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=4.232e^-5)
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

Covariate	χ²	p-value	Significance
In_2L_t	4.7074	0.095

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2407 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	14795131	2L_14795131_DEL [dm3] 2L_14795131_DEL [dm6]	CC	C	2.951e^-7	0.553	UTR_3_PRIME CG18420
3R	26176018	3R_26176018_SNP [dm3] 3R_30350296_SNP [dm6]	C	A	7.866e^-7	0.627	INTRON hdc
3L	12374733	3L_12374733_SNP [dm3] 3L_12381633_SNP [dm6]	T	G	1.002e^-6	0.627	INTRON Ncc69	TF binding site mE1_TFBS_inv
3R	14094242	3R_14094242_SNP [dm3] 3R_18268520_SNP [dm6]	T	C	1.489e^-6	0.636	INTRON CG18599
3R	26088906	3R_26088906_SNP [dm3] 3R_30263184_SNP [dm6]	C	T	1.894e^-6	0.636	INTERGENIC
3R	14094271	3R_14094271_SNP [dm3] 3R_18268549_SNP [dm6]	A	G	2.864e^-6	0.636	INTRON CG18599
2L	3378046	2L_3378046_SNP [dm3] 2L_3378046_SNP [dm6]	A	T	2.890e^-6	0.636	SYNONYMOUS_CODING Ptpa	TF binding site mE1_TFBS_sens
3L	2545668	3L_2545668_DEL [dm3] 3L_2545668_DEL [dm6]	TAAATTAAAGGCTTTGT...	T	3.037e^-6	0.636	INTRON Spn
2R	12861426	2R_12861426_SNP [dm3] 2R_16973921_SNP [dm6]	T	C	3.216e^-6	0.636	UPSTREAM Cbp53E INTERGENIC
3L	18352450	3L_18352450_SNP [dm3] 3L_18359350_SNP [dm6]	T	A	3.392e^-6	0.636	INTERGENIC
2L	7900509	2L_7900509_SNP [dm3] 2L_7900509_SNP [dm6]	A	C	4.675e^-6	0.658	INTRON Snoo
3R	25476842	3R_25476842_SNP [dm3] 3R_29651120_SNP [dm6]	C	T	5.184e^-6	0.658	INTRON Dop1R2	TF binding site mE1_TFBS_chinmo
3L	4726377	3L_4726377_SNP [dm3] 3L_4726377_SNP [dm6]	T	C	5.398e^-6	0.658	INTRON RhoGEF64C
3L	7063391	3L_7063391_SNP [dm3] 3L_7070291_SNP [dm6]	G	A	5.768e^-6	0.658	INTRON CG8641
3L	1081436	3L_1081436_SNP [dm3] 3L_1081436_SNP [dm6]	A	G	5.867e^-6	0.658	INTRON bab1
3L	12374674	3L_12374674_DEL [dm3] 3L_12381574_DEL [dm6]	GAAATTCTTTAACAAGGCGA...	G	5.975e^-6	0.658	INTRON Ncc69	TF binding site mE1_TFBS_inv
X	3483222	X_3483222_SNP [dm3] X_3589189_SNP [dm6]	T	A	6.120e^-6	0.658	INTRON AstA-R1
X	10625028	X_10625028_INS [dm3] X_10730995_INS [dm6]	T	TC	6.316e^-6	0.658	INTRON CG32676	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_Trl
2R	3346733	2R_3346733_DEL [dm3] 2R_7459228_DEL [dm6]	TA	T	7.234e^-6	0.683	UPSTREAM Inos DOWNSTREAM CG11141 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
2L	7900233	2L_7900233_SNP [dm3] 2L_7900233_SNP [dm6]	C	T	7.636e^-6	0.683	INTRON Snoo
X	5872642	X_5872642_SNP [dm3] X_5978609_SNP [dm6]	G	A	7.646e^-6	0.683	INTRON Grip
3L	11649398	3L_11649398_SNP [dm3] 3L_11656298_SNP [dm6]	T	C	8.319e^-6	0.688	UPSTREAM mir-274 INTRON CG32085
3L	12374566	3L_12374566_SNP [dm3] 3L_12381466_SNP [dm6]	G	T	8.432e^-6	0.688	INTRON Ncc69	TF binding site mE1_TFBS_inv
3L	12374579	3L_12374579_SNP [dm3] 3L_12381479_SNP [dm6]	G	A	9.157e^-6	0.705	INTRON Ncc69	TF binding site mE1_TFBS_inv
3L	10369405	3L_10369405_SNP [dm3] 3L_10376305_SNP [dm6]	T	A	1.094e^-5	0.705	INTERGENIC
2L	12588032	2L_12588032_SNP [dm3] 2L_12588032_SNP [dm6]	C	T	1.113e^-5	0.705	START_GAINED nub UTR_5_PRIME nub	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA mE1_TFBS_Trl
2L	7900200	2L_7900200_SNP [dm3] 2L_7900200_SNP [dm6]	T	C	1.206e^-5	0.705	INTRON Snoo
X	3141187	X_3141187_SNP [dm3] X_3247154_SNP [dm6]	T	A	1.246e^-5	0.705	INTRON dnc
2L	10530153	2L_10530153_SNP [dm3] 2L_10530153_SNP [dm6]	T	C	1.341e^-5	0.705	SYNONYMOUS_CODING Lip4
2L	7900235	2L_7900235_SNP [dm3] 2L_7900235_SNP [dm6]	C	G	1.390e^-5	0.705	INTRON Snoo
X	3141181	X_3141181_SNP [dm3] X_3247148_SNP [dm6]	C	A	1.469e^-5	0.705	INTRON dnc
3R	3006133	3R_3006133_SNP [dm3] 3R_7180411_SNP [dm6]	G	A	1.635e^-5	0.705	SYNONYMOUS_CODING sas INTRON sas	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2R	9637295	2R_9637295_SNP [dm3] 2R_13749790_SNP [dm6]	G	A	1.645e^-5	0.705	DOWNSTREAM fas INTERGENIC
3L	12494005	3L_12494005_SNP [dm3] 3L_12500905_SNP [dm6]	C	T	1.648e^-5	0.705	SYNONYMOUS_CODING CG10638 UPSTREAM CG10681 DOWNSTREAM CR43868 INTRON CG10638
X	5736658	X_5736658_SNP [dm3] X_5842625_SNP [dm6]	C	T	1.749e^-5	0.705	INTERGENIC
X	18464207	X_18464207_SNP [dm3] X_18570174_SNP [dm6]	A	C	1.778e^-5	0.705	INTRON Bx	TF binding site BDTNP1_TFBS_da mE1_TFBS_chinmo
3R	11269036	3R_11269036_SNP [dm3] 3R_15443314_SNP [dm6]	T	A	1.804e^-5	0.705	SYNONYMOUS_CODING AdamTS-A	TF binding site mE1_TFBS_cad
3L	12374767	3L_12374767_SNP [dm3] 3L_12381667_SNP [dm6]	T	C	1.851e^-5	0.705	INTRON Ncc69	TF binding site mE1_TFBS_inv
2L	13236971	2L_13236971_SNP [dm3] 2L_13236971_SNP [dm6]	G	A	1.872e^-5	0.705	INTRON CG5867
2R	17868698	2R_17868698_SNP [dm3] 2R_21981193_SNP [dm6]	T	C	1.928e^-5	0.705	DOWNSTREAM Gr58a INTERGENIC
X	6121036	X_6121036_SNP [dm3] X_6227003_SNP [dm6]	C	T	1.971e^-5	0.705	SYNONYMOUS_CODING CG14446	TF binding site BDTNP1_TFBS_dl mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
X	10568445	X_10568445_SNP [dm3] X_10674412_SNP [dm6]	A	C	1.997e^-5	0.705	UPSTREAM CG12637 INTRON X11Lbeta	TF binding site BDTNP1_TFBS_twi mE1_TFBS_chinmo mE1_TFBS_HSA
2R	19573478	2R_19573478_SNP [dm3] 2R_23685955_SNP [dm6]	C	T	2.043e^-5	0.705	UPSTREAM l_2_efl INTRON St3
2L	12587759	2L_12587759_SNP [dm3] 2L_12587759_SNP [dm6]	A	T	2.052e^-5	0.705	UTR_5_PRIME nub	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
2R	11817318	2R_11817318_DEL [dm3] 2R_15929813_DEL [dm6]	GA	G	2.069e^-5	0.705	INTRON bdg	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi
3R	26871778	3R_26871778_SNP [dm3] 3R_31046056_SNP [dm6]	G	A	2.110e^-5	0.705	UPSTREAM CG33920 INTRON CanA1	TF binding site BDTNP1_TFBS_prd
2L	4132014	2L_4132014_SNP [dm3] 2L_4132014_SNP [dm6]	C	T	2.252e^-5	0.705	INTERGENIC	TF binding site BDTNP1_TFBS_twi
3L	14269828	3L_14269828_SNP [dm3] 3L_14276728_SNP [dm6]	T	C	2.314e^-5	0.705	INTRON fz	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_sens
2L	17775496	2L_17775496_SNP [dm3] 2L_17775496_SNP [dm6]	T	A	2.342e^-5	0.705	INTRON CadN
2L	2806636	2L_2806636_SNP [dm3] 2L_2806636_SNP [dm6]	C	A	2.346e^-5	0.705	INTRON daw
2L	7818857	2L_7818857_SNP [dm3] 2L_7818857_SNP [dm6]	C	G	2.374e^-5	0.705	SYNONYMOUS_CODING LanB1	TF binding site mE1_TFBS_cad mE1_TFBS_sens
X	5342912	X_5342912_SNP [dm3] X_5448879_SNP [dm6]	G	A	2.391e^-5	0.705	INTRON SPR
3R	26667352	3R_26667352_SNP [dm3] 3R_30841630_SNP [dm6]	T	A	2.403e^-5	0.705	UTR_3_PRIME CG15544
X	6119168	X_6119168_SNP [dm3] X_6225135_SNP [dm6]	C	G	2.435e^-5	0.705	UTR_5_PRIME sqh UPSTREAM sqh & 1 other	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl mE1_TFBS_zfh1
3L	12374656	3L_12374656_SNP [dm3] 3L_12381556_SNP [dm6]	C	T	2.438e^-5	0.705	INTRON Ncc69	TF binding site mE1_TFBS_inv
2R	12021871	2R_12021871_SNP [dm3] 2R_16134366_SNP [dm6]	G	A	2.555e^-5	0.705	INTRON spin	TF binding site mE1_TFBS_inv
X	3483341	X_3483341_DEL [dm3] X_3589308_DEL [dm6]	AACCAAA	A	2.580e^-5	0.705	INTRON AstA-R1
X	3483218	X_3483218_SNP [dm3] X_3589185_SNP [dm6]	G	C	2.616e^-5	0.705	INTRON AstA-R1
3R	18129037	3R_18129037_SNP [dm3] 3R_22303315_SNP [dm6]	A	G	2.655e^-5	0.705	INTRON CG7084
2R	9679611	2R_9679611_DEL [dm3] 2R_13792106_DEL [dm6]	CC	C	2.661e^-5	0.705	EXON CR43811
3R	14094198	3R_14094198_SNP [dm3] 3R_18268476_SNP [dm6]	G	A	2.678e^-5	0.705	INTRON CG18599
2L	448813	2L_448813_SNP [dm3] 2L_448813_SNP [dm6]	T	G	2.693e^-5	0.705	UTR_3_PRIME crq DOWNSTREAM ex
X	12584129	X_12584129_SNP [dm3] X_12690096_SNP [dm6]	C	A	2.713e^-5	0.705	SYNONYMOUS_CODING Smr	TF binding site BDTNP1_TFBS_ftz BDTNP1_TFBS_kni BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	7994399	2L_7994399_SNP [dm3] 2L_7994399_SNP [dm6]	T	C	2.758e^-5	0.705	UTR_3_PRIME CG7227 UPSTREAM pes & 1 other DOWNSTREAM CG7227	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_en mE1_TFBS_h mE1_TFBS_hkb mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_jumu mE1_TFBS_Trl
3R	17293564	3R_17293564_SNP [dm3] 3R_21467842_SNP [dm6]	C	A	2.759e^-5	0.705	INTERGENIC
3R	17293574	3R_17293574_SNP [dm3] 3R_21467852_SNP [dm6]	A	G	2.759e^-5	0.705	INTERGENIC
3R	17293596	3R_17293596_SNP [dm3] 3R_21467874_SNP [dm6]	T	A	2.759e^-5	0.705	INTERGENIC
2L	9286685	2L_9286685_SNP [dm3] 2L_9286685_SNP [dm6]	T	C	2.822e^-5	0.705	INTRON Ggamma30A
3L	5521724	3L_5521724_SNP [dm3] 3L_5528624_SNP [dm6]	G	A	2.829e^-5	0.705	INTRON Lkr
3L	12374615	3L_12374615_SNP [dm3] 3L_12381515_SNP [dm6]	A	G	2.850e^-5	0.705	INTRON Ncc69	TF binding site mE1_TFBS_inv
3L	12374596	3L_12374596_SNP [dm3] 3L_12381496_SNP [dm6]	C	A	2.866e^-5	0.705	INTRON Ncc69	TF binding site mE1_TFBS_inv
3R	17293551	3R_17293551_SNP [dm3] 3R_21467829_SNP [dm6]	T	G	2.920e^-5	0.705	INTERGENIC
X	5342901	X_5342901_SNP [dm3] X_5448868_SNP [dm6]	C	T	2.978e^-5	0.705	INTRON SPR
3R	17293603	3R_17293603_SNP [dm3] 3R_21467881_SNP [dm6]	C	T	3.071e^-5	0.705	INTERGENIC
3R	23673604	3R_23673604_SNP [dm3] 3R_27847882_SNP [dm6]	G	A	3.099e^-5	0.705	DOWNSTREAM Or98a INTRON CG34353
3L	16036130	3L_16036130_SNP [dm3] 3L_16043030_SNP [dm6]	C	T	3.153e^-5	0.705	UTR_5_PRIME th UPSTREAM th INTRON th	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_inv
3L	12374768	3L_12374768_SNP [dm3] 3L_12381668_SNP [dm6]	G	C	3.167e^-5	0.705	INTRON Ncc69	TF binding site mE1_TFBS_inv
2L	12588392	2L_12588392_SNP [dm3] 2L_12588392_SNP [dm6]	A	G	3.174e^-5	0.705	INTRON nub
X	20443973	X_20443973_SNP [dm3] X_20572946_SNP [dm6]	T	G	3.213e^-5	0.705	INTERGENIC
2L	9888653	2L_9888653_SNP [dm3] 2L_9888653_SNP [dm6]	A	C	3.251e^-5	0.705	INTRON FKBP59	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	19768156	3R_19768156_SNP [dm3] 3R_23942434_SNP [dm6]	T	G	3.260e^-5	0.705	INTRON Gdh	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
X	6119481	X_6119481_SNP [dm3] X_6225448_SNP [dm6]	T	G	3.281e^-5	0.705	UPSTREAM sqh & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_D
3L	12374717	3L_12374717_SNP [dm3] 3L_12381617_SNP [dm6]	A	T	3.308e^-5	0.705	INTRON Ncc69	TF binding site mE1_TFBS_inv
X	10892563	X_10892563_SNP [dm3] X_10998530_SNP [dm6]	G	A	3.321e^-5	0.705	INTRON CG42339
3L	12374759	3L_12374759_SNP [dm3] 3L_12381659_SNP [dm6]	T	G	3.455e^-5	0.705	INTRON Ncc69	TF binding site mE1_TFBS_inv
2L	4897079	2L_4897079_SNP [dm3] 2L_4897079_SNP [dm6]	A	G	3.468e^-5	0.705	INTRON CG3036
3R	18636393	3R_18636393_SNP [dm3] 3R_22810671_SNP [dm6]	T	C	3.489e^-5	0.705	INTERGENIC
2L	1969770	2L_1969770_DEL [dm3] 2L_1969770_DEL [dm6]	AC	A	3.523e^-5	0.705	INTRON erm	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi
2L	4132068	2L_4132068_SNP [dm3] 2L_4132068_SNP [dm6]	T	G	3.576e^-5	0.705	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi
3R	3007748	3R_3007748_SNP [dm3] 3R_7182026_SNP [dm6]	A	C	3.581e^-5	0.705	SYNONYMOUS_CODING sas	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3L	17046469	3L_17046469_SNP [dm3] 3L_17053369_SNP [dm6]	G	T	3.589e^-5	0.705	INTRON rogdi	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	16618743	2R_16618743_SNP [dm3] 2R_20731238_SNP [dm6]	C	T	3.607e^-5	0.705	UPSTREAM CG13442 INTRON dpr
2R	17929699	2R_17929699_SNP [dm3] 2R_22042194_SNP [dm6]	A	G	3.646e^-5	0.705	SYNONYMOUS_CODING PpD5	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
2R	16643013	2R_16643013_SNP [dm3] 2R_20755508_SNP [dm6]	A	T	3.695e^-5	0.705	INTERGENIC
2L	3377824	2L_3377824_SNP [dm3] 2L_3377824_SNP [dm6]	T	C	3.834e^-5	0.705	INTRON Ptpa	TF binding site mE1_TFBS_sens
3R	19649746	3R_19649746_SNP [dm3] 3R_23824024_SNP [dm6]	T	C	3.852e^-5	0.705	INTRON CG34355
2L	5499989	2L_5499989_SNP [dm3] 2L_5499989_SNP [dm6]	G	T	3.852e^-5	0.705	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
X	12288574	X_12288574_SNP [dm3] X_12394541_SNP [dm6]	C	T	3.863e^-5	0.705	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	12702451	2L_12702451_SNP [dm3] 2L_12702451_SNP [dm6]	C	A	3.873e^-5	0.705	SYNONYMOUS_CODING CG5776	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_inv
2L	7281732	2L_7281732_SNP [dm3] 2L_7281732_SNP [dm6]	C	T	3.889e^-5	0.705	INTERGENIC	insulator Insulator_Class_I.mE01 TF binding site BDTNP1_TFBS_da mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_zfh1

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By genomic position
Variant impact
Gene name

mn_Week3_Fecundity phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results