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=1.483e^-4)
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	0.085849

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1776 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
X	6679124	X_6679124_SNP [dm3] X_6785091_SNP [dm6]	A	G	9.355e^-7	0.42	INTRON C3G	TF binding site mE1_TFBS_HSA
3L	10396532	3L_10396532_SNP [dm3] 3L_10403432_SNP [dm6]	C	A	1.527e^-6	0.42	INTERGENIC
3L	21968126	3L_21968126_SNP [dm3] 3L_21975026_SNP [dm6]	T	A	2.019e^-6	0.42	INTRON CG7470
3L	21968129	3L_21968129_SNP [dm3] 3L_21975029_SNP [dm6]	T	C	2.019e^-6	0.42	INTRON CG7470
3L	21968130	3L_21968130_SNP [dm3] 3L_21975030_SNP [dm6]	G	A	2.019e^-6	0.42	INTRON CG7470
X	2888398	X_2888398_SNP [dm3] X_2994365_SNP [dm6]	T	A	2.087e^-6	0.42	INTRON kirre	TF binding site mE1_TFBS_HSA
X	2888399	X_2888399_SNP [dm3] X_2994366_SNP [dm6]	C	G	2.087e^-6	0.42	INTRON kirre	TF binding site mE1_TFBS_HSA
X	2888401	X_2888401_DEL [dm3] X_2994368_DEL [dm6]	AA	A	2.087e^-6	0.42	INTRON kirre	TF binding site mE1_TFBS_HSA
3L	19387043	3L_19387043_SNP [dm3] 3L_19393943_SNP [dm6]	G	T	2.309e^-6	0.42	INTRON CG32206
3L	19387044	3L_19387044_SNP [dm3] 3L_19393944_SNP [dm6]	A	T	2.309e^-6	0.42	INTRON CG32206
2L	7392737	2L_7392737_SNP [dm3] 2L_7392737_SNP [dm6]	T	G	3.237e^-6	0.442	INTRON CG5160
3R	10602855	3R_10602855_SNP [dm3] 3R_14777133_SNP [dm6]	T	C	4.142e^-6	0.442	INTRON jvl	TF binding site BDTNP1_TFBS_twi
2L	3985015	2L_3985015_SNP [dm3] 2L_3985015_SNP [dm6]	C	A	4.820e^-6	0.442	INTRON fred
3L	19386731	3L_19386731_SNP [dm3] 3L_19393631_SNP [dm6]	C	T	4.983e^-6	0.442	INTRON CG32206
3L	19387125	3L_19387125_SNP [dm3] 3L_19394025_SNP [dm6]	A	C	5.111e^-6	0.442	INTRON CG32206
2L	7392474	2L_7392474_SNP [dm3] 2L_7392474_SNP [dm6]	C	T	5.789e^-6	0.442	INTRON CG5160
2L	7392484	2L_7392484_SNP [dm3] 2L_7392484_SNP [dm6]	A	G	5.789e^-6	0.442	INTRON CG5160
2L	7392514	2L_7392514_INS [dm3] 2L_7392514_INS [dm6]	T	TA	5.789e^-6	0.442	INTRON CG5160
2L	7392518	2L_7392518_SNP [dm3] 2L_7392518_SNP [dm6]	C	A	5.789e^-6	0.442	INTRON CG5160
2L	7392551	2L_7392551_SNP [dm3] 2L_7392551_SNP [dm6]	T	A	5.789e^-6	0.442	INTRON CG5160
3L	11148225	3L_11148225_SNP [dm3] 3L_11155125_SNP [dm6]	G	A	5.814e^-6	0.442	INTRON CG32082
X	2888388	X_2888388_SNP [dm3] X_2994355_SNP [dm6]	T	C	5.939e^-6	0.442	INTRON kirre	TF binding site mE1_TFBS_HSA
X	2888410	X_2888410_SNP [dm3] X_2994377_SNP [dm6]	G	A	5.939e^-6	0.442	INTRON kirre	TF binding site mE1_TFBS_HSA
3L	19386848	3L_19386848_SNP [dm3] 3L_19393748_SNP [dm6]	G	T	6.135e^-6	0.442	INTRON CG32206
3L	10396510	3L_10396510_SNP [dm3] 3L_10403410_SNP [dm6]	T	A	6.174e^-6	0.442	INTERGENIC
3L	19386664	3L_19386664_SNP [dm3] 3L_19393564_SNP [dm6]	T	A	6.490e^-6	0.442	INTRON CG32206
3R	11540013	3R_11540013_SNP [dm3] 3R_15714291_SNP [dm6]	T	C	6.567e^-6	0.442	INTERGENIC
2R	16984914	2R_16984914_SNP [dm3] 2R_21097409_SNP [dm6]	G	T	7.480e^-6	0.485	UPSTREAM CG34396 & 1 other INTRON CG34396	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	7392540	2L_7392540_SNP [dm3] 2L_7392540_SNP [dm6]	G	C	8.029e^-6	0.503	INTRON CG5160
3R	26982703	3R_26982703_SNP [dm3] 3R_31156981_SNP [dm6]	G	T	8.734e^-6	0.512	INTRON Gycbeta100B
X	2888414	X_2888414_SNP [dm3] X_2994381_SNP [dm6]	T	G	9.208e^-6	0.512	INTRON kirre	TF binding site mE1_TFBS_HSA
3L	9309606	3L_9309606_SNP [dm3] 3L_9316506_SNP [dm6]	C	G	9.255e^-6	0.512	INTERGENIC
3L	4043937	3L_4043937_SNP [dm3] 3L_4043937_SNP [dm6]	C	G	9.298e^-6	0.512	INTERGENIC
2R	8943727	2R_8943727_SNP [dm3] 2R_13056222_SNP [dm6]	G	T	9.652e^-6	0.516	UTR_3_PRIME Drl-2 DOWNSTREAM Drl-2
3L	11148240	3L_11148240_SNP [dm3] 3L_11155140_SNP [dm6]	G	A	9.974e^-6	0.516	INTRON CG32082
3L	13291564	3L_13291564_SNP [dm3] 3L_13298464_SNP [dm6]	A	G	1.076e^-5	0.516	UPSTREAM CR45255 DOWNSTREAM CR45253 & 1 other EXON CR45254	TF binding site BDTNP1_TFBS_prd
3R	11539917	3R_11539917_DEL [dm3] 3R_15714195_DEL [dm6]	GCGTTGAGTTG...	G	1.084e^-5	0.516	INTERGENIC
X	3360290	X_3360290_SNP [dm3] X_3466257_SNP [dm6]	T	G	1.090e^-5	0.516	INTRON CR44999 & 1 other
3R	26468217	3R_26468217_SNP [dm3] 3R_30642495_SNP [dm6]	T	C	1.107e^-5	0.516	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	8437633	3L_8437633_SNP [dm3] 3L_8444533_SNP [dm6]	G	A	1.153e^-5	0.524	SYNONYMOUS_CODING CG6983	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
X	21850004	X_21850004_SNP [dm3] X_22448168_SNP [dm6]	G	A	1.308e^-5	0.58	DOWNSTREAM CG14621 INTRON CG14615
2R	18968923	2R_18968923_SNP [dm3] 2R_23081400_SNP [dm6]	G	A	1.367e^-5	0.591	SYNONYMOUS_CODING Gr59a UPSTREAM Gr59b	regulatory region REDfly_CRMs
3L	2652798	3L_2652798_SNP [dm3] 3L_2652798_SNP [dm6]	A	C	1.496e^-5	0.632	NON_SYNONYMOUS_CODING Snup UTR_5_PRIME CG42304 UPSTREAM Aats-pro & 1 other	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2L	16558473	2L_16558473_SNP [dm3] 2L_16558473_SNP [dm6]	G	T	1.560e^-5	0.644	SYNONYMOUS_CODING CG42389	TF binding site mE1_TFBS_cad
3L	11125617	3L_11125617_SNP [dm3] 3L_11132517_SNP [dm6]	A	G	1.632e^-5	0.646	UPSTREAM CG32074 INTRON CG42575
X	2888418	X_2888418_SNP [dm3] X_2994385_SNP [dm6]	A	G	1.636e^-5	0.646	INTRON kirre	TF binding site mE1_TFBS_HSA
3L	19386849	3L_19386849_SNP [dm3] 3L_19393749_SNP [dm6]	T	C	1.702e^-5	0.651	INTRON CG32206
2R	12086879	2R_12086879_SNP [dm3] 2R_16199374_SNP [dm6]	T	A	1.720e^-5	0.651	UTR_3_PRIME CG42837 & 1 other DOWNSTREAM shark
X	21850002	X_21850002_SNP [dm3] X_22448166_SNP [dm6]	G	T	1.857e^-5	0.679	DOWNSTREAM CG14621 INTRON CG14615
2R	13994071	2R_13994071_SNP [dm3] 2R_18106566_SNP [dm6]	G	A	1.870e^-5	0.679	INTRON CG5756
3L	9608146	3L_9608146_SNP [dm3] 3L_9615046_SNP [dm6]	T	C	1.953e^-5	0.696	UPSTREAM LanB2 INTRON LanB2	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3L	12129782	3L_12129782_SNP [dm3] 3L_12136682_SNP [dm6]	C	T	2.056e^-5	0.718	UTR_5_PRIME CG5645 UPSTREAM Atg12 DOWNSTREAM l_3_neo18	TF binding site mE1_TFBS_cad
2L	7392808	2L_7392808_SNP [dm3] 2L_7392808_SNP [dm6]	A	G	2.205e^-5	0.756	INTRON CG5160
X	6679129	X_6679129_SNP [dm3] X_6785096_SNP [dm6]	T	A	2.346e^-5	0.762	INTRON C3G	TF binding site mE1_TFBS_HSA
X	3360286	X_3360286_SNP [dm3] X_3466253_SNP [dm6]	C	A	2.363e^-5	0.762	INTRON CR44999 & 1 other
2L	4012537	2L_4012537_SNP [dm3] 2L_4012537_SNP [dm6]	C	T	2.414e^-5	0.762	INTERGENIC
2R	19491538	2R_19491538_SNP [dm3] 2R_23604015_SNP [dm6]	A	G	2.475e^-5	0.762	SYNONYMOUS_CODING CG17664 DOWNSTREAM CG5398
2R	18969255	2R_18969255_SNP [dm3] 2R_23081732_SNP [dm6]	A	G	2.475e^-5	0.762	UPSTREAM Gr59b DOWNSTREAM Gr59a INTERGENIC	regulatory region REDfly_CRMs
2R	18969375	2R_18969375_SNP [dm3] 2R_23081852_SNP [dm6]	A	T	2.475e^-5	0.762	UPSTREAM Gr59b DOWNSTREAM Gr59a INTERGENIC	regulatory region REDfly_CRMs
2R	6801181	2R_6801181_SNP [dm3] 2R_10913676_SNP [dm6]	C	A	2.583e^-5	0.782	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
3L	13551908	3L_13551908_SNP [dm3] 3L_13558808_SNP [dm6]	C	G	2.730e^-5	0.813	DOWNSTREAM CR45178 INTRON bru-3
3R	23410655	3R_23410655_SNP [dm3] 3R_27584933_SNP [dm6]	G	A	2.837e^-5	0.831	NON_SYNONYMOUS_CODING raps	TF binding site mE1_TFBS_chinmo
3L	21968136	3L_21968136_DEL [dm3] 3L_21975036_DEL [dm6]	AA	A	2.916e^-5	0.834	INTRON CG7470
2L	16431241	2L_16431241_SNP [dm3] 2L_16431241_SNP [dm6]	A	G	2.967e^-5	0.834	INTRON CG5888
2R	18969261	2R_18969261_SNP [dm3] 2R_23081738_SNP [dm6]	A	C	3.114e^-5	0.834	UPSTREAM Gr59b DOWNSTREAM Gr59a INTERGENIC	regulatory region REDfly_CRMs
2R	18969392	2R_18969392_SNP [dm3] 2R_23081869_SNP [dm6]	G	C	3.114e^-5	0.834	UPSTREAM Gr59b DOWNSTREAM Gr59a INTERGENIC	regulatory region REDfly_CRMs
3L	9608244	3L_9608244_SNP [dm3] 3L_9615144_SNP [dm6]	G	A	3.433e^-5	0.834	UPSTREAM LanB2 INTRON LanB2	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
2R	1739324	2R_1739324_SNP [dm3] 2R_5851819_SNP [dm6]	T	C	3.448e^-5	0.834	INTRON dpr12
2L	2068780	2L_2068780_SNP [dm3] 2L_2068780_SNP [dm6]	A	G	3.533e^-5	0.834	INTRON dpr3	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	15156377	3R_15156377_SNP [dm3] 3R_19330655_SNP [dm6]	T	C	3.536e^-5	0.834	EXON CR43258	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	2988863	3L_2988863_SNP [dm3] 3L_2988863_SNP [dm6]	G	A	3.536e^-5	0.834	INTERGENIC
3R	24579641	3R_24579641_SNP [dm3] 3R_28753919_SNP [dm6]	C	A	3.615e^-5	0.834	INTERGENIC	TF binding site mE1_TFBS_inv
3L	3106250	3L_3106250_SNP [dm3] 3L_3106250_SNP [dm6]	C	A	3.616e^-5	0.834	INTRON Cht7
2R	16984982	2R_16984982_SNP [dm3] 2R_21097477_SNP [dm6]	T	G	3.630e^-5	0.834	UPSTREAM CG34396 & 1 other INTRON CG34396	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
2L	7392488	2L_7392488_SNP [dm3] 2L_7392488_SNP [dm6]	A	T	3.652e^-5	0.834	INTRON CG5160
2L	7392503	2L_7392503_SNP [dm3] 2L_7392503_SNP [dm6]	A	G	3.652e^-5	0.834	INTRON CG5160
2L	7392506	2L_7392506_SNP [dm3] 2L_7392506_SNP [dm6]	T	A	3.652e^-5	0.834	INTRON CG5160
2L	7392557	2L_7392557_SNP [dm3] 2L_7392557_SNP [dm6]	C	T	3.652e^-5	0.834	INTRON CG5160
3L	1842570	3L_1842570_SNP [dm3] 3L_1842570_SNP [dm6]	G	C	3.675e^-5	0.834	UPSTREAM Cpr62Bc INTERGENIC
X	12923370	X_12923370_SNP [dm3] X_13029337_SNP [dm6]	T	A	3.735e^-5	0.834	INTRON rad
X	12923371	X_12923371_SNP [dm3] X_13029338_SNP [dm6]	A	G	3.735e^-5	0.834	INTRON rad
3L	12131257	3L_12131257_SNP [dm3] 3L_12138157_SNP [dm6]	G	A	3.763e^-5	0.834	SYNONYMOUS_CODING l_3_neo18 UPSTREAM RhoGAP68F DOWNSTREAM Atg12	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_sens mE1_TFBS_Ubx
2R	11156104	2R_11156104_SNP [dm3] 2R_15268599_SNP [dm6]	T	G	3.858e^-5	0.841	INTRON Trpm
X	12388116	X_12388116_SNP [dm3] X_12494083_SNP [dm6]	G	A	3.897e^-5	0.841	DOWNSTREAM Mks1 INTERGENIC
3L	10396489	3L_10396489_INS [dm3] 3L_10403389_INS [dm6]	T	TTA	3.990e^-5	0.841	INTERGENIC
2R	7810946	2R_7810946_SNP [dm3] 2R_11923441_SNP [dm6]	T	C	4.049e^-5	0.841	INTERGENIC
X	6678972	X_6678972_SNP [dm3] X_6784939_SNP [dm6]	C	A	4.104e^-5	0.841	INTRON C3G
3R	26982549	3R_26982549_SNP [dm3] 3R_31156827_SNP [dm6]	A	G	4.171e^-5	0.841	INTRON Gycbeta100B
2R	11900270	2R_11900270_SNP [dm3] 2R_16012765_SNP [dm6]	A	G	4.182e^-5	0.841	SYNONYMOUS_CODING CG8389	TF binding site BDTNP1_TFBS_sna
3L	4511269	3L_4511269_SNP [dm3] 3L_4511269_SNP [dm6]	A	G	4.294e^-5	0.841	SYNONYMOUS_CODING Tie	TF binding site mE1_TFBS_eve mE1_TFBS_HSA
3L	3510493	3L_3510493_SNP [dm3] 3L_3510493_SNP [dm6]	T	G	4.393e^-5	0.841	UTR_3_PRIME CG42324 DOWNSTREAM ImpE2
3R	26982735	3R_26982735_SNP [dm3] 3R_31157013_SNP [dm6]	C	A	4.437e^-5	0.841	INTRON Gycbeta100B
3L	752494	3L_752494_SNP [dm3] 3L_752494_SNP [dm6]	C	G	4.542e^-5	0.841	UTR_3_PRIME emc INTRON hng3	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	11170008	2L_11170008_SNP [dm3] 2L_11170008_SNP [dm6]	C	T	4.552e^-5	0.841	INTRON Ca-beta
X	12387044	X_12387044_SNP [dm3] X_12493011_SNP [dm6]	G	T	4.581e^-5	0.841	DOWNSTREAM Lsp1alpha INTERGENIC
X	12387064	X_12387064_SNP [dm3] X_12493031_SNP [dm6]	G	T	4.581e^-5	0.841	DOWNSTREAM Lsp1alpha INTERGENIC
X	12387065	X_12387065_SNP [dm3] X_12493032_SNP [dm6]	C	T	4.581e^-5	0.841	DOWNSTREAM Lsp1alpha INTERGENIC
X	12387069	X_12387069_SNP [dm3] X_12493036_SNP [dm6]	T	G	4.581e^-5	0.841	DOWNSTREAM Lsp1alpha INTERGENIC
X	12387073	X_12387073_SNP [dm3] X_12493040_SNP [dm6]	A	T	4.581e^-5	0.841	DOWNSTREAM Lsp1alpha INTERGENIC
3L	9312479	3L_9312479_SNP [dm3] 3L_9319379_SNP [dm6]	T	G	4.674e^-5	0.849	INTERGENIC

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Missing results

By genomic position
Variant impact
Gene name

pc_FPKP_PElem_GS phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results