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=2.525e^-1)
Null hypothesis is not rejected (p>0.05).
Interpretation: 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

1866 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	21528351	3R_21528351_SNP [dm3] 3R_25702629_SNP [dm6]	A	C	4.262e^-7	0.504	INTRON LpR2
3R	7168233	3R_7168233_SNP [dm3] 3R_11342511_SNP [dm6]	A	G	6.411e^-7	0.504	INTRON pros
3R	26433094	3R_26433094_SNP [dm3] 3R_30607372_SNP [dm6]	T	C	8.072e^-7	0.504	SYNONYMOUS_CODING CG31016	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	27514710	3R_27514710_SNP [dm3] 3R_31688988_SNP [dm6]	C	T	1.560e^-6	0.594	UPSTREAM CR45564 DOWNSTREAM CR45565 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_Trl
3R	21528368	3R_21528368_SNP [dm3] 3R_25702646_SNP [dm6]	C	T	1.586e^-6	0.594	INTRON LpR2
3R	26433105	3R_26433105_SNP [dm3] 3R_30607383_SNP [dm6]	T	C	2.323e^-6	0.726	SYNONYMOUS_CODING CG31016	TF binding site mE1_TFBS_HSA
3R	23251858	3R_23251858_SNP [dm3] 3R_27426136_SNP [dm6]	A	G	3.750e^-6	0.822	INTRON side	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
3R	9405546	3R_9405546_SNP [dm3] 3R_13579824_SNP [dm6]	C	T	3.946e^-6	0.822	INTERGENIC
3R	19742311	3R_19742311_SNP [dm3] 3R_23916589_SNP [dm6]	A	G	4.732e^-6	0.822	INTRON sba
3R	9410299	3R_9410299_SNP [dm3] 3R_13584577_SNP [dm6]	T	G	4.940e^-6	0.822	INTERGENIC
2R	13482620	2R_13482620_SNP [dm3] 2R_17595115_SNP [dm6]	T	G	5.163e^-6	0.822	UPSTREAM CG11423 INTRON lack
3L	11475004	3L_11475004_SNP [dm3] 3L_11481904_SNP [dm6]	G	T	5.326e^-6	0.822	INTERGENIC
3R	27529361	3R_27529361_SNP [dm3] 3R_31703639_SNP [dm6]	A	G	5.702e^-6	0.822	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_inv
3R	27514532	3R_27514532_SNP [dm3] 3R_31688810_SNP [dm6]	G	A	6.148e^-6	0.823	UPSTREAM CR45564 DOWNSTREAM CR45565 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_Trl
2L	10586705	2L_10586705_SNP [dm3] 2L_10586705_SNP [dm6]	T	C	6.647e^-6	0.831	INTRON Trim9	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	24597238	3R_24597238_SNP [dm3] 3R_28771516_SNP [dm6]	C	G	7.787e^-6	0.912	INTERGENIC
3R	23796610	3R_23796610_SNP [dm3] 3R_27970888_SNP [dm6]	G	T	9.380e^-6	0.961	INTRON betaTub97EF
3R	23251596	3R_23251596_SNP [dm3] 3R_27425874_SNP [dm6]	A	T	1.035e^-5	0.961	INTRON side	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
3R	24922132	3R_24922132_SNP [dm3] 3R_29096410_SNP [dm6]	A	T	1.219e^-5	0.961	INTRON CG11873 EXON CR45030
3R	25960278	3R_25960278_SNP [dm3] 3R_30134556_SNP [dm6]	A	C	1.289e^-5	0.961	UTR_5_PRIME Tpi UPSTREAM Tpi DOWNSTREAM AdoR	TF binding site mE1_TFBS_cad
3R	21444521	3R_21444521_SNP [dm3] 3R_25618799_SNP [dm6]	G	T	1.343e^-5	0.961	NON_SYNONYMOUS_CODING CG5071 INTRON Npl4	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
X	12597357	X_12597357_SNP [dm3] X_12703324_SNP [dm6]	C	T	1.595e^-5	0.961	INTRON Smr	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	16552096	2L_16552096_SNP [dm3] 2L_16552096_SNP [dm6]	G	A	1.625e^-5	0.961	INTRON CG42389	TF binding site mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_zfh1
3L	9262770	3L_9262770_INS [dm3] 3L_9269670_INS [dm6]	A	AAATA	1.681e^-5	0.961	INTRON GluRIB
3R	21444522	3R_21444522_SNP [dm3] 3R_25618800_SNP [dm6]	T	A	1.738e^-5	0.961	NON_SYNONYMOUS_CODING CG5071 INTRON Npl4	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2R	14356571	2R_14356571_SNP [dm3] 2R_18469066_SNP [dm6]	C	T	1.859e^-5	0.961	INTRON CG30116
3R	9410009	3R_9410009_SNP [dm3] 3R_13584287_SNP [dm6]	C	T	1.897e^-5	0.961	INTERGENIC
3R	18788804	3R_18788804_SNP [dm3] 3R_22963082_SNP [dm6]	C	T	1.911e^-5	0.961	DOWNSTREAM CR43655 INTERGENIC
2L	11383645	2L_11383645_DEL [dm3] 2L_11383645_DEL [dm6]	TTATA	T	2.017e^-5	0.961	INTERGENIC	regulatory region REDfly_CRMs
3R	9035531	3R_9035531_SNP [dm3] 3R_13209809_SNP [dm6]	A	C	2.024e^-5	0.961	INTRON CG8483
3R	18458281	3R_18458281_SNP [dm3] 3R_22632559_SNP [dm6]	T	C	2.024e^-5	0.961	INTRON loco	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	25141415	3R_25141415_SNP [dm3] 3R_29315693_SNP [dm6]	T	A	2.087e^-5	0.961	UTR_3_PRIME Cnx99A DOWNSTREAM Cnx99A
3R	23396396	3R_23396396_DEL [dm3] 3R_27570674_DEL [dm6]	TGCTA	T	2.095e^-5	0.961	INTRON wdb	TF binding site BDTNP1_TFBS_da
2L	5472629	2L_5472629_SNP [dm3] 2L_5472629_SNP [dm6]	C	T	2.098e^-5	0.961	INTERGENIC	TF binding site BDTNP1_TFBS_twi
2R	6979872	2R_6979872_SNP [dm3] 2R_11092367_SNP [dm6]	T	C	2.144e^-5	0.961	INTRON luna
2R	9777744	2R_9777744_SNP [dm3] 2R_13890239_SNP [dm6]	C	T	2.184e^-5	0.961	SYNONYMOUS_CODING shot INTRON shot	TF binding site mE1_TFBS_sens
3L	13171658	3L_13171658_SNP [dm3] 3L_13178558_SNP [dm6]	A	C	2.218e^-5	0.961	INTERGENIC
3L	7328017	3L_7328017_SNP [dm3] 3L_7334917_SNP [dm6]	A	T	2.230e^-5	0.961	DOWNSTREAM eco INTRON CG43780 & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_sens
3R	13451789	3R_13451789_SNP [dm3] 3R_17626067_SNP [dm6]	A	T	2.255e^-5	0.961	UTR_3_PRIME AttD
2R	16365130	2R_16365130_SNP [dm3] 2R_20477625_SNP [dm6]	G	T	2.323e^-5	0.961	INTRON CG12484
3R	25134754	3R_25134754_INS [dm3] 3R_29309032_INS [dm6]	A	AC	2.541e^-5	0.961	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	21108954	3R_21108954_INS [dm3] 3R_25283232_INS [dm6]	A	AT	2.617e^-5	0.961	UTR_3_PRIME CG11892 UPSTREAM CG31300
3L	9262772	3L_9262772_SNP [dm3] 3L_9269672_SNP [dm6]	T	A	2.620e^-5	0.961	INTRON GluRIB
3R	9408558	3R_9408558_SNP [dm3] 3R_13582836_SNP [dm6]	A	G	2.726e^-5	0.961	INTERGENIC	TF binding site mE1_TFBS_inv
3R	18902921	3R_18902921_SNP [dm3] 3R_23077199_SNP [dm6]	A	C	2.758e^-5	0.961	INTRON CG13830
3R	23417311	3R_23417311_SNP [dm3] 3R_27591589_SNP [dm6]	G	A	2.777e^-5	0.961	INTRON CG5639
3R	11982059	3R_11982059_SNP [dm3] 3R_16156337_SNP [dm6]	A	G	2.821e^-5	0.961	INTRON CG6006
3R	5682098	3R_5682098_SNP [dm3] 3R_9856376_SNP [dm6]	C	T	2.825e^-5	0.961	INTRON Teh1
X	9327281	X_9327281_SNP [dm3] X_9433248_SNP [dm6]	G	C	2.918e^-5	0.961	INTRON mgl
3R	17758193	3R_17758193_SNP [dm3] 3R_21932471_SNP [dm6]	A	T	2.986e^-5	0.961	INTERGENIC
X	4283162	X_4283162_SNP [dm3] X_4389129_SNP [dm6]	A	C	2.997e^-5	0.961	INTRON CR32773	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	16877075	3R_16877075_SNP [dm3] 3R_21051353_SNP [dm6]	A	T	3.045e^-5	0.961	UPSTREAM CG17279 DOWNSTREAM Mvl INTERGENIC
2L	10412804	2L_10412804_SNP [dm3] 2L_10412804_SNP [dm6]	A	G	3.088e^-5	0.961	SYNONYMOUS_CODING CG5355	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Ubx
2R	4657820	2R_4657820_SNP [dm3] 2R_8770315_SNP [dm6]	C	T	3.293e^-5	0.961	INTERGENIC
3L	12153398	3L_12153398_INS [dm3] 3L_12160298_INS [dm6]	G	GGCAAGTTTTGAGCGCACTC...	3.300e^-5	0.961	INTRON CG9760
2L	9460627	2L_9460627_SNP [dm3] 2L_9460627_SNP [dm6]	A	G	3.336e^-5	0.961	SYNONYMOUS_CODING numb	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
3R	23501386	3R_23501386_SNP [dm3] 3R_27675664_SNP [dm6]	C	G	3.531e^-5	0.961	INTRON unc80	TF binding site BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_chinmo mE1_TFBS_HSA
2R	20805648	2R_20805648_SNP [dm3] 2R_24918125_SNP [dm6]	T	A	3.637e^-5	0.961	NON_SYNONYMOUS_CODING NaCP60E UTR_3_PRIME NaCP60E	TF binding site mE1_TFBS_cad
3R	5693676	3R_5693676_SNP [dm3] 3R_9867954_SNP [dm6]	A	C	3.786e^-5	0.961	UTR_5_PRIME Teh1	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1
3R	21444511	3R_21444511_SNP [dm3] 3R_25618789_SNP [dm6]	C	T	3.924e^-5	0.961	NON_SYNONYMOUS_CODING CG5071 INTRON Npl4	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	11581555	3L_11581555_SNP [dm3] 3L_11588455_SNP [dm6]	A	G	3.963e^-5	0.961	UPSTREAM rt INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med
2R	8699269	2R_8699269_SNP [dm3] 2R_12811764_SNP [dm6]	C	T	4.093e^-5	0.961	INTERGENIC
2R	19920212	2R_19920212_SNP [dm3] 2R_24032689_SNP [dm6]	G	A	4.202e^-5	0.961	SYNONYMOUS_CODING Chi	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_sens
3R	23250529	3R_23250529_SNP [dm3] 3R_27424807_SNP [dm6]	A	C	4.303e^-5	0.961	INTRON side
3L	15685869	3L_15685869_SNP [dm3] 3L_15692769_SNP [dm6]	A	G	4.309e^-5	0.961	UPSTREAM CG34451 INTERGENIC
3L	19260084	3L_19260084_SNP [dm3] 3L_19266984_SNP [dm6]	A	T	4.318e^-5	0.961	SYNONYMOUS_CODING CG9629 DOWNSTREAM CG45081 & 2 others	TF binding site mE1_TFBS_cad
2R	7056990	2R_7056990_SNP [dm3] 2R_11169485_SNP [dm6]	C	G	4.319e^-5	0.961	INTRON shn & 1 other
2R	14341572	2R_14341572_SNP [dm3] 2R_18454067_SNP [dm6]	C	T	4.357e^-5	0.961	SYNONYMOUS_CODING CG17669	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	14968312	2R_14968312_SNP [dm3] 2R_19080807_SNP [dm6]	C	T	4.519e^-5	0.961	INTRON 5-HT1A
2L	10412604	2L_10412604_SNP [dm3] 2L_10412604_SNP [dm6]	C	A	4.520e^-5	0.961	INTRON CG5355	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	12462736	2R_12462736_SNP [dm3] 2R_16575231_SNP [dm6]	C	T	4.538e^-5	0.961	SYNONYMOUS_CODING CG8317	TF binding site mE1_TFBS_inv
X	10867965	X_10867965_SNP [dm3] X_10973932_SNP [dm6]	G	A	4.564e^-5	0.961	INTRON CG42339
3R	23244259	3R_23244259_SNP [dm3] 3R_27418537_SNP [dm6]	T	C	4.575e^-5	0.961	UTR_5_PRIME side	TF binding site mE1_TFBS_HSA
X	5954122	X_5954122_SNP [dm3] X_6060089_SNP [dm6]	C	A	4.613e^-5	0.961	SYNONYMOUS_CODING CG5921	TF binding site mE1_TFBS_chinmo
3R	16686222	3R_16686222_SNP [dm3] 3R_20860500_SNP [dm6]	A	T	4.704e^-5	0.961	UTR_3_PRIME CG3822 UPSTREAM Ir93a
2L	10585873	2L_10585873_SNP [dm3] 2L_10585873_SNP [dm6]	C	A	4.706e^-5	0.961	INTRON Trim9
3R	24922664	3R_24922664_SNP [dm3] 3R_29096942_SNP [dm6]	C	T	4.779e^-5	0.961	DOWNSTREAM CR45030 INTRON CG11873
3L	5959851	3L_5959851_SNP [dm3] 3L_5966751_SNP [dm6]	C	T	4.789e^-5	0.961	DOWNSTREAM CG10479 INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA
3L	16048632	3L_16048632_SNP [dm3] 3L_16055532_SNP [dm6]	G	A	4.806e^-5	0.961	INTRON Mbs	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb mE1_TFBS_HSA
2L	11383643	2L_11383643_SNP [dm3] 2L_11383643_SNP [dm6]	A	T	4.829e^-5	0.961	INTERGENIC	regulatory region REDfly_CRMs
3R	22983234	3R_22983234_SNP [dm3] 3R_27157512_SNP [dm6]	A	T	4.867e^-5	0.961	UTR_3_PRIME Men-b UPSTREAM grass	TF binding site mE1_TFBS_Trl
2L	16798239	2L_16798239_SNP [dm3] 2L_16798239_SNP [dm6]	G	A	4.881e^-5	0.961	NON_SYNONYMOUS_CODING Ugt36Bb UPSTREAM Ugt36Bc
2L	16380515	2L_16380515_SNP [dm3] 2L_16380515_SNP [dm6]	T	A	4.965e^-5	0.961	INTERGENIC
3R	19207422	3R_19207422_SNP [dm3] 3R_23381700_SNP [dm6]	G	C	5.016e^-5	0.961	SYNONYMOUS_CODING CG4393	TF binding site mE1_TFBS_cad
2L	10585916	2L_10585916_SNP [dm3] 2L_10585916_SNP [dm6]	T	C	5.023e^-5	0.961	INTRON Trim9
X	2372952	X_2372952_SNP [dm3] X_2478919_SNP [dm6]	G	T	5.090e^-5	0.961	UTR_3_PRIME trol DOWNSTREAM trol INTRON trol
3L	5520122	3L_5520122_SNP [dm3] 3L_5527022_SNP [dm6]	G	C	5.177e^-5	0.961	INTRON Lkr
2L	9440547	2L_9440547_SNP [dm3] 2L_9440547_SNP [dm6]	G	A	5.253e^-5	0.961	SYNONYMOUS_CODING CG33723 INTRON numb
3R	6827471	3R_6827471_SNP [dm3] 3R_11001749_SNP [dm6]	C	T	5.663e^-5	0.961	INTRON CG34114
2R	7056991	2R_7056991_DEL [dm3] 2R_11169486_DEL [dm6]	TGC	T	5.718e^-5	0.961	INTRON shn & 1 other
2L	20491447	2L_20491447_SNP [dm3] 2L_20491447_SNP [dm6]	C	T	5.809e^-5	0.961	INTERGENIC
2L	6771880	2L_6771880_SNP [dm3] 2L_6771880_SNP [dm6]	A	C	5.820e^-5	0.961	UPSTREAM CG11321 INTRON CG11321
2R	15078229	2R_15078229_SNP [dm3] 2R_19190724_SNP [dm6]	G	A	5.867e^-5	0.961	INTRON hppy
3R	23186580	3R_23186580_SNP [dm3] 3R_27360858_SNP [dm6]	T	A	5.881e^-5	0.961	INTRON CG42534
2R	4655545	2R_4655545_SNP [dm3] 2R_8768040_SNP [dm6]	G	T	5.884e^-5	0.961	DOWNSTREAM CR44278 INTERGENIC	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
4	170407	4_170407_SNP [dm3] 4_149781_SNP [dm6]	G	C	5.940e^-5	0.961	UPSTREAM CG32006 INTERGENIC
2L	6159103	2L_6159103_SNP [dm3] 2L_6159103_SNP [dm6]	C	T	6.127e^-5	0.961	INTERGENIC	TF binding site mE1_TFBS_chinmo
3R	21444402	3R_21444402_SNP [dm3] 3R_25618680_SNP [dm6]	G	C	6.174e^-5	0.961	NON_SYNONYMOUS_CODING CG5071 INTRON Npl4	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	19742106	3R_19742106_SNP [dm3] 3R_23916384_SNP [dm6]	T	G	6.476e^-5	0.961	INTRON sba
2R	16834430	2R_16834430_SNP [dm3] 2R_20946925_SNP [dm6]	A	C	6.510e^-5	0.961	DOWNSTREAM snoRNA:660 & 1 other INTERGENIC	TF binding site mE1_TFBS_inv

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By genomic position
Variant impact
Gene name

ERStress_t50 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results