRON Nrk	TF binding site BDTNP1_TFBS_twi
3L	16735429	3L_16735429_SNP [dm3] 3L_16742329_SNP [dm6]	G	A	4.247e^-6	0.867	INTERGENIC
3L	6480167	3L_6480167_SNP [dm3] 3L_6487067_SNP [dm6]	C	T	4.312e^-6	0.867	SYNONYMOUS_CODING CG10147	TF binding site BDTNP1_TFBS_twi
3R	5045687	3R_5045687_SNP [dm3] 3R_9219965_SNP [dm6]	A	T	5.233e^-6	0.867	INTRON pum	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_Trl
3L	18446458	3L_18446458_SNP [dm3] 3L_18453358_SNP [dm6]	C	G	5.424e^-6	0.867	INTERGENIC	TF binding site mE1_TFBS_HSA
2R	9048826	2R_9048826_SNP [dm3] 2R_13161321_SNP [dm6]	A	C	5.759e^-6	0.867	INTRON Nrk	TF binding site BDTNP1_TFBS_twi
3R	26527703	3R_26527703_SNP [dm3] 3R_30701981_SNP [dm6]	T	A	5.774e^-6	0.867	INTERGENIC	TF binding site mE1_TFBS_inv
2R	9048897	2R_9048897_SNP [dm3] 2R_13161392_SNP [dm6]	T	G	6.122e^-6	0.867	NON_SYNONYMOUS_CODING Nrk	TF binding site BDTNP1_TFBS_twi
3R	26895815	3R_26895815_SNP [dm3] 3R_31070093_SNP [dm6]	G	T	6.506e^-6	0.867	INTRON Sox100B	TF binding site BDTNP1_TFBS_twi
2L	9822575	2L_9822575_SNP [dm3] 2L_9822575_SNP [dm6]	T	G	7.612e^-6	0.946	INTRON nAChRalpha6
3R	10264754	3R_10264754_SNP [dm3] 3R_14439032_SNP [dm6]	G	A	8.192e^-6	0.955	INTRON cv-c
X	15860115	X_15860115_SNP [dm3] X_15966082_SNP [dm6]	A	T	9.541e^-6	0.971	UPSTREAM mir-927 INTRON mmd
2R	9151999	2R_9151999_SNP [dm3] 2R_13264494_SNP [dm6]	A	G	9.752e^-6	0.971	SYNONYMOUS_CODING CG42319 DOWNSTREAM CG42319
3L	5873664	3L_5873664_SNP [dm3] 3L_5880564_SNP [dm6]	A	T	1.232e^-5	0.971	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
X	8274164	X_8274164_SNP [dm3] X_8380131_SNP [dm6]	A	G	1.238e^-5	0.971	INTERGENIC
X	749623	X_749623_SNP [dm3] X_855590_SNP [dm6]	A	G	1.241e^-5	0.971	INTRON CG43867	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2L	19413335	2L_19413335_SNP [dm3] 2L_19413335_SNP [dm6]	A	T	1.269e^-5	0.971	INTRON Pax	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
3L	5857291	3L_5857291_SNP [dm3] 3L_5864191_SNP [dm6]	C	T	1.314e^-5	0.971	INTERGENIC
2R	8613586	2R_8613586_SNP [dm3] 2R_12726081_SNP [dm6]	G	A	1.339e^-5	0.971	INTRON CG42663
3R	26527620	3R_26527620_DEL [dm3] 3R_30701898_DEL [dm6]	CG	C	1.340e^-5	0.971	INTERGENIC	TF binding site mE1_TFBS_inv
2R	9892328	2R_9892328_SNP [dm3] 2R_14004823_SNP [dm6]	T	G	1.391e^-5	0.971	INTRON mam	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
2L	3794426	2L_3794426_SNP [dm3] 2L_3794426_SNP [dm6]	T	C	1.429e^-5	0.971	SYNONYMOUS_CODING CG3921	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	15594610	3L_15594610_SNP [dm3] 3L_15601510_SNP [dm6]	C	T	1.699e^-5	0.971	INTRON RhoGAP71E	TF binding site mE1_TFBS_chinmo
3R	7321521	3R_7321521_SNP [dm3] 3R_11495799_SNP [dm6]	C	T	1.762e^-5	0.971	INTERGENIC
2R	8613576	2R_8613576_SNP [dm3] 2R_12726071_SNP [dm6]	C	T	1.772e^-5	0.971	INTRON CG42663
2L	2177108	2L_2177108_SNP [dm3] 2L_2177108_SNP [dm6]	A	T	1.948e^-5	0.971	INTRON aop	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_sens mE1_TFBS_Trl
X	14221635	X_14221635_SNP [dm3] X_14327602_SNP [dm6]	C	T	1.957e^-5	0.971	INTRON dpr8
3R	13530932	3R_13530932_SNP [dm3] 3R_17705210_SNP [dm6]	C	A	1.989e^-5	0.971	INTRON osa
3R	26895754	3R_26895754_SNP [dm3] 3R_31070032_SNP [dm6]	A	C	2.022e^-5	0.971	INTRON Sox100B	TF binding site BDTNP1_TFBS_twi
3L	13528516	3L_13528516_SNP [dm3] 3L_13535416_SNP [dm6]	A	G	2.023e^-5	0.971	UTR_3_PRIME bru-3 DOWNSTREAM bru-3	TF binding site mE1_TFBS_kn
2R	9146272	2R_9146272_SNP [dm3] 2R_13258767_SNP [dm6]	T	A	2.134e^-5	0.971	DOWNSTREAM CG10799 INTERGENIC
2R	9146260	2R_9146260_SNP [dm3] 2R_13258755_SNP [dm6]	T	C	2.254e^-5	0.971	DOWNSTREAM CG10799 INTERGENIC
2R	9146173	2R_9146173_SNP [dm3] 2R_13258668_SNP [dm6]	C	G	2.326e^-5	0.971	DOWNSTREAM CG10799 INTERGENIC
3R	8141669	3R_8141669_SNP [dm3] 3R_12315947_SNP [dm6]	A	C	2.376e^-5	0.971	INTERGENIC
3L	19769316	3L_19769316_SNP [dm3] 3L_19776216_SNP [dm6]	G	A	2.566e^-5	0.971	INTRON CG42637 & 1 other
2R	9754197	2R_9754197_SNP [dm3] 2R_13866692_SNP [dm6]	T	C	2.635e^-5	0.971	INTRON shot
2R	6888738	2R_6888738_SNP [dm3] 2R_11001233_SNP [dm6]	A	G	2.760e^-5	0.971	INTRON luna
3L	9361423	3L_9361423_SNP [dm3] 3L_9368323_SNP [dm6]	A	G	2.935e^-5	0.971	INTRON CG4452	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	1979606	2L_1979606_SNP [dm3] 2L_1979606_SNP [dm6]	A	C	2.983e^-5	0.971	INTRON CG15356	TF binding site mE1_TFBS_HSA
3L	13229180	3L_13229180_SNP [dm3] 3L_13236080_SNP [dm6]	A	G	3.014e^-5	0.971	INTRON caps
3L	5873662	3L_5873662_SNP [dm3] 3L_5880562_SNP [dm6]	A	G	3.259e^-5	0.971	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
3L	13024874	3L_13024874_SNP [dm3] 3L_13031774_SNP [dm6]	A	T	3.274e^-5	0.971	DOWNSTREAM CR45157 INTRON CG17672	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
3L	6607449	3L_6607449_SNP [dm3] 3L_6614349_SNP [dm6]	T	C	3.287e^-5	0.971	INTRON CG8398
3R	27513292	3R_27513292_SNP [dm3] 3R_31687570_SNP [dm6]	C	T	3.406e^-5	0.971	DOWNSTREAM CR45564 INTERGENIC	TF binding site mE1_TFBS_chinmo
2R	11443576	2R_11443576_SNP [dm3] 2R_15556071_SNP [dm6]	T	G	3.431e^-5	0.971	UPSTREAM CG12963 INTRON CG12963
2R	10841794	2R_10841794_SNP [dm3] 2R_14954289_SNP [dm6]	G	A	3.506e^-5	0.971	INTRON aPKC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3L	5899172	3L_5899172_SNP [dm3] 3L_5906072_SNP [dm6]	G	A	3.519e^-5	0.971	SYNONYMOUS_CODING CG10486
3R	10229978	3R_10229978_SNP [dm3] 3R_14404256_SNP [dm6]	G	A	3.532e^-5	0.971	INTRON cv-c
3L	16661482	3L_16661482_SNP [dm3] 3L_16668382_SNP [dm6]	T	A	3.613e^-5	0.971	UPSTREAM Galphaf INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Trl
3L	16735436	3L_16735436_SNP [dm3] 3L_16742336_SNP [dm6]	C	T	3.626e^-5	0.971	INTERGENIC
3R	23300059	3R_23300059_SNP [dm3] 3R_27474337_SNP [dm6]	T	A	3.640e^-5	0.971	INTERGENIC
2L	8348181	2L_8348181_SNP [dm3] 2L_8348181_SNP [dm6]	C	T	3.729e^-5	0.971	INTRON CG7778
3R	25357177	3R_25357177_DEL [dm3] 3R_29531455_DEL [dm6]	ACAACAA	A	3.832e^-5	0.971	INTERGENIC	TF binding site mE1_TFBS_sens
3R	8513395	3R_8513395_SNP [dm3] 3R_12687673_SNP [dm6]	T	C	3.846e^-5	0.971	INTRON kar	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2L	3173257	2L_3173257_SNP [dm3] 2L_3173257_SNP [dm6]	C	T	3.995e^-5	0.971	UTR_3_PRIME CG31698 UPSTREAM CR44003 & 2 others DOWNSTREAM CG31698	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi
2R	17436207	2R_17436207_SNP [dm3] 2R_21548702_SNP [dm6]	T	C	4.053e^-5	0.971	INTRON Egfr	TF binding site BDTNP1_TFBS_dl
X	13931521	X_13931521_SNP [dm3] X_14037488_SNP [dm6]	A	G	4.105e^-5	0.971	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi
3L	5976368	3L_5976368_SNP [dm3] 3L_5983268_SNP [dm6]	G	T	4.143e^-5	0.971	DOWNSTREAM CR45439 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_eve mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_sens
2R	10547476	2R_10547476_DEL [dm3] 2R_14659971_DEL [dm6]	CAGACACCC	C	4.145e^-5	0.971	INTERGENIC
3L	2060412	3L_2060412_SNP [dm3] 3L_2060412_SNP [dm6]	C	T	4.196e^-5	0.971	NON_SYNONYMOUS_CODING sls INTRON sls
3R	19465242	3R_19465242_SNP [dm3] 3R_23639520_SNP [dm6]	G	A	4.222e^-5	0.971	INTRON CG31145	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
X	4208879	X_4208879_SNP [dm3] X_4314846_SNP [dm6]	A	C	4.290e^-5	0.971	UTR_3_PRIME mei-9 UPSTREAM CR44957
3L	10842341	3L_10842341_SNP [dm3] 3L_10849241_SNP [dm6]	T	C	4.308e^-5	0.971	DOWNSTREAM CR45169 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_sens mE1_TFBS_Trl
3R	20232542	3R_20232542_SNP [dm3] 3R_24406820_SNP [dm6]	C	T	4.320e^-5	0.971	INTRON nAChRalpha1
3L	10396532	3L_10396532_SNP [dm3] 3L_10403432_SNP [dm6]	C	A	4.404e^-5	0.971	INTERGENIC
3R	27515687	3R_27515687_SNP [dm3] 3R_31689965_SNP [dm6]	G	C	4.462e^-5	0.971	UPSTREAM CR45565 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2R	17320976	2R_17320976_SNP [dm3] 2R_21433471_SNP [dm6]	G	C	4.509e^-5	0.971	INTRON Sdc
2L	5377325	2L_5377325_SNP [dm3] 2L_5377325_SNP [dm6]	A	G	4.560e^-5	0.971	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	9775485	2R_9775485_SNP [dm3] 2R_13887980_SNP [dm6]	G	A	4.564e^-5	0.971	SYNONYMOUS_CODING shot INTRON shot	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	26896083	3R_26896083_SNP [dm3] 3R_31070361_SNP [dm6]	C	G	4.618e^-5	0.971	INTRON Sox100B	TF binding site BDTNP1_TFBS_twi
2R	19991068	2R_19991068_SNP [dm3] 2R_24103545_SNP [dm6]	A	G	4.669e^-5	0.971	SYNONYMOUS_CODING enok	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	14938555	3L_14938555_SNP [dm3] 3L_14945455_SNP [dm6]	G	T	4.687e^-5	0.971	DOWNSTREAM BobA INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi
3L	5857216	3L_5857216_INS [dm3] 3L_5864116_INS [dm6]	G	GG	4.717e^-5	0.971	INTERGENIC
2L	13621081	2L_13621081_SNP [dm3] 2L_13621081_SNP [dm6]	G	A	4.794e^-5	0.971	INTRON kuz
2R	3463587	2R_3463587_SNP [dm3] 2R_7576082_SNP [dm6]	C	T	4.826e^-5	0.971	SYNONYMOUS_CODING Vps13
3R	22683355	3R_22683355_SNP [dm3] 3R_26857633_SNP [dm6]	A	G	5.037e^-5	0.971	INTRON Lerp
X	7769889	X_7769889_SNP [dm3] X_7875856_SNP [dm6]	C	T	5.040e^-5	0.971	NON_SYNONYMOUS_CODING Ir7c
X	13155756	X_13155756_SNP [dm3] X_13261723_SNP [dm6]	T	C	5.051e^-5	0.971	DOWNSTREAM HDAC4 INTRON comt
3R	20500099	3R_20500099_SNP [dm3] 3R_24674377_SNP [dm6]	T	G	5.117e^-5	0.971	INTRON slo
3R	13679866	3R_13679866_SNP [dm3] 3R_17854144_SNP [dm6]	C	T	5.249e^-5	0.971	INTRON tinc	TF binding site mE1_TFBS_inv
2L	19516846	2L_19516846_SNP [dm3] 2L_19516846_SNP [dm6]	T	A	5.278e^-5	0.971	UTR_5_PRIME CG10186 UPSTREAM CG10186
3L	14424076	3L_14424076_SNP [dm3] 3L_14430976_SNP [dm6]	T	A	5.402e^-5	0.971	INTRON bbg
2R	19100744	2R_19100744_SNP [dm3] 2R_23213221_SNP [dm6]	T	C	5.747e^-5	0.971	INTERGENIC
2R	17519211	2R_17519211_SNP [dm3] 2R_21631706_SNP [dm6]	T	A	5.835e^-5	0.971	UPSTREAM CG15674 DOWNSTREAM mahj EXON CR42547
3L	3814085	3L_3814085_SNP [dm3] 3L_3814085_SNP [dm6]	G	T	5.847e^-5	0.971	UPSTREAM Scsalpha DOWNSTREAM CR43932 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_kn
X	6491114	X_6491114_SNP [dm3] X_6597081_SNP [dm6]	G	T	5.867e^-5	0.971	UPSTREAM APC7 DOWNSTREAM Pat1 INTERGENIC
X	14221632	X_14221632_SNP [dm3] X_14327599_SNP [dm6]	A	T	5.888e^-5	0.971	INTRON dpr8
3L	19388797	3L_19388797_SNP [dm3] 3L_19395697_SNP [dm6]	A	G	5.895e^-5	0.971	INTRON CG32206
3R	26137458	3R_26137458_INS [dm3] 3R_30311736_INS [dm6]	T	TG	5.935e^-5	0.971	INTRON hdc
3R	10416177	3R_10416177_SNP [dm3] 3R_14590455_SNP [dm6]	A	C	6.015e^-5	0.971	INTRON stumps	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	20565703	3R_20565703_SNP [dm3] 3R_24739981_SNP [dm6]	T	C	6.025e^-5	0.971	INTRON tok
3L	14432999	3L_14432999_SNP [dm3] 3L_14439899_SNP [dm6]	T	C	6.049e^-5	0.971	INTRON bbg
2R	9148445	2R_9148445_SNP [dm3] 2R_13260940_SNP [dm6]	C	T	6.114e^-5	0.971	INTRON CG42319
3R	26897488	3R_26897488_SNP [dm3] 3R_31071766_SNP [dm6]	T	C	6.143e^-5	0.971	INTRON Sox100B	TF binding site BDTNP1_TFBS_twi
X	754179	X_754179_SNP [dm3] X_860146_SNP [dm6]	T	C	6.261e^-5	0.971	INTRON CG43867

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By genomic position
Variant impact
Gene name

PE_FracDead_3d phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results