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=1.187e^-8)
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

Covariate	χ²	p-value	Significance
In_2L_t	5.09	0.0785
In_2R_NS	4.9683	0.0834

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1954 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	8089676	2R_8089676_SNP [dm3] 2R_12202171_SNP [dm6]	A	T	1.689e^-7	0.29	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	8078685	2R_8078685_SNP [dm3] 2R_12191180_SNP [dm6]	G	A	3.090e^-7	0.29	NON_SYNONYMOUS_CODING Cyp6t3 UPSTREAM Cyp6g2
2R	8091687	2R_8091687_SNP [dm3] 2R_12204182_SNP [dm6]	A	G	6.872e^-7	0.373	INTERGENIC
2R	8072884	2R_8072884_INS [dm3] 2R_12185379_INS [dm6]	G	GAGTTACGGGTGCCTCCGTT...	7.953e^-7	0.373	UTR_3_PRIME CG13175 & 1 other UPSTREAM Cyp6g1	regulatory region REDfly_CRMs
2R	8090560	2R_8090560_SNP [dm3] 2R_12203055_SNP [dm6]	A	T	1.324e^-6	0.434	INTERGENIC
2R	8091181	2R_8091181_SNP [dm3] 2R_12203676_SNP [dm6]	A	C	1.500e^-6	0.434	INTERGENIC
2R	8090564	2R_8090564_SNP [dm3] 2R_12203059_SNP [dm6]	G	A	1.619e^-6	0.434	INTERGENIC
2R	8078684	2R_8078684_SNP [dm3] 2R_12191179_SNP [dm6]	A	G	2.165e^-6	0.484	NON_SYNONYMOUS_CODING Cyp6t3 UPSTREAM Cyp6g2
2R	8095372	2R_8095372_INS [dm3] 2R_12207867_INS [dm6]	T	TT	2.324e^-6	0.484	DOWNSTREAM CR45276 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
2R	19132875	2R_19132875_SNP [dm3] 2R_23245352_SNP [dm6]	A	G	2.634e^-6	0.492	UTR_5_PRIME yip3
2R	8078974	2R_8078974_SNP [dm3] 2R_12191469_SNP [dm6]	G	C	2.896e^-6	0.492	NON_SYNONYMOUS_CODING Cyp6t3 DOWNSTREAM CG8858
2R	8100594	2R_8100594_SNP [dm3] 2R_12213089_SNP [dm6]	G	A	3.480e^-6	0.492	UPSTREAM Sr-CII & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_da
2R	15070156	2R_15070156_SNP [dm3] 2R_19182651_SNP [dm6]	C	G	3.500e^-6	0.492	INTRON hppy
2L	7752065	2L_7752065_INS [dm3] 2L_7752065_INS [dm6]	A	AGAA	3.818e^-6	0.492	DOWNSTREAM CG7203 INTERGENIC
2L	4417004	2L_4417004_SNP [dm3] 2L_4417004_SNP [dm6]	T	G	3.933e^-6	0.492	INTRON CG15431	TF binding site mE1_TFBS_chinmo
3L	4715162	3L_4715162_SNP [dm3] 3L_4715162_SNP [dm6]	C	T	5.556e^-6	0.613	INTRON RhoGEF64C
3L	4715229	3L_4715229_SNP [dm3] 3L_4715229_SNP [dm6]	A	T	5.902e^-6	0.613	INTRON RhoGEF64C
2R	8091180	2R_8091180_SNP [dm3] 2R_12203675_SNP [dm6]	C	A	6.436e^-6	0.613	INTERGENIC
2L	3974165	2L_3974165_SNP [dm3] 2L_3974165_SNP [dm6]	C	T	6.453e^-6	0.613	INTRON fred	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	8091158	2R_8091158_SNP [dm3] 2R_12203653_SNP [dm6]	G	C	6.540e^-6	0.613	INTERGENIC
3L	8248329	3L_8248329_SNP [dm3] 3L_8255229_SNP [dm6]	G	T	7.328e^-6	0.624	INTRON Dscam4
2L	7752047	2L_7752047_SNP [dm3] 2L_7752047_SNP [dm6]	C	A	7.634e^-6	0.624	DOWNSTREAM CG7203 INTERGENIC
2L	7752033	2L_7752033_SNP [dm3] 2L_7752033_SNP [dm6]	A	G	7.656e^-6	0.624	DOWNSTREAM CG7203 INTERGENIC
X	10565810	X_10565810_SNP [dm3] X_10671777_SNP [dm6]	G	A	8.693e^-6	0.641	DOWNSTREAM CG12637 INTRON X11Lbeta
3L	18691141	3L_18691141_SNP [dm3] 3L_18698041_SNP [dm6]	A	T	8.968e^-6	0.641	INTRON Dic4
2R	10850673	2R_10850673_SNP [dm3] 2R_14963168_SNP [dm6]	A	T	9.340e^-6	0.641	UPSTREAM ckn & 1 other INTERGENIC	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_hkb mE1_TFBS_HSA mE1_TFBS_run mE1_TFBS_sens mE1_TFBS_Trl mE1_TFBS_Ubx
2R	10851502	2R_10851502_SNP [dm3] 2R_14963997_SNP [dm6]	A	G	9.496e^-6	0.641	INTRON ckn	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
3L	11317609	3L_11317609_SNP [dm3] 3L_11324509_SNP [dm6]	G	A	9.566e^-6	0.641	UPSTREAM CR44721 DOWNSTREAM CR44722 EXON CR44723	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA
X	9657929	X_9657929_SNP [dm3] X_9763896_SNP [dm6]	T	C	1.051e^-5	0.65	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_sens
2R	8098232	2R_8098232_SNP [dm3] 2R_12210727_SNP [dm6]	G	A	1.060e^-5	0.65	SYNONYMOUS_CODING Sr-CII	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
X	3329903	X_3329903_SNP [dm3] X_3435870_SNP [dm6]	G	T	1.075e^-5	0.65	UPSTREAM CG14269 INTRON CR44999 & 1 other
2R	8092269	2R_8092269_SNP [dm3] 2R_12204764_SNP [dm6]	T	A	1.152e^-5	0.667	INTERGENIC
X	944800	X_944800_SNP [dm3] X_1050767_SNP [dm6]	C	T	1.216e^-5	0.667	UPSTREAM CG14629 INTRON CR44779	TF binding site BDTNP1_TFBS_z
2R	19133250	2R_19133250_SNP [dm3] 2R_23245727_SNP [dm6]	A	T	1.324e^-5	0.667	UPSTREAM yip3 DOWNSTREAM RpL22-like INTERGENIC
2L	4339206	2L_4339206_SNP [dm3] 2L_4339206_SNP [dm6]	G	C	1.408e^-5	0.667	INTRON Atet	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_inv
3L	10125260	3L_10125260_SNP [dm3] 3L_10132160_SNP [dm6]	C	A	1.448e^-5	0.667	INTRON dpr6
2L	19062736	2L_19062736_SNP [dm3] 2L_19062736_SNP [dm6]	T	A	1.473e^-5	0.667	NON_SYNONYMOUS_CODING Phlpp UPSTREAM CG10495	TF binding site mE1_TFBS_chinmo mE1_TFBS_sens
2L	15134617	2L_15134617_SNP [dm3] 2L_15134617_SNP [dm6]	G	T	1.485e^-5	0.667	INTERGENIC
2L	4279798	2L_4279798_SNP [dm3] 2L_4279798_SNP [dm6]	A	G	1.489e^-5	0.667	UPSTREAM Art2 INTRON Art2	TF binding site BDTNP1_TFBS_dl
3L	4715234	3L_4715234_SNP [dm3] 3L_4715234_SNP [dm6]	T	C	1.528e^-5	0.667	INTRON RhoGEF64C
3L	14367854	3L_14367854_SNP [dm3] 3L_14374754_SNP [dm6]	T	C	1.529e^-5	0.667	INTERGENIC
2L	4415907	2L_4415907_SNP [dm3] 2L_4415907_SNP [dm6]	C	T	1.541e^-5	0.667	INTRON CG15431
2R	8092306	2R_8092306_SNP [dm3] 2R_12204801_SNP [dm6]	C	T	1.561e^-5	0.667	INTERGENIC
2L	8229046	2L_8229046_SNP [dm3] 2L_8229046_SNP [dm6]	T	A	1.572e^-5	0.667	INTRON Pvr
2R	8100454	2R_8100454_SNP [dm3] 2R_12212949_SNP [dm6]	G	T	1.619e^-5	0.667	UPSTREAM Sr-CII INTERGENIC
2R	10925043	2R_10925043_SNP [dm3] 2R_15037538_SNP [dm6]	T	C	1.637e^-5	0.667	SYNONYMOUS_CODING hbs
2L	19062735	2L_19062735_SNP [dm3] 2L_19062735_SNP [dm6]	G	A	1.706e^-5	0.681	NON_SYNONYMOUS_CODING Phlpp UPSTREAM CG10495	TF binding site mE1_TFBS_chinmo mE1_TFBS_sens
3L	14367875	3L_14367875_SNP [dm3] 3L_14374775_SNP [dm6]	A	C	1.792e^-5	0.7	INTERGENIC
3L	8225007	3L_8225007_SNP [dm3] 3L_8231907_SNP [dm6]	G	A	1.866e^-5	0.709	UTR_3_PRIME CG7213 DOWNSTREAM CR43953
3L	10613368	3L_10613368_SNP [dm3] 3L_10620268_SNP [dm6]	C	T	1.897e^-5	0.709	INTERGENIC
2L	7752063	2L_7752063_SNP [dm3] 2L_7752063_SNP [dm6]	A	G	1.944e^-5	0.709	DOWNSTREAM CG7203 INTERGENIC
3R	26575911	3R_26575911_DEL [dm3] 3R_30750189_DEL [dm6]	TCCTGTTT	T	1.967e^-5	0.709	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	26581271	3R_26581271_SNP [dm3] 3R_30755549_SNP [dm6]	T	A	2.009e^-5	0.711	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3L	10897475	3L_10897475_SNP [dm3] 3L_10904375_SNP [dm6]	G	A	2.054e^-5	0.713	INTERGENIC
3L	8248346	3L_8248346_SNP [dm3] 3L_8255246_SNP [dm6]	A	C	2.197e^-5	0.749	INTRON Dscam4
2L	7752077	2L_7752077_SNP [dm3] 2L_7752077_SNP [dm6]	A	T	2.264e^-5	0.756	DOWNSTREAM CG7203 INTERGENIC
2R	11518388	2R_11518388_SNP [dm3] 2R_15630883_SNP [dm6]	G	A	2.298e^-5	0.756	INTRON CG42524
3L	10780345	3L_10780345_SNP [dm3] 3L_10787245_SNP [dm6]	C	T	2.400e^-5	0.776	INTERGENIC
X	10477460	X_10477460_SNP [dm3] X_10583427_SNP [dm6]	C	A	2.572e^-5	0.811	INTRON spri	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	5499967	2L_5499967_SNP [dm3] 2L_5499967_SNP [dm6]	G	A	2.597e^-5	0.811	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	10851404	2R_10851404_SNP [dm3] 2R_14963899_SNP [dm6]	T	C	2.667e^-5	0.811	UTR_5_PRIME ckn UPSTREAM aPKC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_Trl
2L	13697175	2L_13697175_SNP [dm3] 2L_13697175_SNP [dm6]	C	A	2.682e^-5	0.811	INTRON CG31814
2L	7752072	2L_7752072_SNP [dm3] 2L_7752072_SNP [dm6]	G	T	2.747e^-5	0.815	DOWNSTREAM CG7203 INTERGENIC
2R	10925067	2R_10925067_SNP [dm3] 2R_15037562_SNP [dm6]	A	C	2.783e^-5	0.815	SYNONYMOUS_CODING hbs
3R	18990840	3R_18990840_SNP [dm3] 3R_23165118_SNP [dm6]	A	G	2.874e^-5	0.829	INTERGENIC
2R	8090749	2R_8090749_SNP [dm3] 2R_12203244_SNP [dm6]	T	A	3.073e^-5	0.873	INTERGENIC
2R	10851929	2R_10851929_SNP [dm3] 2R_14964424_SNP [dm6]	T	G	3.135e^-5	0.877	INTRON ckn	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2R	10925064	2R_10925064_SNP [dm3] 2R_15037559_SNP [dm6]	T	C	3.182e^-5	0.877	SYNONYMOUS_CODING hbs
2R	8070658	2R_8070658_SNP [dm3] 2R_12183153_SNP [dm6]	T	G	3.235e^-5	0.877	NON_SYNONYMOUS_CODING CG13175 UTR_5_PRIME CG33964 DOWNSTREAM wash & 1 other	TF binding site mE1_TFBS_sens
2R	10851839	2R_10851839_SNP [dm3] 2R_14964334_SNP [dm6]	T	A	3.311e^-5	0.877	INTRON ckn	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2R	10850663	2R_10850663_SNP [dm3] 2R_14963158_SNP [dm6]	T	C	3.320e^-5	0.877	UPSTREAM ckn & 1 other INTERGENIC	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_hkb mE1_TFBS_HSA mE1_TFBS_run mE1_TFBS_sens mE1_TFBS_Trl mE1_TFBS_Ubx
X	10477387	X_10477387_SNP [dm3] X_10583354_SNP [dm6]	C	G	3.462e^-5	0.893	INTRON spri	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	10852296	2R_10852296_SNP [dm3] 2R_14964791_SNP [dm6]	T	C	3.498e^-5	0.893	UPSTREAM ckn INTRON ckn	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
2R	8497621	2R_8497621_SNP [dm3] 2R_12610116_SNP [dm6]	C	T	3.580e^-5	0.893	INTRON Amph	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	10851471	2R_10851471_SNP [dm3] 2R_14963966_SNP [dm6]	A	C	3.694e^-5	0.893	UPSTREAM aPKC INTRON ckn	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
2R	10852011	2R_10852011_SNP [dm3] 2R_14964506_SNP [dm6]	T	C	3.762e^-5	0.893	INTRON ckn	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2R	19197363	2R_19197363_SNP [dm3] 2R_23309840_SNP [dm6]	C	A	3.827e^-5	0.893	UPSTREAM Prosbeta5R1 INTERGENIC
3L	14367753	3L_14367753_SNP [dm3] 3L_14374653_SNP [dm6]	A	G	3.827e^-5	0.893	INTERGENIC
2R	12186362	2R_12186362_SNP [dm3] 2R_16298857_SNP [dm6]	C	T	3.926e^-5	0.893	UTR_5_PRIME CG43265
X	8093828	X_8093828_SNP [dm3] X_8199795_SNP [dm6]	A	G	4.101e^-5	0.893	INTRON sdt
2L	3770009	2L_3770009_SNP [dm3] 2L_3770009_SNP [dm6]	C	T	4.239e^-5	0.893	DOWNSTREAM CG43707 EXON CR43704	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
X	2682430	X_2682430_INS [dm3] X_2788397_INS [dm6]	A	ATA	4.260e^-5	0.893	INTRON kirre & 1 other	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
2L	3869340	2L_3869340_SNP [dm3] 2L_3869340_SNP [dm6]	C	T	4.262e^-5	0.893	SYNONYMOUS_CODING Cep97 UPSTREAM Cep97
X	2291813	X_2291813_SNP [dm3] X_2397780_SNP [dm6]	T	C	4.287e^-5	0.893	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_Kr mE1_TFBS_sens
2R	10851680	2R_10851680_SNP [dm3] 2R_14964175_SNP [dm6]	G	A	4.299e^-5	0.893	INTRON ckn	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2L	955429	2L_955429_INS [dm3] 2L_955429_INS [dm6]	G	GCTTG	4.334e^-5	0.893	INTRON CG4341
3L	5518333	3L_5518333_SNP [dm3] 3L_5525233_SNP [dm6]	G	T	4.345e^-5	0.893	INTRON Lkr
X	9432629	X_9432629_SNP [dm3] X_9538596_SNP [dm6]	T	A	4.384e^-5	0.893	INTRON CG32700
2R	8061931	2R_8061931_SNP [dm3] 2R_12174426_SNP [dm6]	C	A	4.581e^-5	0.893	UPSTREAM Cct5 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_GATAe mE1_TFBS_HSA mE1_TFBS_Ubx
3R	26119050	3R_26119050_SNP [dm3] 3R_30293328_SNP [dm6]	T	G	4.588e^-5	0.893	INTRON hdc
2L	8230692	2L_8230692_SNP [dm3] 2L_8230692_SNP [dm6]	T	G	4.719e^-5	0.893	UPSTREAM Pvr INTRON Pvr
2R	7967256	2R_7967256_SNP [dm3] 2R_12079751_SNP [dm6]	G	A	4.790e^-5	0.893	UPSTREAM CG8888 INTERGENIC	TF binding site mE1_TFBS_inv
3L	14367878	3L_14367878_SNP [dm3] 3L_14374778_SNP [dm6]	A	C	4.808e^-5	0.893	INTERGENIC
3R	19923890	3R_19923890_SNP [dm3] 3R_24098168_SNP [dm6]	T	C	4.816e^-5	0.893	INTRON 4EHP
3L	14367882	3L_14367882_INS [dm3] 3L_14374782_INS [dm6]	C	CC	4.823e^-5	0.893	INTERGENIC
2L	7240000	2L_7240000_SNP [dm3] 2L_7240000_SNP [dm6]	T	C	4.886e^-5	0.893	INTRON Ndae1
2L	19087980	2L_19087980_SNP [dm3] 2L_19087980_SNP [dm6]	T	C	4.953e^-5	0.893	INTRON Lim3
2R	9511846	2R_9511846_INS [dm3] 2R_13624341_INS [dm6]	A	ACCTAGATATGAAAA...	5.015e^-5	0.893	INTRON fas	TF binding site mE1_TFBS_HSA
X	13372549	X_13372549_SNP [dm3] X_13478516_SNP [dm6]	G	A	5.134e^-5	0.893	INTRON Neto
2L	8229054	2L_8229054_SNP [dm3] 2L_8229054_SNP [dm6]	A	G	5.221e^-5	0.893	INTRON Pvr

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By genomic position
Variant impact
Gene name

mn_Surv_Azinpho_0_5 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results