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=1.470e^-13)
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_3R_P	0.01003

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_3R_P	5.1202	0.0773

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1917 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	8124467	2R_8124467_SNP [dm3] 2R_12236962_SNP [dm6]	A	G	1.885e^-6	0.808	INTERGENIC	TF binding site mE1_TFBS_HSA
2R	8124481	2R_8124481_SNP [dm3] 2R_12236976_SNP [dm6]	T	G	2.979e^-6	0.808	INTERGENIC	TF binding site mE1_TFBS_HSA
X	2707113	X_2707113_SNP [dm3] X_2813080_SNP [dm6]	A	G	3.510e^-6	0.808	INTRON kirre
3L	18109144	3L_18109144_SNP [dm3] 3L_18116044_SNP [dm6]	C	G	3.664e^-6	0.808	UTR_3_PRIME CG32195 DOWNSTREAM CG32195 INTRON CG7341
X	2266612	X_2266612_SNP [dm3] X_2372579_SNP [dm6]	A	T	4.170e^-6	0.808	UTR_3_PRIME PsGEF INTRON PsGEF	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	8124488	2R_8124488_SNP [dm3] 2R_12236983_SNP [dm6]	T	A	4.731e^-6	0.808	INTERGENIC	TF binding site mE1_TFBS_HSA
2L	660395	2L_660395_SNP [dm3] 2L_660395_SNP [dm6]	C	A	5.784e^-6	0.808	INTRON ds	TF binding site BDTNP1_TFBS_prd mE1_TFBS_HSA
3R	20115134	3R_20115134_SNP [dm3] 3R_24289412_SNP [dm6]	A	C	6.066e^-6	0.808	UPSTREAM CG6364 DOWNSTREAM CG6356 INTRON CG34290	TF binding site mE1_TFBS_HSA
X	5367856	X_5367856_SNP [dm3] X_5473823_SNP [dm6]	A	T	6.304e^-6	0.808	INTRON SPR
2R	8124473	2R_8124473_SNP [dm3] 2R_12236968_SNP [dm6]	A	C	6.482e^-6	0.808	INTERGENIC	TF binding site mE1_TFBS_HSA
2R	8124497	2R_8124497_SNP [dm3] 2R_12236992_SNP [dm6]	G	T	7.897e^-6	0.808	INTERGENIC	TF binding site mE1_TFBS_HSA
3L	18112024	3L_18112024_SNP [dm3] 3L_18118924_SNP [dm6]	C	G	7.905e^-6	0.808	UTR_3_PRIME CG32195 INTRON CG7341	TF binding site mE1_TFBS_cad
3L	18112023	3L_18112023_SNP [dm3] 3L_18118923_SNP [dm6]	G	A	8.707e^-6	0.808	UTR_3_PRIME CG32195 INTRON CG7341	TF binding site mE1_TFBS_cad
2R	8124458	2R_8124458_SNP [dm3] 2R_12236953_SNP [dm6]	T	C	8.811e^-6	0.808	INTERGENIC	TF binding site mE1_TFBS_HSA
2R	16665456	2R_16665456_SNP [dm3] 2R_20777951_SNP [dm6]	C	A	8.917e^-6	0.808	UPSTREAM CG43710 DOWNSTREAM CG43711 INTERGENIC
3R	9195632	3R_9195632_SNP [dm3] 3R_13369910_SNP [dm6]	T	C	9.032e^-6	0.808	DOWNSTREAM Dic1 & 1 other INTRON CheA87a
3R	6385465	3R_6385465_SNP [dm3] 3R_10559743_SNP [dm6]	A	G	9.080e^-6	0.808	INTRON hth
2R	8124472	2R_8124472_SNP [dm3] 2R_12236967_SNP [dm6]	A	G	9.226e^-6	0.808	INTERGENIC	TF binding site mE1_TFBS_HSA
X	5367861	X_5367861_SNP [dm3] X_5473828_SNP [dm6]	C	T	9.532e^-6	0.808	INTRON SPR
2R	11784257	2R_11784257_SNP [dm3] 2R_15896752_SNP [dm6]	T	C	9.701e^-6	0.808	UPSTREAM CG33463 INTRON sli	TF binding site mE1_TFBS_cad
X	2266611	X_2266611_SNP [dm3] X_2372578_SNP [dm6]	A	T	9.740e^-6	0.808	UTR_3_PRIME PsGEF INTRON PsGEF	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	9195636	3R_9195636_SNP [dm3] 3R_13369914_SNP [dm6]	A	T	1.017e^-5	0.808	DOWNSTREAM Dic1 & 1 other INTRON CheA87a
2R	8124487	2R_8124487_SNP [dm3] 2R_12236982_SNP [dm6]	G	A	1.044e^-5	0.808	INTERGENIC	TF binding site mE1_TFBS_HSA
3L	18109193	3L_18109193_DEL [dm3] 3L_18116093_DEL [dm6]	AA	A	1.110e^-5	0.808	UTR_3_PRIME CG32195 DOWNSTREAM CG32195 INTRON CG7341
2R	10319981	2R_10319981_SNP [dm3] 2R_14432476_SNP [dm6]	A	G	1.120e^-5	0.808	UPSTREAM phyl DOWNSTREAM CR45277 INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_HSA
3R	22790433	3R_22790433_SNP [dm3] 3R_26964711_SNP [dm6]	A	T	1.138e^-5	0.808	UTR_5_PRIME Tsp97E DOWNSTREAM Gr97a	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_h mE1_TFBS_HSA
2R	8119607	2R_8119607_SNP [dm3] 2R_12232102_SNP [dm6]	T	C	1.211e^-5	0.808	INTERGENIC
2R	8117968	2R_8117968_SNP [dm3] 2R_12230463_SNP [dm6]	G	A	1.337e^-5	0.808	INTERGENIC	TF binding site BDTNP1_TFBS_da
3L	16241835	3L_16241835_SNP [dm3] 3L_16248735_SNP [dm6]	C	T	1.401e^-5	0.808	DOWNSTREAM CG13055 INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	16241933	3L_16241933_SNP [dm3] 3L_16248833_SNP [dm6]	C	T	1.443e^-5	0.808	DOWNSTREAM CG13055 INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
X	5367855	X_5367855_SNP [dm3] X_5473822_SNP [dm6]	A	G	1.447e^-5	0.808	INTRON SPR
2R	8118979	2R_8118979_SNP [dm3] 2R_12231474_SNP [dm6]	C	T	1.473e^-5	0.808	INTERGENIC
3L	13922660	3L_13922660_SNP [dm3] 3L_13929560_SNP [dm6]	A	G	1.516e^-5	0.808	UPSTREAM CG8833 INTRON Gl	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_HSA mE1_TFBS_zfh1
X	5850545	X_5850545_SNP [dm3] X_5956512_SNP [dm6]	C	G	1.666e^-5	0.808	INTRON CG6067
2R	8117922	2R_8117922_SNP [dm3] 2R_12230417_SNP [dm6]	A	C	1.683e^-5	0.808	INTERGENIC	TF binding site BDTNP1_TFBS_da
3R	15623343	3R_15623343_SNP [dm3] 3R_19797621_SNP [dm6]	A	C	1.690e^-5	0.808	INTRON bnl	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv
3L	18109147	3L_18109147_SNP [dm3] 3L_18116047_SNP [dm6]	A	C	1.814e^-5	0.808	UTR_3_PRIME CG32195 DOWNSTREAM CG32195 INTRON CG7341
2R	8120391	2R_8120391_SNP [dm3] 2R_12232886_SNP [dm6]	A	T	1.877e^-5	0.808	INTERGENIC
2R	8113708	2R_8113708_SNP [dm3] 2R_12226203_SNP [dm6]	G	T	1.914e^-5	0.808	SYNONYMOUS_CODING CG8854	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2R	8117938	2R_8117938_SNP [dm3] 2R_12230433_SNP [dm6]	A	C	1.980e^-5	0.808	INTERGENIC	TF binding site BDTNP1_TFBS_da
X	6260049	X_6260049_SNP [dm3] X_6366016_SNP [dm6]	A	G	2.008e^-5	0.808	START_GAINED Marf UTR_5_PRIME Marf UPSTREAM swa	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Ubx
2R	7838913	2R_7838913_SNP [dm3] 2R_11951408_SNP [dm6]	A	C	2.009e^-5	0.808	INTRON CG13188
3R	20115145	3R_20115145_SNP [dm3] 3R_24289423_SNP [dm6]	G	A	2.072e^-5	0.808	UPSTREAM CG6364 DOWNSTREAM CG6356 INTRON CG34290	TF binding site mE1_TFBS_HSA
2R	8112997	2R_8112997_SNP [dm3] 2R_12225492_SNP [dm6]	C	G	2.099e^-5	0.808	INTRON CG8854
2R	8669459	2R_8669459_SNP [dm3] 2R_12781954_SNP [dm6]	T	G	2.179e^-5	0.808	INTRON sca	TF binding site BDTNP1_TFBS_dl
2R	8117959	2R_8117959_SNP [dm3] 2R_12230454_SNP [dm6]	C	T	2.179e^-5	0.808	INTERGENIC	TF binding site BDTNP1_TFBS_da
2R	8117970	2R_8117970_DEL [dm3] 2R_12230465_DEL [dm6]	TAGTAT	T	2.179e^-5	0.808	INTERGENIC	TF binding site BDTNP1_TFBS_da
2R	8124504	2R_8124504_SNP [dm3] 2R_12236999_SNP [dm6]	A	T	2.222e^-5	0.808	INTERGENIC	TF binding site mE1_TFBS_HSA
3L	12931658	3L_12931658_INS [dm3] 3L_12938558_INS [dm6]	A	ACTT	2.240e^-5	0.808	INTERGENIC
3L	18109155	3L_18109155_SNP [dm3] 3L_18116055_SNP [dm6]	T	A	2.273e^-5	0.808	UTR_3_PRIME CG32195 DOWNSTREAM CG32195 INTRON CG7341
2R	8117934	2R_8117934_DEL [dm3] 2R_12230429_DEL [dm6]	TTA	T	2.281e^-5	0.808	INTERGENIC	TF binding site BDTNP1_TFBS_da
2R	8117950	2R_8117950_INS [dm3] 2R_12230445_INS [dm6]	T	TTCT	2.281e^-5	0.808	INTERGENIC	TF binding site BDTNP1_TFBS_da
3R	24131873	3R_24131873_SNP [dm3] 3R_28306151_SNP [dm6]	T	C	2.329e^-5	0.808	INTERGENIC
2R	8117958	2R_8117958_SNP [dm3] 2R_12230453_SNP [dm6]	C	A	2.395e^-5	0.808	INTERGENIC	TF binding site BDTNP1_TFBS_da
X	5710688	X_5710688_SNP [dm3] X_5816655_SNP [dm6]	T	C	2.478e^-5	0.808	UPSTREAM CG15766 INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2R	8118689	2R_8118689_DEL [dm3] 2R_12231184_DEL [dm6]	ACTATGTATCCTAAAGATAT...	A	2.583e^-5	0.808	INTERGENIC	TF binding site BDTNP1_TFBS_da
2L	4895154	2L_4895154_SNP [dm3] 2L_4895154_SNP [dm6]	A	C	2.663e^-5	0.808	INTRON CG3036
3L	18093070	3L_18093070_SNP [dm3] 3L_18099970_SNP [dm6]	C	T	2.793e^-5	0.808	INTRON CG13698
2R	8112985	2R_8112985_SNP [dm3] 2R_12225480_SNP [dm6]	G	T	2.832e^-5	0.808	INTRON CG8854
2R	8117933	2R_8117933_SNP [dm3] 2R_12230428_SNP [dm6]	C	A	2.925e^-5	0.808	INTERGENIC	TF binding site BDTNP1_TFBS_da
2R	11708952	2R_11708952_SNP [dm3] 2R_15821447_SNP [dm6]	T	C	2.941e^-5	0.808	UPSTREAM CG33465 INTRON tun	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA
X	14411994	X_14411994_SNP [dm3] X_14517961_SNP [dm6]	G	T	3.021e^-5	0.808	INTRON CR44110	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2L	3832062	2L_3832062_SNP [dm3] 2L_3832062_SNP [dm6]	T	A	3.079e^-5	0.808	INTERGENIC	regulatory region REDfly_CRMs silencer mE1_HDAC_PRE
3L	16240056	3L_16240056_SNP [dm3] 3L_16246956_SNP [dm6]	G	A	3.092e^-5	0.808	INTERGENIC
2R	8117930	2R_8117930_SNP [dm3] 2R_12230425_SNP [dm6]	C	G	3.098e^-5	0.808	INTERGENIC	TF binding site BDTNP1_TFBS_da
3L	1321254	3L_1321254_SNP [dm3] 3L_1321254_SNP [dm6]	G	A	3.125e^-5	0.808	DOWNSTREAM CG9184 INTRON Myo61F
3L	14237250	3L_14237250_SNP [dm3] 3L_14244150_SNP [dm6]	G	A	3.127e^-5	0.808	DOWNSTREAM CR44561 INTERGENIC
3R	26544416	3R_26544416_SNP [dm3] 3R_30718694_SNP [dm6]	G	A	3.213e^-5	0.808	INTERGENIC	TF binding site BDTNP1_TFBS_da
2R	11708755	2R_11708755_DEL [dm3] 2R_15821250_DEL [dm6]	AT	A	3.257e^-5	0.808	UPSTREAM CG33465 INTRON tun	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA
3L	20530667	3L_20530667_DEL [dm3] 3L_20537567_DEL [dm6]	TAT	T	3.305e^-5	0.808	INTRON Rcd2
2R	8118725	2R_8118725_SNP [dm3] 2R_12231220_SNP [dm6]	A	T	3.432e^-5	0.808	INTERGENIC
2R	8117929	2R_8117929_SNP [dm3] 2R_12230424_SNP [dm6]	G	T	3.443e^-5	0.808	INTERGENIC	TF binding site BDTNP1_TFBS_da
3L	21917558	3L_21917558_SNP [dm3] 3L_21924458_SNP [dm6]	T	G	3.471e^-5	0.808	DOWNSTREAM mub INTRON mub
3R	22790443	3R_22790443_SNP [dm3] 3R_26964721_SNP [dm6]	A	C	3.526e^-5	0.808	UTR_5_PRIME Tsp97E DOWNSTREAM Gr97a	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_h mE1_TFBS_HSA
2R	10319990	2R_10319990_SNP [dm3] 2R_14432485_SNP [dm6]	A	G	3.582e^-5	0.808	UPSTREAM phyl DOWNSTREAM CR45277 INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_HSA
2R	8120283	2R_8120283_SNP [dm3] 2R_12232778_SNP [dm6]	A	G	3.584e^-5	0.808	INTERGENIC
2R	8117948	2R_8117948_SNP [dm3] 2R_12230443_SNP [dm6]	A	T	3.633e^-5	0.808	INTERGENIC	TF binding site BDTNP1_TFBS_da
2R	8119562	2R_8119562_SNP [dm3] 2R_12232057_SNP [dm6]	A	T	3.646e^-5	0.808	INTERGENIC
3L	18109159	3L_18109159_SNP [dm3] 3L_18116059_SNP [dm6]	G	A	3.673e^-5	0.808	UTR_3_PRIME CG32195 DOWNSTREAM CG32195 INTRON CG7341
2R	18455306	2R_18455306_SNP [dm3] 2R_22567801_SNP [dm6]	T	G	3.679e^-5	0.808	INTRON dnr1
3R	20113116	3R_20113116_SNP [dm3] 3R_24287394_SNP [dm6]	G	T	3.742e^-5	0.808	INTRON CG6356
3R	20115133	3R_20115133_SNP [dm3] 3R_24289411_SNP [dm6]	A	G	3.762e^-5	0.808	UPSTREAM CG6364 DOWNSTREAM CG6356 INTRON CG34290	TF binding site mE1_TFBS_HSA
2R	8117308	2R_8117308_SNP [dm3] 2R_12229803_SNP [dm6]	G	A	3.779e^-5	0.808	UPSTREAM CG8854 INTERGENIC
3L	11338090	3L_11338090_SNP [dm3] 3L_11344990_SNP [dm6]	T	C	3.839e^-5	0.808	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	4118965	2R_4118965_SNP [dm3] 2R_8231460_SNP [dm6]	G	T	3.860e^-5	0.808	DOWNSTREAM CR44275 INTRON dpn	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_z mE1_TFBS_HSA
2R	8118777	2R_8118777_SNP [dm3] 2R_12231272_SNP [dm6]	C	G	3.939e^-5	0.808	INTERGENIC
3R	23976735	3R_23976735_SNP [dm3] 3R_28151013_SNP [dm6]	T	G	3.980e^-5	0.808	INTRON CG34354	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	16792158	3R_16792158_SNP [dm3] 3R_20966436_SNP [dm6]	C	T	3.992e^-5	0.808	SYNONYMOUS_CODING Atpalpha
3L	1592404	3L_1592404_SNP [dm3] 3L_1592404_SNP [dm6]	G	A	4.038e^-5	0.808	INTRON CG13917	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_Trl
2R	11708754	2R_11708754_SNP [dm3] 2R_15821249_SNP [dm6]	A	T	4.100e^-5	0.808	UPSTREAM CG33465 INTRON tun	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA
3L	8571637	3L_8571637_SNP [dm3] 3L_8578537_SNP [dm6]	C	T	4.141e^-5	0.808	START_GAINED CG43078 UTR_5_PRIME CG43078 UPSTREAM CG43078
2R	8117977	2R_8117977_MNP [dm3] 2R_12230472_MNP [dm6]	TATA	CCGG	4.188e^-5	0.808	INTERGENIC	TF binding site BDTNP1_TFBS_da
3R	14938112	3R_14938112_SNP [dm3] 3R_19112390_SNP [dm6]	A	G	4.202e^-5	0.808	INTRON CG6040
3L	8262377	3L_8262377_SNP [dm3] 3L_8269277_SNP [dm6]	C	G	4.216e^-5	0.808	INTRON Dscam4
2R	3079375	2R_3079375_SNP [dm3] 2R_7191870_SNP [dm6]	T	C	4.346e^-5	0.808	INTRON pk	TF binding site BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	8117987	2R_8117987_SNP [dm3] 2R_12230482_SNP [dm6]	T	G	4.426e^-5	0.808	INTERGENIC	TF binding site BDTNP1_TFBS_da
2L	7302446	2L_7302446_SNP [dm3] 2L_7302446_SNP [dm6]	T	C	4.441e^-5	0.808	INTERGENIC	regulatory region REDfly_CRMs TF binding site mE1_TFBS_cad
3R	24537389	3R_24537389_SNP [dm3] 3R_28711667_SNP [dm6]	C	A	4.454e^-5	0.808	INTRON htt
2R	8119392	2R_8119392_SNP [dm3] 2R_12231887_SNP [dm6]	T	G	4.457e^-5	0.808	INTERGENIC
3R	17040003	3R_17040003_INS [dm3] 3R_21214281_INS [dm6]	A	AGA	4.531e^-5	0.808	UPSTREAM CG5862 DOWNSTREAM SNF4Agamma INTERGENIC	TF binding site BDTNP1_TFBS_dl

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By genomic position
Variant impact
Gene name

Surv_AAmanitin_2ug phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results