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=4.144e^-1)
Null hypothesis is not rejected (p>0.05).
Interpretation: 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
wolba	3.2769	0.0703

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1764 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	12653734	X_12653734_SNP [dm3] X_12759701_SNP [dm6]	T	A	9.185e^-7	0.487	DOWNSTREAM CG12717 INTRON ade5	TF binding site mE1_TFBS_inv
2R	18726393	2R_18726393_SNP [dm3] 2R_22838870_SNP [dm6]	T	C	1.195e^-6	0.487	SYNONYMOUS_CODING CG9825	TF binding site mE1_TFBS_cad mE1_TFBS_sens
3L	11508784	3L_11508784_SNP [dm3] 3L_11515684_SNP [dm6]	C	A	1.364e^-6	0.487	INTRON CG7512
3L	11508520	3L_11508520_SNP [dm3] 3L_11515420_SNP [dm6]	T	C	1.483e^-6	0.487	INTRON CG7512
3L	5231686	3L_5231686_DEL [dm3] 3L_5238586_DEL [dm6]	GCC	G	1.817e^-6	0.487	INTRON shep
3L	5231689	3L_5231689_DEL [dm3] 3L_5238589_DEL [dm6]	GTAAAAATGCGA...	G	1.817e^-6	0.487	INTRON shep
3L	5231716	3L_5231716_SNP [dm3] 3L_5238616_SNP [dm6]	G	T	2.099e^-6	0.487	INTRON shep
3L	5231642	3L_5231642_DEL [dm3] 3L_5238542_DEL [dm6]	TGGCG	T	2.412e^-6	0.487	INTRON shep
3L	5231662	3L_5231662_SNP [dm3] 3L_5238562_SNP [dm6]	T	C	2.412e^-6	0.487	INTRON shep
2R	18726642	2R_18726642_SNP [dm3] 2R_22839119_SNP [dm6]	T	C	2.599e^-6	0.487	SYNONYMOUS_CODING CG9825
2L	14639412	2L_14639412_SNP [dm3] 2L_14639412_SNP [dm6]	G	A	2.987e^-6	0.493	INTRON osp
2R	16931871	2R_16931871_SNP [dm3] 2R_21044366_SNP [dm6]	T	C	3.219e^-6	0.493	INTERGENIC
X	11754215	X_11754215_SNP [dm3] X_11860182_SNP [dm6]	C	T	3.798e^-6	0.493	INTRON ATP7	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	5231602	3L_5231602_DEL [dm3] 3L_5238502_DEL [dm6]	GGACTCAATACAATCCTGTA...	G	3.991e^-6	0.493	INTRON shep
3L	5231661	3L_5231661_SNP [dm3] 3L_5238561_SNP [dm6]	C	T	4.019e^-6	0.493	INTRON shep
3L	11509003	3L_11509003_SNP [dm3] 3L_11515903_SNP [dm6]	A	C	4.447e^-6	0.493	INTRON CG7512
3L	5231715	3L_5231715_SNP [dm3] 3L_5238615_SNP [dm6]	A	G	4.694e^-6	0.493	INTRON shep
3L	5231649	3L_5231649_SNP [dm3] 3L_5238549_SNP [dm6]	C	A	4.731e^-6	0.493	INTRON shep
3R	13891963	3R_13891963_SNP [dm3] 3R_18066241_SNP [dm6]	G	A	5.526e^-6	0.545	INTERGENIC
3L	11102990	3L_11102990_SNP [dm3] 3L_11109890_SNP [dm6]	G	A	6.195e^-6	0.551	UPSTREAM CG34012 INTRON CG7638	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	11508999	3L_11508999_SNP [dm3] 3L_11515899_SNP [dm6]	C	G	6.321e^-6	0.551	INTRON CG7512
2R	7645025	2R_7645025_SNP [dm3] 2R_11757520_SNP [dm6]	A	T	6.469e^-6	0.551	UTR_5_PRIME ths
3L	5231719	3L_5231719_INS [dm3] 3L_5238619_INS [dm6]	T	TATAATAGATAA...	6.800e^-6	0.554	INTRON shep
2L	1523356	2L_1523356_SNP [dm3] 2L_1523356_SNP [dm6]	C	A	7.504e^-6	0.579	SYNONYMOUS_CODING Or22b
3L	5231732	3L_5231732_DEL [dm3] 3L_5238632_DEL [dm6]	GAG	G	7.729e^-6	0.579	INTRON shep
2R	18726395	2R_18726395_SNP [dm3] 2R_22838872_SNP [dm6]	A	G	8.386e^-6	0.605	SYNONYMOUS_CODING CG9825	TF binding site mE1_TFBS_cad mE1_TFBS_sens
3L	5231825	3L_5231825_SNP [dm3] 3L_5238725_SNP [dm6]	A	C	8.901e^-6	0.618	INTRON shep
3L	5231770	3L_5231770_SNP [dm3] 3L_5238670_SNP [dm6]	T	A	9.446e^-6	0.632	INTRON shep
3R	25795369	3R_25795369_SNP [dm3] 3R_29969647_SNP [dm6]	T	A	9.850e^-6	0.637	UPSTREAM TkR99D INTERGENIC
3L	5231849	3L_5231849_SNP [dm3] 3L_5238749_SNP [dm6]	C	A	1.075e^-5	0.654	INTRON shep
3L	19497550	3L_19497550_SNP [dm3] 3L_19504450_SNP [dm6]	G	A	1.135e^-5	0.654	UPSTREAM CG9452 DOWNSTREAM CR45731 INTERGENIC
3L	2363986	3L_2363986_INS [dm3] 3L_2363986_INS [dm6]	G	GG	1.148e^-5	0.654	INTERGENIC
2L	4227607	2L_4227607_SNP [dm3] 2L_4227607_SNP [dm6]	G	T	1.170e^-5	0.654	UPSTREAM RpL40 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_Kr
3L	5231821	3L_5231821_SNP [dm3] 3L_5238721_SNP [dm6]	G	T	1.186e^-5	0.654	INTRON shep
2R	16875344	2R_16875344_SNP [dm3] 2R_20987839_SNP [dm6]	T	C	1.327e^-5	0.663	SYNONYMOUS_CODING CG3216	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	11508979	3L_11508979_SNP [dm3] 3L_11515879_SNP [dm6]	G	A	1.338e^-5	0.663	INTRON CG7512
3L	5231718	3L_5231718_SNP [dm3] 3L_5238618_SNP [dm6]	C	A	1.358e^-5	0.663	INTRON shep
2R	16987557	2R_16987557_SNP [dm3] 2R_21100052_SNP [dm6]	G	A	1.367e^-5	0.663	SYNONYMOUS_CODING CG34396 INTRON CG34396	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_inv
3L	11102992	3L_11102992_SNP [dm3] 3L_11109892_SNP [dm6]	C	T	1.379e^-5	0.663	UPSTREAM CG34012 INTRON CG7638	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	2626348	3L_2626348_SNP [dm3] 3L_2626348_SNP [dm6]	A	T	1.504e^-5	0.705	INTRON Pxn
3L	16326022	3L_16326022_SNP [dm3] 3L_16332922_SNP [dm6]	C	T	1.648e^-5	0.737	UPSTREAM CG13056 DOWNSTREAM retinin INTERGENIC
2L	284303	2L_284303_SNP [dm3] 2L_284303_SNP [dm6]	T	C	1.655e^-5	0.737	INTRON CG3625	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	3795336	3L_3795336_SNP [dm3] 3L_3795336_SNP [dm6]	A	G	1.843e^-5	0.737	UPSTREAM CG32264 INTRON CG32264
2R	16985709	2R_16985709_SNP [dm3] 2R_21098204_SNP [dm6]	C	A	1.865e^-5	0.737	SYNONYMOUS_CODING CG34396 UPSTREAM CG4038 INTRON CG34396	TF binding site BDTNP1_TFBS_dl mE1_TFBS_chinmo mE1_TFBS_HSA
3R	21827449	3R_21827449_SNP [dm3] 3R_26001727_SNP [dm6]	G	A	1.907e^-5	0.737	DOWNSTREAM E_spl_mgamma-HLH INTRON CR45037	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_HSA
3R	21833740	3R_21833740_SNP [dm3] 3R_26008018_SNP [dm6]	C	A	1.923e^-5	0.737	UPSTREAM CR45039 INTERGENIC	TF binding site BDTNP1_TFBS_dl
2R	16875177	2R_16875177_SNP [dm3] 2R_20987672_SNP [dm6]	A	G	2.005e^-5	0.737	INTRON CG3216	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2R	7645014	2R_7645014_SNP [dm3] 2R_11757509_SNP [dm6]	C	T	2.028e^-5	0.737	UTR_5_PRIME ths
3L	5231658	3L_5231658_SNP [dm3] 3L_5238558_SNP [dm6]	T	A	2.028e^-5	0.737	INTRON shep
2R	12392100	2R_12392100_SNP [dm3] 2R_16504595_SNP [dm6]	T	C	2.043e^-5	0.737	INTRON Sema-2a
X	6807221	X_6807221_INS [dm3] X_6913188_INS [dm6]	C	CTACCATACACACAC...	2.057e^-5	0.737	INTRON CG14431
2R	5228425	2R_5228425_SNP [dm3] 2R_9340920_SNP [dm6]	A	G	2.085e^-5	0.737	INTRON CG13954 & 1 other
3R	24545175	3R_24545175_SNP [dm3] 3R_28719453_SNP [dm6]	C	T	2.105e^-5	0.737	INTRON htt	TF binding site mE1_TFBS_chinmo
2R	16875166	2R_16875166_SNP [dm3] 2R_20987661_SNP [dm6]	G	A	2.209e^-5	0.737	SYNONYMOUS_CODING CG3216	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3L	5231807	3L_5231807_DEL [dm3] 3L_5238707_DEL [dm6]	TT	T	2.217e^-5	0.737	INTRON shep
2L	11621793	2L_11621793_SNP [dm3] 2L_11621793_SNP [dm6]	T	C	2.231e^-5	0.737	UTR_5_PRIME kek2
3R	21236940	3R_21236940_SNP [dm3] 3R_25411218_SNP [dm6]	C	T	2.258e^-5	0.737	INTRON Fur1
X	19501643	X_19501643_SNP [dm3] X_19607610_SNP [dm6]	A	T	2.312e^-5	0.737	INTRON CG14207	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cnc mE1_TFBS_Trl
2L	3720667	2L_3720667_SNP [dm3] 2L_3720667_SNP [dm6]	T	C	2.321e^-5	0.737	UPSTREAM Shaw INTRON Shaw
3L	11102967	3L_11102967_SNP [dm3] 3L_11109867_SNP [dm6]	T	C	2.463e^-5	0.749	UPSTREAM CG34012 INTRON CG7638	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	1838116	2L_1838116_SNP [dm3] 2L_1838116_SNP [dm6]	T	C	2.482e^-5	0.749	INTRON wry
2R	6735376	2R_6735376_SNP [dm3] 2R_10847871_SNP [dm6]	A	G	2.483e^-5	0.749	INTRON CG30015
2L	10208160	2L_10208160_SNP [dm3] 2L_10208160_SNP [dm6]	A	G	2.516e^-5	0.749	SYNONYMOUS_CODING CG5731 UPSTREAM CR44845	TF binding site BDTNP1_TFBS_dl
3R	25795346	3R_25795346_SNP [dm3] 3R_29969624_SNP [dm6]	T	C	2.679e^-5	0.777	UPSTREAM TkR99D INTERGENIC
2R	6735422	2R_6735422_SNP [dm3] 2R_10847917_SNP [dm6]	T	C	2.720e^-5	0.777	INTRON CG30015
3L	12770248	3L_12770248_SNP [dm3] 3L_12777148_SNP [dm6]	G	A	2.748e^-5	0.777	NON_SYNONYMOUS_CODING CG32106	TF binding site mE1_TFBS_sens
2R	12577434	2R_12577434_INS [dm3] 2R_16689929_INS [dm6]	C	CC	2.779e^-5	0.777	INTRON CG30463
3L	11102966	3L_11102966_SNP [dm3] 3L_11109866_SNP [dm6]	C	G	2.828e^-5	0.78	UPSTREAM CG34012 INTRON CG7638	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	11102687	3L_11102687_SNP [dm3] 3L_11109587_SNP [dm6]	T	C	2.927e^-5	0.79	UPSTREAM CG7638 & 1 other DOWNSTREAM CG12522 INTERGENIC	TF binding site BDTNP1_TFBS_dl
X	13872525	X_13872525_SNP [dm3] X_13978492_SNP [dm6]	T	A	2.966e^-5	0.79	INTRON mamo
3R	21236935	3R_21236935_SNP [dm3] 3R_25411213_SNP [dm6]	T	A	2.991e^-5	0.79	INTRON Fur1
2R	12315660	2R_12315660_SNP [dm3] 2R_16428155_SNP [dm6]	A	T	3.340e^-5	0.866	INTRON Sema-2b
2R	5228436	2R_5228436_SNP [dm3] 2R_9340931_SNP [dm6]	C	T	3.411e^-5	0.866	INTRON CG13954 & 1 other
2L	10208159	2L_10208159_SNP [dm3] 2L_10208159_SNP [dm6]	G	T	3.446e^-5	0.866	SYNONYMOUS_CODING CG5731 UPSTREAM CR44845	TF binding site BDTNP1_TFBS_dl
3L	20929326	3L_20929326_SNP [dm3] 3L_20936226_SNP [dm6]	G	A	3.464e^-5	0.866	INTRON fng
2L	5239391	2L_5239391_SNP [dm3] 2L_5239391_SNP [dm6]	A	T	3.523e^-5	0.869	INTRON tkv	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_Stat92E mE1_TFBS_Trl
2L	4227613	2L_4227613_SNP [dm3] 2L_4227613_SNP [dm6]	G	A	3.636e^-5	0.872	UPSTREAM RpL40 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_Kr
2R	1299839	2R_1299839_SNP [dm3] 2R_5412334_SNP [dm6]	C	A	3.740e^-5	0.872	INTERGENIC	transposable element FlyBase
3L	16424073	3L_16424073_SNP [dm3] 3L_16430973_SNP [dm6]	T	C	3.760e^-5	0.872	INTRON CG33158 & 1 other
3L	16424074	3L_16424074_SNP [dm3] 3L_16430974_SNP [dm6]	C	A	3.760e^-5	0.872	INTRON CG33158 & 1 other
3R	21236936	3R_21236936_SNP [dm3] 3R_25411214_SNP [dm6]	A	G	3.784e^-5	0.872	INTRON Fur1
3L	6699658	3L_6699658_SNP [dm3] 3L_6706558_SNP [dm6]	C	T	3.813e^-5	0.872	INTRON CG8519
3L	11102685	3L_11102685_SNP [dm3] 3L_11109585_SNP [dm6]	A	T	3.956e^-5	0.891	UPSTREAM CG7638 & 1 other DOWNSTREAM CG12522 INTERGENIC	TF binding site BDTNP1_TFBS_dl
X	6557334	X_6557334_SNP [dm3] X_6663301_SNP [dm6]	A	T	3.994e^-5	0.891	INTRON Ctr1A	TF binding site BDTNP1_TFBS_dl
3L	2855550	3L_2855550_SNP [dm3] 3L_2855550_SNP [dm6]	A	G	4.110e^-5	0.894	INTRON CG43444	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	13843155	2R_13843155_SNP [dm3] 2R_17955650_SNP [dm6]	C	T	4.148e^-5	0.894	NON_SYNONYMOUS_CODING PpY-55A DOWNSTREAM CR44418
2L	1523293	2L_1523293_SNP [dm3] 2L_1523293_SNP [dm6]	C	T	4.150e^-5	0.894	SYNONYMOUS_CODING Or22b
3L	11367891	3L_11367891_SNP [dm3] 3L_11374791_SNP [dm6]	T	A	4.437e^-5	0.907	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_HSA
3L	624758	3L_624758_SNP [dm3] 3L_624758_SNP [dm6]	C	T	4.499e^-5	0.907	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
2L	11826647	2L_11826647_SNP [dm3] 2L_11826647_SNP [dm6]	A	G	4.546e^-5	0.907	DOWNSTREAM esc INTRON Pde1c
3R	21236795	3R_21236795_SNP [dm3] 3R_25411073_SNP [dm6]	G	A	4.572e^-5	0.907	INTRON Fur1
3R	6561940	3R_6561940_SNP [dm3] 3R_10736218_SNP [dm6]	T	C	4.609e^-5	0.907	UPSTREAM tomboy20 INTERGENIC
2L	2287718	2L_2287718_SNP [dm3] 2L_2287718_SNP [dm6]	A	T	4.619e^-5	0.907	SYNONYMOUS_CODING CG42658 UPSTREAM CG31681 DOWNSTREAM CG17237
2R	7647473	2R_7647473_SNP [dm3] 2R_11759968_SNP [dm6]	C	A	4.669e^-5	0.907	INTRON ths
2L	14977708	2L_14977708_SNP [dm3] 2L_14977708_SNP [dm6]	A	T	4.691e^-5	0.907	INTRON mol
2R	13339191	2R_13339191_SNP [dm3] 2R_17451686_SNP [dm6]	A	G	4.700e^-5	0.907	UPSTREAM mthl3 INTRON mthl3	transposable element FlyBase
X	19506217	X_19506217_SNP [dm3] X_19612184_SNP [dm6]	G	C	4.704e^-5	0.907	SYNONYMOUS_CODING Tyler UTR_5_PRIME Shawn DOWNSTREAM CG14207	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	5283119	3L_5283119_SNP [dm3] 3L_5290019_SNP [dm6]	C	G	4.743e^-5	0.907	INTERGENIC
3L	16542828	3L_16542828_SNP [dm3] 3L_16549728_SNP [dm6]	C	A	4.807e^-5	0.91	INTERGENIC	TF binding site mE1_TFBS_cad
2L	3180353	2L_3180353_SNP [dm3] 2L_3180353_SNP [dm6]	G	A	4.911e^-5	0.919	INTRON CG34393

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By genomic position
Variant impact
Gene name

mn_Glycerol_HighDiet phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results