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=1.464e^-2)
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	0.05473

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	6.3495	0.0418
In_2R_NS	5.0762	0.079

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2075 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	14287527	3R_14287527_SNP [dm3] 3R_18461805_SNP [dm6]	T	C	8.183e^-8	0.153	INTRON fru
2L	20099842	2L_20099842_SNP [dm3] 2L_20099842_SNP [dm6]	A	G	8.968e^-7	0.812	INTRON Kua
3R	18444145	3R_18444145_SNP [dm3] 3R_22618423_SNP [dm6]	G	A	1.898e^-6	0.812	UPSTREAM mRpL45 DOWNSTREAM CG31161 INTERGENIC	TF binding site BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	4314990	2L_4314990_SNP [dm3] 2L_4314990_SNP [dm6]	A	T	2.338e^-6	0.812	UTR_3_PRIME tutl INTRON tutl
2L	14959399	2L_14959399_SNP [dm3] 2L_14959399_SNP [dm6]	T	G	2.456e^-6	0.812	INTRON CG42313
2L	20098796	2L_20098796_SNP [dm3] 2L_20098796_SNP [dm6]	A	T	3.722e^-6	0.812	INTRON Kua	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna mE1_TFBS_HSA
3R	13559050	3R_13559050_SNP [dm3] 3R_17733328_SNP [dm6]	C	T	4.860e^-6	0.812	UPSTREAM CG14321 DOWNSTREAM Lgr1 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_HSA transposable element FlyBase
2L	4858454	2L_4858454_INS [dm3] 2L_4858454_INS [dm6]	T	TTGTAT	4.861e^-6	0.812	INTRON pog
2L	8059650	2L_8059650_SNP [dm3] 2L_8059650_SNP [dm6]	A	C	5.156e^-6	0.812	SYNONYMOUS_CODING poe
2L	20029874	2L_20029874_SNP [dm3] 2L_20029874_SNP [dm6]	C	A	5.473e^-6	0.812	INTRON sNPF
3R	26064247	3R_26064247_SNP [dm3] 3R_30238525_SNP [dm6]	C	G	5.548e^-6	0.812	UPSTREAM CG43448 INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
3L	18248331	3L_18248331_INS [dm3] 3L_18255231_INS [dm6]	T	AA	5.553e^-6	0.812	INTERGENIC
2L	16114052	2L_16114052_SNP [dm3] 2L_16114052_SNP [dm6]	G	A	6.450e^-6	0.812	INTERGENIC
3R	10661151	3R_10661151_SNP [dm3] 3R_14835429_SNP [dm6]	T	A	7.790e^-6	0.812	INTRON btsz
3L	12108285	3L_12108285_SNP [dm3] 3L_12115185_SNP [dm6]	T	A	8.230e^-6	0.812	UPSTREAM l_3_j2D3 INTERGENIC
3L	3288632	3L_3288632_SNP [dm3] 3L_3288632_SNP [dm6]	G	A	8.446e^-6	0.812	INTRON CG12017
X	9741235	X_9741235_SNP [dm3] X_9847202_SNP [dm6]	A	T	9.830e^-6	0.812	INTRON CG32698
3L	13928885	3L_13928885_SNP [dm3] 3L_13935785_SNP [dm6]	C	A	9.959e^-6	0.812	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
X	17866031	X_17866031_SNP [dm3] X_17971998_SNP [dm6]	C	T	1.008e^-5	0.812	INTRON Sh
3R	14284834	3R_14284834_DEL [dm3] 3R_18459112_DEL [dm6]	AG	A	1.064e^-5	0.812	INTRON fru	TF binding site mE1_TFBS_inv
3R	16618705	3R_16618705_SNP [dm3] 3R_20792983_SNP [dm6]	T	A	1.065e^-5	0.812	INTRON Syp	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
3R	14451804	3R_14451804_SNP [dm3] 3R_18626082_SNP [dm6]	T	G	1.106e^-5	0.812	INTRON qin
2L	20234799	2L_20234799_SNP [dm3] 2L_20234799_SNP [dm6]	G	A	1.114e^-5	0.812	INTERGENIC
3L	8552639	3L_8552639_SNP [dm3] 3L_8559539_SNP [dm6]	T	C	1.174e^-5	0.812	UPSTREAM rhea INTRON rhea	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
3L	11690671	3L_11690671_SNP [dm3] 3L_11697571_SNP [dm6]	T	G	1.289e^-5	0.812	SPLICE_SITE_REGION CG6053 UPSTREAM CG11652 INTRON CG6053	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Ubx
3L	16242283	3L_16242283_SNP [dm3] 3L_16249183_SNP [dm6]	G	A	1.320e^-5	0.812	DOWNSTREAM CG13055 INTERGENIC
3R	14287601	3R_14287601_SNP [dm3] 3R_18461879_SNP [dm6]	A	C	1.338e^-5	0.812	INTRON fru
3R	10662828	3R_10662828_SNP [dm3] 3R_14837106_SNP [dm6]	C	G	1.409e^-5	0.812	INTRON btsz
2R	17599829	2R_17599829_SNP [dm3] 2R_21712324_SNP [dm6]	C	G	1.423e^-5	0.812	UPSTREAM CG30403 INTRON HmgD	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
3R	11601416	3R_11601416_SNP [dm3] 3R_15775694_SNP [dm6]	G	C	1.444e^-5	0.812	UPSTREAM CR45206 & 1 other INTRON CG4525
3R	14153754	3R_14153754_SNP [dm3] 3R_18328032_SNP [dm6]	G	T	1.566e^-5	0.812	INTRON CG31235
3R	14451805	3R_14451805_DEL [dm3] 3R_18626083_DEL [dm6]	TTCTACTACATATATCTT...	T	1.605e^-5	0.812	INTRON qin
3R	14284739	3R_14284739_SNP [dm3] 3R_18459017_SNP [dm6]	A	G	1.628e^-5	0.812	INTRON fru	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
3L	9179724	3L_9179724_SNP [dm3] 3L_9186624_SNP [dm6]	G	A	1.645e^-5	0.812	INTERGENIC
2L	20029875	2L_20029875_SNP [dm3] 2L_20029875_SNP [dm6]	A	T	1.706e^-5	0.812	INTRON sNPF
2L	20104634	2L_20104634_SNP [dm3] 2L_20104634_SNP [dm6]	G	A	1.722e^-5	0.812	UPSTREAM CG13970 INTERGENIC	TF binding site BDTNP1_TFBS_dl
3L	8552650	3L_8552650_SNP [dm3] 3L_8559550_SNP [dm6]	A	T	1.806e^-5	0.812	UPSTREAM rhea INTRON rhea	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
3L	5894878	3L_5894878_SNP [dm3] 3L_5901778_SNP [dm6]	A	G	1.889e^-5	0.812	DOWNSTREAM CG32409 INTRON QC
3L	8552777	3L_8552777_SNP [dm3] 3L_8559677_SNP [dm6]	G	A	1.913e^-5	0.812	UPSTREAM rhea INTRON rhea	TF binding site BDTNP1_TFBS_dl mE1_TFBS_sens mE1_TFBS_Trl
2L	11290612	2L_11290612_SNP [dm3] 2L_11290612_SNP [dm6]	C	A	1.989e^-5	0.812	DOWNSTREAM CR43409 INTERGENIC
2L	7908053	2L_7908053_SNP [dm3] 2L_7908053_SNP [dm6]	T	C	1.999e^-5	0.812	INTRON Snoo
2L	12588760	2L_12588760_SNP [dm3] 2L_12588760_SNP [dm6]	T	A	2.062e^-5	0.812	INTRON nub	TF binding site mE1_TFBS_cad
3R	21816941	3R_21816941_SNP [dm3] 3R_25991219_SNP [dm6]	T	C	2.099e^-5	0.812	SYNONYMOUS_CODING Nf1	TF binding site mE1_TFBS_sens
2R	4919016	2R_4919016_SNP [dm3] 2R_9031511_SNP [dm6]	A	T	2.212e^-5	0.812	UPSTREAM CG8170 INTERGENIC
2L	20099188	2L_20099188_SNP [dm3] 2L_20099188_SNP [dm6]	A	T	2.238e^-5	0.812	UTR_5_PRIME Kua INTRON Kua	TF binding site BDTNP1_TFBS_dl
3L	13928901	3L_13928901_SNP [dm3] 3L_13935801_SNP [dm6]	C	A	2.239e^-5	0.812	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3R	16122891	3R_16122891_SNP [dm3] 3R_20297169_SNP [dm6]	C	T	2.281e^-5	0.812	NON_SYNONYMOUS_CODING cic INTRON cic
2L	20108220	2L_20108220_DEL [dm3] 2L_20108220_DEL [dm6]	CCAG	C	2.296e^-5	0.812	INTERGENIC	transposable element FlyBase
2L	18386545	2L_18386545_SNP [dm3] 2L_18386545_SNP [dm6]	T	A	2.299e^-5	0.812	UTR_3_PRIME Fas3 INTRON Fas3
3R	16337358	3R_16337358_SNP [dm3] 3R_20511636_SNP [dm6]	A	C	2.359e^-5	0.812	INTRON CG4288	TF binding site mE1_TFBS_sbb
2L	10244591	2L_10244591_SNP [dm3] 2L_10244591_SNP [dm6]	T	A	2.372e^-5	0.812	INTRON CR44995 & 1 other
3R	10414414	3R_10414414_INS [dm3] 3R_14588692_INS [dm6]	G	GGA	2.383e^-5	0.812	INTRON stumps	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
3R	14026130	3R_14026130_DEL [dm3] 3R_18200408_DEL [dm6]	CAA	C	2.387e^-5	0.812	UTR_5_PRIME CG7985 UPSTREAM Ssdp INTRON CG7985	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 mE1_TFBS_GATAe mE1_TFBS_HSA mE1_TFBS_jumu
3L	18248294	3L_18248294_SNP [dm3] 3L_18255194_SNP [dm6]	T	C	2.446e^-5	0.812	INTERGENIC
2L	20085024	2L_20085024_SNP [dm3] 2L_20085024_SNP [dm6]	C	T	2.470e^-5	0.812	UTR_5_PRIME fok INTRON neb	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
2R	7150750	2R_7150750_SNP [dm3] 2R_11263245_SNP [dm6]	C	G	2.478e^-5	0.812	INTERGENIC
3R	5466392	3R_5466392_SNP [dm3] 3R_9640670_SNP [dm6]	C	T	2.518e^-5	0.812	UTR_5_PRIME Dh44 INTRON Dh44
3L	12108294	3L_12108294_SNP [dm3] 3L_12115194_SNP [dm6]	C	A	2.568e^-5	0.812	UPSTREAM l_3_j2D3 INTERGENIC
2L	6125692	2L_6125692_SNP [dm3] 2L_6125692_SNP [dm6]	A	G	2.592e^-5	0.812	SYNONYMOUS_CODING Arpc4 DOWNSTREAM WDR79	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3L	11418980	3L_11418980_SNP [dm3] 3L_11425880_SNP [dm6]	C	G	2.665e^-5	0.812	INTRON CG7560	TF binding site mE1_TFBS_cad
3L	12108453	3L_12108453_SNP [dm3] 3L_12115353_SNP [dm6]	G	T	2.698e^-5	0.812	UPSTREAM l_3_j2D3 INTERGENIC
2R	17859455	2R_17859455_SNP [dm3] 2R_21971950_SNP [dm6]	A	G	2.701e^-5	0.812	UPSTREAM CG34029 INTERGENIC
2L	20093349	2L_20093349_SNP [dm3] 2L_20093349_SNP [dm6]	T	C	2.768e^-5	0.812	SYNONYMOUS_CODING Taf13 UPSTREAM nesd DOWNSTREAM CG10721	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_sens
2L	8061568	2L_8061568_SNP [dm3] 2L_8061568_SNP [dm6]	A	G	2.800e^-5	0.812	SPLICE_SITE_DONOR poe INTRON poe	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2L	8060331	2L_8060331_SNP [dm3] 2L_8060331_SNP [dm6]	A	G	2.889e^-5	0.812	SYNONYMOUS_CODING poe
2L	8059758	2L_8059758_SNP [dm3] 2L_8059758_SNP [dm6]	A	G	2.908e^-5	0.812	SYNONYMOUS_CODING poe
2R	1361405	2R_1361405_SNP [dm3] 2R_5473900_SNP [dm6]	G	T	2.943e^-5	0.812	INTRON CG30440	transposable element FlyBase
2R	3812216	2R_3812216_SNP [dm3] 2R_7924711_SNP [dm6]	T	A	3.001e^-5	0.812	INTRON Kdm4A	TF binding site BDTNP1_TFBS_prd mE1_TFBS_cad
2R	3812221	2R_3812221_SNP [dm3] 2R_7924716_SNP [dm6]	T	C	3.001e^-5	0.812	INTRON Kdm4A	TF binding site BDTNP1_TFBS_prd mE1_TFBS_cad
2L	15786165	2L_15786165_SNP [dm3] 2L_15786165_SNP [dm6]	T	C	3.083e^-5	0.816	SYNONYMOUS_CODING CG18109
2L	20095646	2L_20095646_SNP [dm3] 2L_20095646_SNP [dm6]	A	G	3.106e^-5	0.816	SYNONYMOUS_CODING nesd DOWNSTREAM mRpS18B	TF binding site mE1_TFBS_sens
2L	20087184	2L_20087184_SNP [dm3] 2L_20087184_SNP [dm6]	G	A	3.199e^-5	0.819	INTRON neb
3R	15645735	3R_15645735_SNP [dm3] 3R_19820013_SNP [dm6]	G	A	3.406e^-5	0.819	INTRON bnl	TF binding site mE1_TFBS_chinmo
3L	5399975	3L_5399975_SNP [dm3] 3L_5406875_SNP [dm6]	T	C	3.427e^-5	0.819	INTERGENIC
3R	26017101	3R_26017101_SNP [dm3] 3R_30191379_SNP [dm6]	C	G	3.580e^-5	0.819	UPSTREAM CG9747 INTERGENIC
3R	18289486	3R_18289486_SNP [dm3] 3R_22463764_SNP [dm6]	T	C	3.600e^-5	0.819	SYNONYMOUS_CODING AP-2mu	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2R	17034461	2R_17034461_SNP [dm3] 2R_21146956_SNP [dm6]	T	C	3.629e^-5	0.819	SYNONYMOUS_CODING Hmg-2 DOWNSTREAM CG15657	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3R	14012352	3R_14012352_SNP [dm3] 3R_18186630_SNP [dm6]	G	A	3.656e^-5	0.819	SYNONYMOUS_CODING Arp5 UPSTREAM CG7208	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2L	20039976	2L_20039976_SNP [dm3] 2L_20039976_SNP [dm6]	G	A	3.744e^-5	0.819	INTRON sNPF
2L	20101000	2L_20101000_SNP [dm3] 2L_20101000_SNP [dm6]	T	C	3.754e^-5	0.819	SYNONYMOUS_CODING Kua
3L	2224444	3L_2224444_SNP [dm3] 3L_2224444_SNP [dm6]	A	G	3.826e^-5	0.819	INTERGENIC
3R	15476930	3R_15476930_SNP [dm3] 3R_19651208_SNP [dm6]	A	T	3.924e^-5	0.819	UTR_5_PRIME CG31219 DOWNSTREAM CG31220 INTRON CG31219
2L	20464375	2L_20464375_SNP [dm3] 2L_20464375_SNP [dm6]	T	A	3.932e^-5	0.819	UPSTREAM CG2493 DOWNSTREAM CR44980 INTERGENIC	TF binding site mE1_TFBS_HSA
3L	16908351	3L_16908351_SNP [dm3] 3L_16915251_SNP [dm6]	G	A	3.942e^-5	0.819	INTRON Lmpt
2L	8059656	2L_8059656_SNP [dm3] 2L_8059656_SNP [dm6]	T	C	3.944e^-5	0.819	SYNONYMOUS_CODING poe
2R	5016991	2R_5016991_SNP [dm3] 2R_9129486_SNP [dm6]	T	C	3.957e^-5	0.819	INTRON CG18659
3L	8553458	3L_8553458_DEL [dm3] 3L_8560358_DEL [dm6]	TCGT	C	3.959e^-5	0.819	INTRON rhea	TF binding site mE1_TFBS_Trl
3L	14849628	3L_14849628_SNP [dm3] 3L_14856528_SNP [dm6]	T	A	3.980e^-5	0.819	INTRON CG17839
X	11591320	X_11591320_SNP [dm3] X_11697287_SNP [dm6]	A	T	4.028e^-5	0.819	INTRON PhKgamma	TF binding site mE1_TFBS_sens
2L	20039917	2L_20039917_DEL [dm3] 2L_20039917_DEL [dm6]	TGAGACGGTAATC...	A	4.041e^-5	0.819	INTRON sNPF
2L	20087501	2L_20087501_SNP [dm3] 2L_20087501_SNP [dm6]	C	T	4.046e^-5	0.819	INTRON neb	TF binding site mE1_TFBS_cad
3L	1979990	3L_1979990_SNP [dm3] 3L_1979990_SNP [dm6]	T	A	4.193e^-5	0.819	INTERGENIC
2L	7458167	2L_7458167_SNP [dm3] 2L_7458167_SNP [dm6]	G	C	4.256e^-5	0.819	SYNONYMOUS_CODING Gr28b UPSTREAM Gr28b INTRON Gr28b
2R	4752490	2R_4752490_SNP [dm3] 2R_8864985_SNP [dm6]	G	C	4.405e^-5	0.819	INTRON RyR
3L	4392460	3L_4392460_DEL [dm3] 3L_4392460_DEL [dm6]	ATGAATGGGG	A	4.437e^-5	0.819	INTRON slow
2L	7909376	2L_7909376_SNP [dm3] 2L_7909376_SNP [dm6]	G	A	4.453e^-5	0.819	INTRON Snoo
3L	3288330	3L_3288330_SNP [dm3] 3L_3288330_SNP [dm6]	T	G	4.478e^-5	0.819	INTRON CG12017	TF binding site mE1_TFBS_cad
3R	10673376	3R_10673376_SNP [dm3] 3R_14847654_SNP [dm6]	G	A	4.579e^-5	0.819	DOWNSTREAM CG3610 INTRON btsz
X	1052596	X_1052596_DEL [dm3] X_1158563_DEL [dm6]	ACACTCTCCAA...	A	4.581e^-5	0.819	DOWNSTREAM eIF4E-7 INTERGENIC	TF binding site BDTNP1_TFBS_da mE1_TFBS_GATAe mE1_TFBS_HSA
2R	12612490	2R_12612490_SNP [dm3] 2R_16724985_SNP [dm6]	G	A	4.597e^-5	0.819	INTRON CG30463

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Missing results

By genomic position
Variant impact
Gene name

Fecundity phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results