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=2.738e^-19)
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
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2377 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
2R	6994275	2R_6994275_SNP [dm3] 2R_11106770_SNP [dm6]	G	T	3.425e^-7	0.351	UTR_5_PRIME luna INTRON luna	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
3L	1286335	3L_1286335_SNP [dm3] 3L_1286335_SNP [dm6]	G	A	3.741e^-7	0.351	INTRON CG32333
2R	7007339	2R_7007339_SNP [dm3] 2R_11119834_SNP [dm6]	T	C	8.290e^-7	0.478	UTR_3_PRIME Cyp12d1-p DOWNSTREAM Cyp12d1-p
X	5940506	X_5940506_SNP [dm3] X_6046473_SNP [dm6]	C	T	1.492e^-6	0.478	SYNONYMOUS_CODING CG5937	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3L	14962751	3L_14962751_SNP [dm3] 3L_14969651_SNP [dm6]	C	T	1.847e^-6	0.478	SYNONYMOUS_CODING Tom	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_hb BDTNP1_TFBS_Mad BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
X	5940191	X_5940191_SNP [dm3] X_6046158_SNP [dm6]	T	G	2.027e^-6	0.478	SYNONYMOUS_CODING CG5937	TF binding site mE1_TFBS_sens
2R	6999812	2R_6999812_SNP [dm3] 2R_11112307_SNP [dm6]	A	G	2.194e^-6	0.478	INTRON luna
2R	6999263	2R_6999263_SNP [dm3] 2R_11111758_SNP [dm6]	T	G	2.382e^-6	0.478	INTRON luna	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sbb
2L	5134794	2L_5134794_SNP [dm3] 2L_5134794_SNP [dm6]	A	G	2.445e^-6	0.478	SYNONYMOUS_CODING Msp300 INTRON Msp300
X	5940384	X_5940384_SNP [dm3] X_6046351_SNP [dm6]	C	T	2.633e^-6	0.478	SYNONYMOUS_CODING CG5937	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	16667721	2R_16667721_SNP [dm3] 2R_20780216_SNP [dm6]	G	A	2.804e^-6	0.478	UPSTREAM CG43711 DOWNSTREAM CR44666 INTERGENIC	TF binding site mE1_TFBS_sens
X	5940326	X_5940326_SNP [dm3] X_6046293_SNP [dm6]	C	T	3.430e^-6	0.499	SYNONYMOUS_CODING CG5937	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
X	5940380	X_5940380_SNP [dm3] X_6046347_SNP [dm6]	A	G	3.460e^-6	0.499	SYNONYMOUS_CODING CG5937	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	16667377	2R_16667377_SNP [dm3] 2R_20779872_SNP [dm6]	A	T	3.934e^-6	0.509	UPSTREAM CG43711 DOWNSTREAM CR44666 INTERGENIC
3R	22139517	3R_22139517_SNP [dm3] 3R_26313795_SNP [dm6]	G	C	4.725e^-6	0.509	INTERGENIC
2R	6994584	2R_6994584_INS [dm3] 2R_11107079_INS [dm6]	A	ACATAC	4.801e^-6	0.509	UPSTREAM luna INTRON luna	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
3L	13240443	3L_13240443_SNP [dm3] 3L_13247343_SNP [dm6]	G	C	5.005e^-6	0.509	SYNONYMOUS_CODING CG32119 INTRON caps	TF binding site mE1_TFBS_HSA
3L	11266387	3L_11266387_SNP [dm3] 3L_11273287_SNP [dm6]	G	A	5.053e^-6	0.509	DOWNSTREAM CR44720 INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
X	5939714	X_5939714_SNP [dm3] X_6045681_SNP [dm6]	C	T	5.229e^-6	0.509	SYNONYMOUS_CODING CG5937	TF binding site mE1_TFBS_chinmo
2L	2264650	2L_2264650_SNP [dm3] 2L_2264650_SNP [dm6]	A	T	5.640e^-6	0.509	SYNONYMOUS_CODING CG34049 DOWNSTREAM CG4270
3L	5839105	3L_5839105_SNP [dm3] 3L_5846005_SNP [dm6]	A	T	5.704e^-6	0.509	UPSTREAM vn INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
2R	16665509	2R_16665509_SNP [dm3] 2R_20778004_SNP [dm6]	A	C	6.077e^-6	0.518	UPSTREAM CG43710 DOWNSTREAM CG43711 INTERGENIC
2R	16667474	2R_16667474_INS [dm3] 2R_20779969_INS [dm6]	A	AAG	6.736e^-6	0.548	UPSTREAM CG43711 DOWNSTREAM CR44666 INTERGENIC
2L	1035901	2L_1035901_SNP [dm3] 2L_1035901_SNP [dm6]	C	T	7.018e^-6	0.548	INTRON IA-2
2R	9924871	2R_9924871_SNP [dm3] 2R_14037366_SNP [dm6]	G	A	7.979e^-6	0.58	INTRON mam	TF binding site mE1_TFBS_HSA
3L	5845082	3L_5845082_SNP [dm3] 3L_5851982_SNP [dm6]	G	A	8.039e^-6	0.58	INTERGENIC
X	5940725	X_5940725_SNP [dm3] X_6046692_SNP [dm6]	A	T	9.168e^-6	0.621	SYNONYMOUS_CODING CG5937	TF binding site mE1_TFBS_chinmo mE1_TFBS_sens
2L	5134713	2L_5134713_SNP [dm3] 2L_5134713_SNP [dm6]	C	T	9.276e^-6	0.621	SYNONYMOUS_CODING Msp300 INTRON Msp300
X	4416638	X_4416638_SNP [dm3] X_4522605_SNP [dm6]	C	T	1.000e^-5	0.626	INTRON CR32773
3L	7796285	3L_7796285_SNP [dm3] 3L_7803185_SNP [dm6]	G	A	1.027e^-5	0.626	INTRON CG32369	TF binding site mE1_TFBS_cad
2R	16665531	2R_16665531_INS [dm3] 2R_20778026_INS [dm6]	G	GTTTAG	1.049e^-5	0.626	UPSTREAM CG43710 DOWNSTREAM CG43711 INTERGENIC
2L	18955294	2L_18955294_SNP [dm3] 2L_18955294_SNP [dm6]	G	A	1.087e^-5	0.626	UPSTREAM CG10621 DOWNSTREAM CG10623 & 1 other INTERGENIC
2L	14863186	2L_14863186_SNP [dm3] 2L_14863186_SNP [dm6]	G	A	1.165e^-5	0.626	INTERGENIC
2R	16667463	2R_16667463_SNP [dm3] 2R_20779958_SNP [dm6]	C	T	1.199e^-5	0.626	UPSTREAM CG43711 DOWNSTREAM CR44666 INTERGENIC
3L	8323062	3L_8323062_SNP [dm3] 3L_8329962_SNP [dm6]	A	C	1.233e^-5	0.626	NON_SYNONYMOUS_CODING CG34462
3R	9894341	3R_9894341_SNP [dm3] 3R_14068619_SNP [dm6]	G	A	1.265e^-5	0.626	INTRON foxo
2L	18955323	2L_18955323_SNP [dm3] 2L_18955323_SNP [dm6]	G	T	1.317e^-5	0.626	UPSTREAM CG10621 DOWNSTREAM CG10623 & 1 other INTERGENIC
2L	18955282	2L_18955282_SNP [dm3] 2L_18955282_SNP [dm6]	A	T	1.366e^-5	0.626	UPSTREAM CG10621 DOWNSTREAM CG10623 & 1 other INTERGENIC
2R	16376332	2R_16376332_SNP [dm3] 2R_20488827_SNP [dm6]	T	A	1.368e^-5	0.626	INTERGENIC
2R	16666807	2R_16666807_SNP [dm3] 2R_20779302_SNP [dm6]	A	T	1.418e^-5	0.626	SYNONYMOUS_CODING CG43711 DOWNSTREAM CR44666
2R	6995302	2R_6995302_SNP [dm3] 2R_11107797_SNP [dm6]	T	A	1.419e^-5	0.626	UPSTREAM luna INTRON luna	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
2L	732000	2L_732000_SNP [dm3] 2L_732000_SNP [dm6]	C	G	1.444e^-5	0.626	INTERGENIC
3R	22312916	3R_22312916_SNP [dm3] 3R_26487194_SNP [dm6]	A	G	1.459e^-5	0.626	INTRON plum	TF binding site mE1_TFBS_inv
3L	11898847	3L_11898847_SNP [dm3] 3L_11905747_SNP [dm6]	G	A	1.489e^-5	0.626	INTRON CG44837
X	5940458	X_5940458_SNP [dm3] X_6046425_SNP [dm6]	T	C	1.765e^-5	0.626	SYNONYMOUS_CODING CG5937	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2L	1266122	2L_1266122_SNP [dm3] 2L_1266122_SNP [dm6]	A	G	1.823e^-5	0.626	INTRON robo3
2R	7007374	2R_7007374_SNP [dm3] 2R_11119869_SNP [dm6]	C	T	1.829e^-5	0.626	UTR_3_PRIME Cyp12d1-p DOWNSTREAM Cyp12d1-p
2L	9618352	2L_9618352_SNP [dm3] 2L_9618352_SNP [dm6]	C	T	1.836e^-5	0.626	INTRON GlcAT-S
2L	14394945	2L_14394945_SNP [dm3] 2L_14394945_SNP [dm6]	C	T	1.854e^-5	0.626	INTRON elB	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
2L	7297922	2L_7297922_SNP [dm3] 2L_7297922_SNP [dm6]	A	G	1.856e^-5	0.626	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_twi
2R	18117876	2R_18117876_SNP [dm3] 2R_22230371_SNP [dm6]	A	C	1.877e^-5	0.626	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
2R	6995229	2R_6995229_SNP [dm3] 2R_11107724_SNP [dm6]	A	T	1.900e^-5	0.626	UPSTREAM luna INTRON luna	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3L	11702873	3L_11702873_SNP [dm3] 3L_11709773_SNP [dm6]	C	A	1.901e^-5	0.626	NON_SYNONYMOUS_CODING mtTFB1 UTR_3_PRIME Ccdc56 DOWNSTREAM crim	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2R	9924958	2R_9924958_SNP [dm3] 2R_14037453_SNP [dm6]	G	T	2.005e^-5	0.626	INTRON mam	TF binding site mE1_TFBS_HSA
3R	21457268	3R_21457268_SNP [dm3] 3R_25631546_SNP [dm6]	A	T	2.022e^-5	0.626	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
2R	17088175	2R_17088175_SNP [dm3] 2R_21200670_SNP [dm6]	C	T	2.032e^-5	0.626	INTRON Glycogenin & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
2R	17087840	2R_17087840_SNP [dm3] 2R_21200335_SNP [dm6]	C	G	2.092e^-5	0.626	UPSTREAM Glycogenin & 1 other DOWNSTREAM Lapsyn INTERGENIC	TF binding site BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_Trl
2R	17089888	2R_17089888_SNP [dm3] 2R_21202383_SNP [dm6]	A	T	2.106e^-5	0.626	UPSTREAM Glycogenin INTRON Glycogenin & 1 other	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
X	21353129	X_21353129_SNP [dm3] X_21482102_SNP [dm6]	A	G	2.107e^-5	0.626	UPSTREAM CR45510 DOWNSTREAM CR45511 INTERGENIC
2L	18955312	2L_18955312_DEL [dm3] 2L_18955312_DEL [dm6]	AA	A	2.124e^-5	0.626	UPSTREAM CG10621 DOWNSTREAM CG10623 & 1 other INTERGENIC
2L	18955324	2L_18955324_SNP [dm3] 2L_18955324_SNP [dm6]	G	T	2.126e^-5	0.626	UPSTREAM CG10621 DOWNSTREAM CG10623 & 1 other INTERGENIC
2R	16666693	2R_16666693_SNP [dm3] 2R_20779188_SNP [dm6]	A	G	2.133e^-5	0.626	SYNONYMOUS_CODING CG43711
3R	22136677	3R_22136677_SNP [dm3] 3R_26310955_SNP [dm6]	A	T	2.288e^-5	0.626	INTERGENIC
2R	1737954	2R_1737954_SNP [dm3] 2R_5850449_SNP [dm6]	C	T	2.338e^-5	0.626	INTRON dpr12
2R	4301411	2R_4301411_SNP [dm3] 2R_8413906_SNP [dm6]	C	G	2.461e^-5	0.626	INTERGENIC
2R	17089857	2R_17089857_SNP [dm3] 2R_21202352_SNP [dm6]	A	C	2.526e^-5	0.626	INTRON Glycogenin & 1 other	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
X	21353374	X_21353374_SNP [dm3] X_21482347_SNP [dm6]	A	G	2.665e^-5	0.626	DOWNSTREAM CR45511 INTERGENIC
X	21353182	X_21353182_INS [dm3] X_21482155_INS [dm6]	C	CTGCGTCTTTGTCTCTAGAA...	2.748e^-5	0.626	DOWNSTREAM CR45511 INTERGENIC
3R	21457267	3R_21457267_SNP [dm3] 3R_25631545_SNP [dm6]	G	A	2.807e^-5	0.626	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
X	21353413	X_21353413_SNP [dm3] X_21482386_SNP [dm6]	A	G	2.868e^-5	0.626	DOWNSTREAM CR45511 INTERGENIC
2R	6999236	2R_6999236_SNP [dm3] 2R_11111731_SNP [dm6]	A	T	2.894e^-5	0.626	INTRON luna	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	11117578	3L_11117578_SNP [dm3] 3L_11124478_SNP [dm6]	T	G	2.930e^-5	0.626	INTRON CG42575	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_jumu mE1_TFBS_Trl
2R	7016080	2R_7016080_SNP [dm3] 2R_11128575_SNP [dm6]	C	A	2.939e^-5	0.626	INTERGENIC	TF binding site BDTNP1_TFBS_twi
3R	4631968	3R_4631968_SNP [dm3] 3R_8806246_SNP [dm6]	T	C	2.942e^-5	0.626	UPSTREAM hng2 & 1 other DOWNSTREAM Tcp-1eta INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	89612	2R_89612_SNP [dm3] 2R_4202107_SNP [dm6]	G	T	2.945e^-5	0.626	INTERGENIC
2L	9092538	2L_9092538_SNP [dm3] 2L_9092538_SNP [dm6]	C	T	3.076e^-5	0.626	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_inv
2L	9090547	2L_9090547_SNP [dm3] 2L_9090547_SNP [dm6]	C	T	3.089e^-5	0.626	INTERGENIC
3L	9617491	3L_9617491_SNP [dm3] 3L_9624391_SNP [dm6]	T	A	3.137e^-5	0.626	DOWNSTREAM LanB2 INTRON CG3335
3R	22312913	3R_22312913_INS [dm3] 3R_26487191_INS [dm6]	T	TCT	3.162e^-5	0.626	INTRON plum	TF binding site mE1_TFBS_inv
2L	10586705	2L_10586705_SNP [dm3] 2L_10586705_SNP [dm6]	T	C	3.208e^-5	0.626	INTRON Trim9	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2L	1501244	2L_1501244_SNP [dm3] 2L_1501244_SNP [dm6]	G	T	3.274e^-5	0.626	NON_SYNONYMOUS_CODING CG7420 UPSTREAM CG18131 EXON CR44064
2R	17089852	2R_17089852_SNP [dm3] 2R_21202347_SNP [dm6]	A	T	3.282e^-5	0.626	INTRON Glycogenin & 1 other	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
2L	773298	2L_773298_SNP [dm3] 2L_773298_SNP [dm6]	G	T	3.338e^-5	0.626	UPSTREAM CG12506 DOWNSTREAM CR44614 INTERGENIC
3L	1670311	3L_1670311_SNP [dm3] 3L_1670311_SNP [dm6]	C	T	3.348e^-5	0.626	UPSTREAM RabX5 DOWNSTREAM CG13930 INTERGENIC	TF binding site mE1_TFBS_chinmo
2L	11868532	2L_11868532_SNP [dm3] 2L_11868532_SNP [dm6]	A	G	3.367e^-5	0.626	INTRON Pde1c
X	3485383	X_3485383_SNP [dm3] X_3591350_SNP [dm6]	T	A	3.368e^-5	0.626	INTRON AstA-R1
X	5380042	X_5380042_SNP [dm3] X_5486009_SNP [dm6]	A	T	3.386e^-5	0.626	INTRON SPR
2L	18955315	2L_18955315_SNP [dm3] 2L_18955315_SNP [dm6]	A	T	3.404e^-5	0.626	UPSTREAM CG10621 DOWNSTREAM CG10623 & 1 other INTERGENIC
2L	18955317	2L_18955317_DEL [dm3] 2L_18955317_DEL [dm6]	TA	T	3.404e^-5	0.626	UPSTREAM CG10621 DOWNSTREAM CG10623 & 1 other INTERGENIC
3L	12641483	3L_12641483_SNP [dm3] 3L_12648383_SNP [dm6]	G	C	3.488e^-5	0.626	DOWNSTREAM CR43431 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd mE1_TFBS_HSA
X	4102943	X_4102943_SNP [dm3] X_4208910_SNP [dm6]	T	A	3.550e^-5	0.626	INTERGENIC
2L	9090506	2L_9090506_SNP [dm3] 2L_9090506_SNP [dm6]	A	G	3.561e^-5	0.626	INTERGENIC
2L	960188	2L_960188_SNP [dm3] 2L_960188_SNP [dm6]	A	C	3.571e^-5	0.626	INTERGENIC	TF binding site mE1_TFBS_chinmo
3R	17560453	3R_17560453_SNP [dm3] 3R_21734731_SNP [dm6]	G	T	3.588e^-5	0.626	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	8531246	2L_8531246_SNP [dm3] 2L_8531246_SNP [dm6]	A	T	3.657e^-5	0.626	INTRON CG17834
X	4983768	X_4983768_SNP [dm3] X_5089735_SNP [dm6]	A	G	3.681e^-5	0.626	START_GAINED rg & 1 other UTR_5_PRIME rg & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	3563598	3L_3563598_SNP [dm3] 3L_3563598_SNP [dm6]	A	G	3.697e^-5	0.626	INTRON Eip63E
3L	18332348	3L_18332348_SNP [dm3] 3L_18339248_SNP [dm6]	A	G	3.704e^-5	0.626	INTERGENIC	TF binding site mE1_TFBS_cad
2L	9753242	2L_9753242_SNP [dm3] 2L_9753242_SNP [dm6]	G	A	3.784e^-5	0.626	INTERGENIC
2R	17087653	2R_17087653_SNP [dm3] 2R_21200148_SNP [dm6]	T	C	3.869e^-5	0.626	UPSTREAM Glycogenin & 1 other DOWNSTREAM Lapsyn INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_Trl

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By genomic position
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LC50 phenotype phenotype

Phenotype distribution and association to known covariates

QQplot

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GWAS results