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=1.010e^-9)
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
wolba	0.060538
In_2R_NS	0.005681

Kruskal-Wallis test

Covariate	χ²	p-value
In_2L_t	6.9916	0.0303
In_2R_NS	11.0145	0.0041
In_3R_K	5.6038	0.0607
In_3R_Mo	5.6429	0.0595

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2083 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	19412618	2L_19412618_SNP [dm3] 2L_19412618_SNP [dm6]	T	C	3.860e^-7	0.724	UPSTREAM Pax INTRON Pax
X	15009353	X_15009353_SNP [dm3] X_15115320_SNP [dm6]	T	C	8.278e^-7	0.756	SYNONYMOUS_CODING Cyp4s3
X	15009264	X_15009264_SNP [dm3] X_15115231_SNP [dm6]	C	G	1.209e^-6	0.756	NON_SYNONYMOUS_CODING Cyp4s3
2R	14012048	2R_14012048_SNP [dm3] 2R_18124543_SNP [dm6]	C	G	2.227e^-6	0.783	UPSTREAM stau INTRON stau	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_hkb mE1_TFBS_HSA
X	15453776	X_15453776_SNP [dm3] X_15559743_SNP [dm6]	C	A	2.332e^-6	0.783	INTERGENIC
X	16010164	X_16010164_SNP [dm3] X_16116131_SNP [dm6]	T	A	4.565e^-6	0.783	INTERGENIC
X	15009365	X_15009365_SNP [dm3] X_15115332_SNP [dm6]	C	T	4.841e^-6	0.783	SYNONYMOUS_CODING Cyp4s3
X	15009356	X_15009356_SNP [dm3] X_15115323_SNP [dm6]	C	T	5.061e^-6	0.783	SYNONYMOUS_CODING Cyp4s3
X	16010160	X_16010160_SNP [dm3] X_16116127_SNP [dm6]	G	T	5.430e^-6	0.783	INTERGENIC
X	16010161	X_16010161_SNP [dm3] X_16116128_SNP [dm6]	T	A	5.430e^-6	0.783	INTERGENIC
3R	10885534	3R_10885534_SNP [dm3] 3R_15059812_SNP [dm6]	G	A	5.468e^-6	0.783	INTRON dpr9
2R	14012035	2R_14012035_SNP [dm3] 2R_18124530_SNP [dm6]	C	T	6.387e^-6	0.783	UPSTREAM stau INTRON stau	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_hkb mE1_TFBS_HSA
2L	1823977	2L_1823977_SNP [dm3] 2L_1823977_SNP [dm6]	G	A	7.448e^-6	0.783	UPSTREAM CG31933 DOWNSTREAM CG31664 INTERGENIC
X	16010168	X_16010168_SNP [dm3] X_16116135_SNP [dm6]	T	C	7.989e^-6	0.783	INTERGENIC
X	16010151	X_16010151_DEL [dm3] X_16116118_DEL [dm6]	TC	T	8.960e^-6	0.783	INTERGENIC
2L	7199181	2L_7199181_DEL [dm3] 2L_7199181_DEL [dm6]	CA	T	9.054e^-6	0.783	INTRON CG4502
X	19800301	X_19800301_SNP [dm3] X_19906268_SNP [dm6]	G	T	1.070e^-5	0.783	UTR_3_PRIME Hers
3R	12248271	3R_12248271_SNP [dm3] 3R_16422549_SNP [dm6]	T	C	1.110e^-5	0.783	INTERGENIC	regulatory region REDfly_CRMs
2L	1820129	2L_1820129_SNP [dm3] 2L_1820129_SNP [dm6]	G	C	1.168e^-5	0.783	INTERGENIC
3L	1277532	3L_1277532_SNP [dm3] 3L_1277532_SNP [dm6]	T	C	1.216e^-5	0.783	INTRON CG32333
2L	5934698	2L_5934698_SNP [dm3] 2L_5934698_SNP [dm6]	T	C	1.226e^-5	0.783	INTRON dsf	TF binding site BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 mE1_TFBS_HSA
X	15009717	X_15009717_SNP [dm3] X_15115684_SNP [dm6]	G	A	1.253e^-5	0.783	SYNONYMOUS_CODING Cyp4s3
2R	14012123	2R_14012123_SNP [dm3] 2R_18124618_SNP [dm6]	C	T	1.309e^-5	0.783	UPSTREAM stau INTRON stau	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_hkb mE1_TFBS_HSA
2L	1434480	2L_1434480_SNP [dm3] 2L_1434480_SNP [dm6]	G	T	1.314e^-5	0.783	INTERGENIC	TF binding site mE1_TFBS_cad
3R	12250664	3R_12250664_SNP [dm3] 3R_16424942_SNP [dm6]	A	T	1.345e^-5	0.783	DOWNSTREAM tRNA:CR31497 INTERGENIC	regulatory region REDfly_CRMs
2L	1820635	2L_1820635_SNP [dm3] 2L_1820635_SNP [dm6]	G	A	1.354e^-5	0.783	DOWNSTREAM CG31933 INTERGENIC
2L	1434481	2L_1434481_SNP [dm3] 2L_1434481_SNP [dm6]	A	G	1.364e^-5	0.783	INTERGENIC	TF binding site mE1_TFBS_cad
2R	14809906	2R_14809906_SNP [dm3] 2R_18922401_SNP [dm6]	G	C	1.425e^-5	0.783	INTRON sano	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2R	18583911	2R_18583911_SNP [dm3] 2R_22696406_SNP [dm6]	T	G	1.430e^-5	0.783	INTRON robo
X	17505888	X_17505888_SNP [dm3] X_17611855_SNP [dm6]	C	A	1.463e^-5	0.783	INTERGENIC
2R	7374927	2R_7374927_SNP [dm3] 2R_11487422_SNP [dm6]	A	G	1.516e^-5	0.783	INTRON inv
3L	5983698	3L_5983698_SNP [dm3] 3L_5990598_SNP [dm6]	G	A	1.517e^-5	0.783	INTERGENIC
X	19795320	X_19795320_SNP [dm3] X_19901287_SNP [dm6]	C	T	1.552e^-5	0.783	NON_SYNONYMOUS_CODING Hers	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_chinmo mE1_TFBS_HSA
X	6840769	X_6840769_SNP [dm3] X_6946736_SNP [dm6]	C	T	1.556e^-5	0.783	INTRON CG14431
3R	12250654	3R_12250654_SNP [dm3] 3R_16424932_SNP [dm6]	A	G	1.565e^-5	0.783	DOWNSTREAM tRNA:CR31497 INTERGENIC	regulatory region REDfly_CRMs
2L	19286329	2L_19286329_SNP [dm3] 2L_19286329_SNP [dm6]	G	T	1.633e^-5	0.783	INTERGENIC
3L	12238431	3L_12238431_DEL [dm3] 3L_12245331_DEL [dm6]	AATGGCCCGAA...	A	1.689e^-5	0.783	DOWNSTREAM CR43991 INTRON app
3L	10283129	3L_10283129_SNP [dm3] 3L_10290029_SNP [dm6]	C	A	1.710e^-5	0.783	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad
3L	14879666	3L_14879666_SNP [dm3] 3L_14886566_SNP [dm6]	T	G	1.735e^-5	0.783	DOWNSTREAM CR44702 INTERGENIC
3R	10486695	3R_10486695_SNP [dm3] 3R_14660973_SNP [dm6]	C	T	1.761e^-5	0.783	UTR_3_PRIME Hexim DOWNSTREAM Rad17
2L	5923670	2L_5923670_SNP [dm3] 2L_5923670_SNP [dm6]	A	C	1.804e^-5	0.783	UPSTREAM CG9016 DOWNSTREAM bchs INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	4104610	2L_4104610_SNP [dm3] 2L_4104610_SNP [dm6]	G	A	1.872e^-5	0.783	INTRON ed
X	16010144	X_16010144_SNP [dm3] X_16116111_SNP [dm6]	A	G	1.978e^-5	0.783	INTERGENIC
3R	12250650	3R_12250650_SNP [dm3] 3R_16424928_SNP [dm6]	T	A	2.006e^-5	0.783	DOWNSTREAM tRNA:CR31497 INTERGENIC	regulatory region REDfly_CRMs
2L	16472261	2L_16472261_SNP [dm3] 2L_16472261_SNP [dm6]	G	T	2.014e^-5	0.783	SYNONYMOUS_CODING dac	TF binding site mE1_TFBS_cad
2R	18985930	2R_18985930_SNP [dm3] 2R_23098407_SNP [dm6]	A	C	2.027e^-5	0.783	INTERGENIC
X	19800262	X_19800262_SNP [dm3] X_19906229_SNP [dm6]	A	C	2.027e^-5	0.783	UTR_3_PRIME Hers
3L	2959712	3L_2959712_SNP [dm3] 3L_2959712_SNP [dm6]	A	T	2.034e^-5	0.783	DOWNSTREAM CG34025 & 1 other INTERGENIC
3R	9956564	3R_9956564_SNP [dm3] 3R_14130842_SNP [dm6]	T	A	2.133e^-5	0.783	SYNONYMOUS_CODING CG14356 DOWNSTREAM RpII140	TF binding site mE1_TFBS_cad
3R	6458723	3R_6458723_SNP [dm3] 3R_10633001_SNP [dm6]	A	G	2.165e^-5	0.783	INTRON hth	TF binding site mE1_TFBS_cad
3R	6456997	3R_6456997_SNP [dm3] 3R_10631275_SNP [dm6]	A	C	2.182e^-5	0.783	INTRON hth	TF binding site mE1_TFBS_cad
3R	9648695	3R_9648695_SNP [dm3] 3R_13822973_SNP [dm6]	G	C	2.191e^-5	0.783	INTERGENIC
X	15994868	X_15994868_DEL [dm3] X_16100835_DEL [dm6]	TT	T	2.233e^-5	0.783	INTRON CG42354 & 1 other	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	16751380	3L_16751380_SNP [dm3] 3L_16758280_SNP [dm6]	G	T	2.312e^-5	0.783	INTERGENIC
2L	17603404	2L_17603404_SNP [dm3] 2L_17603404_SNP [dm6]	T	G	2.394e^-5	0.783	UTR_3_PRIME Sytalpha	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA
3R	12251001	3R_12251001_SNP [dm3] 3R_16425279_SNP [dm6]	A	G	2.394e^-5	0.783	UPSTREAM tRNA:CR31497 INTERGENIC	regulatory region REDfly_CRMs
2L	8480063	2L_8480063_SNP [dm3] 2L_8480063_SNP [dm6]	C	G	2.423e^-5	0.783	INTRON d	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
X	19800303	X_19800303_SNP [dm3] X_19906270_SNP [dm6]	C	G	2.500e^-5	0.783	UTR_3_PRIME Hers
3R	25785297	3R_25785297_SNP [dm3] 3R_29959575_SNP [dm6]	G	C	2.502e^-5	0.783	INTRON TkR99D
2R	6207920	2R_6207920_SNP [dm3] 2R_10320415_SNP [dm6]	C	T	2.505e^-5	0.783	INTRON Ndg & 1 other
X	1539515	X_1539515_SNP [dm3] X_1645482_SNP [dm6]	G	A	2.592e^-5	0.797	DOWNSTREAM br INTRON Mur2B & 1 other
X	19800289	X_19800289_SNP [dm3] X_19906256_SNP [dm6]	T	A	2.674e^-5	0.809	UTR_3_PRIME Hers
2L	6009463	2L_6009463_SNP [dm3] 2L_6009463_SNP [dm6]	G	A	2.900e^-5	0.846	SYNONYMOUS_CODING CG9098	TF binding site mE1_TFBS_chinmo
3L	21615063	3L_21615063_SNP [dm3] 3L_21621963_SNP [dm6]	A	T	2.988e^-5	0.846	SYNONYMOUS_CODING CG7166
3L	1817356	3L_1817356_SNP [dm3] 3L_1817356_SNP [dm6]	C	A	3.014e^-5	0.846	INTRON GV1
3L	10283149	3L_10283149_SNP [dm3] 3L_10290049_SNP [dm6]	C	T	3.105e^-5	0.846	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi
2L	5736952	2L_5736952_SNP [dm3] 2L_5736952_SNP [dm6]	A	C	3.253e^-5	0.846	INTRON CG11030 & 1 other
2L	1792767	2L_1792767_SNP [dm3] 2L_1792767_SNP [dm6]	G	T	3.301e^-5	0.846	NON_SYNONYMOUS_CODING Gr22b UPSTREAM Gr22c DOWNSTREAM Gr22a	regulatory region REDfly_CRMs
2L	16170031	2L_16170031_SNP [dm3] 2L_16170031_SNP [dm6]	C	T	3.330e^-5	0.846	INTRON Ca-alpha1D
X	15009732	X_15009732_SNP [dm3] X_15115699_SNP [dm6]	G	A	3.408e^-5	0.846	SYNONYMOUS_CODING Cyp4s3
3R	27168511	3R_27168511_SNP [dm3] 3R_31342789_SNP [dm6]	T	A	3.502e^-5	0.846	INTRON CG34347
X	19800846	X_19800846_DEL [dm3] X_19906813_DEL [dm6]	TA	T	3.539e^-5	0.846	UTR_3_PRIME Hers DOWNSTREAM Hers	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	4348757	2L_4348757_SNP [dm3] 2L_4348757_SNP [dm6]	C	T	3.607e^-5	0.846	UPSTREAM CR44699 DOWNSTREAM CR44697 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_twi
2R	8718128	2R_8718128_SNP [dm3] 2R_12830623_SNP [dm6]	A	G	3.617e^-5	0.846	INTERGENIC
2L	13690722	2L_13690722_SNP [dm3] 2L_13690722_SNP [dm6]	G	A	3.674e^-5	0.846	INTRON CG31814
2L	5736943	2L_5736943_SNP [dm3] 2L_5736943_SNP [dm6]	G	T	3.690e^-5	0.846	SPLICE_SITE_REGION CG11147 INTRON CG11030 & 1 other
3R	10883642	3R_10883642_SNP [dm3] 3R_15057920_SNP [dm6]	A	G	3.702e^-5	0.846	INTRON dpr9
3L	16030080	3L_16030080_SNP [dm3] 3L_16036980_SNP [dm6]	G	A	3.805e^-5	0.846	NON_SYNONYMOUS_CODING CG5895	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_HSA
X	17897118	X_17897118_SNP [dm3] X_18003085_SNP [dm6]	T	A	3.807e^-5	0.846	INTRON Sh
3L	5984163	3L_5984163_SNP [dm3] 3L_5991063_SNP [dm6]	A	G	3.836e^-5	0.846	INTERGENIC	TF binding site BDTNP1_TFBS_twi
X	6224157	X_6224157_SNP [dm3] X_6330124_SNP [dm6]	C	G	3.857e^-5	0.846	UPSTREAM CG42240 DOWNSTREAM CG15894 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
3R	12250667	3R_12250667_SNP [dm3] 3R_16424945_SNP [dm6]	G	A	3.894e^-5	0.846	DOWNSTREAM tRNA:CR31497 INTERGENIC	regulatory region REDfly_CRMs
3L	4505054	3L_4505054_SNP [dm3] 3L_4505054_SNP [dm6]	C	T	3.994e^-5	0.846	SYNONYMOUS_CODING NT1	TF binding site mE1_TFBS_cad
X	10346166	X_10346166_SNP [dm3] X_10452133_SNP [dm6]	T	A	4.004e^-5	0.846	INTRON CG32683
X	1542845	X_1542845_SNP [dm3] X_1648812_SNP [dm6]	G	A	4.049e^-5	0.846	SYNONYMOUS_CODING br UTR_3_PRIME br INTRON Mur2B & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_sna mE1_TFBS_chinmo mE1_TFBS_HSA
3R	6458797	3R_6458797_SNP [dm3] 3R_10633075_SNP [dm6]	A	G	4.060e^-5	0.846	INTRON hth	TF binding site mE1_TFBS_cad
3R	25599748	3R_25599748_SNP [dm3] 3R_29774026_SNP [dm6]	T	A	4.073e^-5	0.846	INTRON kay	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_GATAe mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
X	17896711	X_17896711_SNP [dm3] X_18002678_SNP [dm6]	A	G	4.242e^-5	0.846	INTRON Sh
2L	3523392	2L_3523392_SNP [dm3] 2L_3523392_SNP [dm6]	A	T	4.281e^-5	0.846	SYNONYMOUS_CODING Sr-CIV DOWNSTREAM CG8851
X	6126797	X_6126797_INS [dm3] X_6232764_INS [dm6]	G	GCCAAA	4.307e^-5	0.846	UTR_3_PRIME CG14446
2L	1820226	2L_1820226_SNP [dm3] 2L_1820226_SNP [dm6]	T	A	4.440e^-5	0.846	INTERGENIC
X	15009726	X_15009726_SNP [dm3] X_15115693_SNP [dm6]	A	T	4.489e^-5	0.846	SYNONYMOUS_CODING Cyp4s3
2R	17760464	2R_17760464_SNP [dm3] 2R_21872959_SNP [dm6]	T	C	4.529e^-5	0.846	INTRON Fili	TF binding site mE1_TFBS_D
2L	9427305	2L_9427305_SNP [dm3] 2L_9427305_SNP [dm6]	A	T	4.531e^-5	0.846	UPSTREAM CG42847 DOWNSTREAM Mco1 INTRON Fbp2	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	18844373	2R_18844373_SNP [dm3] 2R_22956850_SNP [dm6]	G	T	4.532e^-5	0.846	DOWNSTREAM CR44780 INTERGENIC
X	16804970	X_16804970_SNP [dm3] X_16910937_SNP [dm6]	T	C	4.763e^-5	0.846	INTRON CR44754
X	8013096	X_8013096_SNP [dm3] X_8119063_SNP [dm6]	T	C	4.791e^-5	0.846	UTR_3_PRIME CG1575 DOWNSTREAM CG2260
X	8013106	X_8013106_SNP [dm3] X_8119073_SNP [dm6]	G	C	4.791e^-5	0.846	UTR_3_PRIME CG1575 DOWNSTREAM CG2260
3L	13260742	3L_13260742_SNP [dm3] 3L_13267642_SNP [dm6]	T	G	4.842e^-5	0.846	INTRON caps	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	23431307	3R_23431307_SNP [dm3] 3R_27605585_SNP [dm6]	G	T	4.852e^-5	0.846	INTRON dsd	TF binding site mE1_TFBS_cad mE1_TFBS_HSA

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By genomic position
Variant impact
Gene name

pc_Surv_MeHg_0_CAFF phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results