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=8.694e^-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

Covariate	p-value	Significance
In_2R_NS	0.06537

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2R_NS	2.7143	0.0995

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

962 significant hits at p-value < 0.001.

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
2L	10268784	2L_10268784_SNP [dm3] 2L_10268784_SNP [dm6]	T	A	7.768e^-6	0.846	UPSTREAM CG4957 DOWNSTREAM CG4953 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med
2L	226835	2L_226835_SNP [dm3] 2L_226835_SNP [dm6]	T	C	1.110e^-5	0.846	INTRON kis
X	7079117	X_7079117_INS [dm3] X_7185084_INS [dm6]	G	GTG	1.110e^-5	0.846	INTRON CG9650 & 1 other
2L	14786577	2L_14786577_DEL [dm3] 2L_14786577_DEL [dm6]	TGATACTTTT	T	1.228e^-5	0.846	INTERGENIC
2L	14786590	2L_14786590_SNP [dm3] 2L_14786590_SNP [dm6]	T	G	1.228e^-5	0.846	INTERGENIC
2L	14786591	2L_14786591_SNP [dm3] 2L_14786591_SNP [dm6]	T	G	1.228e^-5	0.846	INTERGENIC
2L	17254881	2L_17254881_SNP [dm3] 2L_17254881_SNP [dm6]	G	T	1.228e^-5	0.846	INTRON beat-IIIc
3R	25810994	3R_25810994_SNP [dm3] 3R_29985272_SNP [dm6]	C	A	2.749e^-5	0.846	INTRON CG7896	TF binding site mE1_TFBS_cad
3R	6960166	3R_6960166_SNP [dm3] 3R_11134444_SNP [dm6]	G	T	2.749e^-5	0.846	INTERGENIC
2L	225718	2L_225718_SNP [dm3] 2L_225718_SNP [dm6]	T	A	3.106e^-5	0.846	INTRON kis	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	20977818	2R_20977818_DEL [dm3] 2R_25090295_DEL [dm6]	AA	A	3.328e^-5	0.846	INTRON lov	transposable element FlyBase
3R	6960171	3R_6960171_SNP [dm3] 3R_11134449_SNP [dm6]	T	A	3.502e^-5	0.846	INTERGENIC
3R	6960173	3R_6960173_SNP [dm3] 3R_11134451_SNP [dm6]	T	C	3.502e^-5	0.846	INTERGENIC
3R	6960185	3R_6960185_SNP [dm3] 3R_11134463_SNP [dm6]	A	G	3.502e^-5	0.846	INTERGENIC
3R	6960194	3R_6960194_SNP [dm3] 3R_11134472_SNP [dm6]	A	C	3.502e^-5	0.846	INTERGENIC
2R	17094655	2R_17094655_SNP [dm3] 2R_21207150_SNP [dm6]	C	T	3.588e^-5	0.846	NON_SYNONYMOUS_CODING Glycogenin INTRON CG44245 & 1 other
2L	9571290	2L_9571290_SNP [dm3] 2L_9571290_SNP [dm6]	A	C	3.705e^-5	0.846	START_GAINED CG3838 UTR_5_PRIME CG3838 INTRON CG3838	TF binding site BDTNP1_TFBS_dl
2L	9573156	2L_9573156_SNP [dm3] 2L_9573156_SNP [dm6]	C	T	3.705e^-5	0.846	UTR_3_PRIME CG3838 DOWNSTREAM Mtpalpha
2R	17587284	2R_17587284_SNP [dm3] 2R_21699779_SNP [dm6]	G	A	3.705e^-5	0.846	INTRON HmgZ
X	10702282	X_10702282_INS [dm3] X_10808249_INS [dm6]	C	CACTTTCTTTTCGTTTTGGC...	3.705e^-5	0.846	INTRON Imp	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Kr
X	16523231	X_16523231_SNP [dm3] X_16629198_SNP [dm6]	T	G	3.705e^-5	0.846	SYNONYMOUS_CODING Rok	TF binding site mE1_TFBS_chinmo
X	16523453	X_16523453_SNP [dm3] X_16629420_SNP [dm6]	T	C	3.705e^-5	0.846	SYNONYMOUS_CODING Rok	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	7637860	2L_7637860_SNP [dm3] 2L_7637860_SNP [dm6]	G	T	4.076e^-5	0.846	DOWNSTREAM CR44800 INTERGENIC	TF binding site BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Kr
2L	7637861	2L_7637861_SNP [dm3] 2L_7637861_SNP [dm6]	G	T	4.076e^-5	0.846	DOWNSTREAM CR44800 INTERGENIC	TF binding site BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Kr
3L	485731	3L_485731_SNP [dm3] 3L_485731_SNP [dm6]	C	G	4.100e^-5	0.846	INTRON klar	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	11693039	3L_11693039_DEL [dm3] 3L_11699939_DEL [dm6]	AGGA	A	4.335e^-5	0.846	UTR_3_PRIME CG11658 UPSTREAM CG6053 DOWNSTREAM CG11658
X	21281649	X_21281649_SNP [dm3] X_21410622_SNP [dm6]	A	T	4.943e^-5	0.846	UPSTREAM CR45003 INTERGENIC
3L	7719686	3L_7719686_SNP [dm3] 3L_7726586_SNP [dm6]	G	A	5.610e^-5	0.846	UPSTREAM CG7457 INTRON CG32373	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	17088352	3R_17088352_SNP [dm3] 3R_21262630_SNP [dm6]	T	G	5.617e^-5	0.846	SYNONYMOUS_CODING ETHR INTRON ETHR	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2R	17299720	2R_17299720_SNP [dm3] 2R_21412215_SNP [dm6]	G	T	6.180e^-5	0.846	INTRON Sdc	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2R	17806402	2R_17806402_SNP [dm3] 2R_21918897_SNP [dm6]	T	C	6.472e^-5	0.846	INTRON Fili
3R	21061664	3R_21061664_SNP [dm3] 3R_25235942_SNP [dm6]	G	A	6.620e^-5	0.846	UPSTREAM CG10420 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	10355750	3L_10355750_SNP [dm3] 3L_10362650_SNP [dm6]	T	C	6.889e^-5	0.846	EXON CR44327	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
3L	10355803	3L_10355803_SNP [dm3] 3L_10362703_SNP [dm6]	C	T	6.889e^-5	0.846	EXON CR44327	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
3L	11531845	3L_11531845_SNP [dm3] 3L_11538745_SNP [dm6]	T	C	6.889e^-5	0.846	INTRON Mob2
3L	13254530	3L_13254530_DEL [dm3] 3L_13261430_DEL [dm6]	TAG	T	6.889e^-5	0.846	INTRON caps
3L	1422679	3L_1422679_SNP [dm3] 3L_1422679_SNP [dm6]	C	A	6.889e^-5	0.846	NON_SYNONYMOUS_CODING CG9173 INTRON Ptp61F	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3L	5185782	3L_5185782_SNP [dm3] 3L_5192682_SNP [dm6]	C	T	6.889e^-5	0.846	INTRON shep
3L	8729191	3L_8729191_SNP [dm3] 3L_8736091_SNP [dm6]	C	T	6.889e^-5	0.846	DOWNSTREAM Prm INTRON Prm	TF binding site mE1_TFBS_inv
3L	8729201	3L_8729201_SNP [dm3] 3L_8736101_SNP [dm6]	A	T	6.889e^-5	0.846	DOWNSTREAM Prm INTRON Prm	TF binding site mE1_TFBS_inv
X	4942739	X_4942739_SNP [dm3] X_5048706_SNP [dm6]	T	A	6.889e^-5	0.846	UTR_5_PRIME ovo INTRON CR44833	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
3L	7728262	3L_7728262_DEL [dm3] 3L_7735162_DEL [dm6]	AA	A	6.926e^-5	0.846	INTRON CG32373 & 1 other
3L	2530442	3L_2530442_INS [dm3] 3L_2530442_INS [dm6]	T	TT	6.948e^-5	0.846	INTRON Spn
3R	5224115	3R_5224115_SNP [dm3] 3R_9398393_SNP [dm6]	C	T	7.040e^-5	0.846	SYNONYMOUS_CODING Or85f	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna mE1_TFBS_sens
3R	5224118	3R_5224118_SNP [dm3] 3R_9398396_SNP [dm6]	T	C	7.040e^-5	0.846	SYNONYMOUS_CODING Or85f	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna mE1_TFBS_sens
3R	5224121	3R_5224121_SNP [dm3] 3R_9398399_SNP [dm6]	T	G	7.040e^-5	0.846	SYNONYMOUS_CODING Or85f	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna mE1_TFBS_sens
X	2565297	X_2565297_SNP [dm3] X_2671264_SNP [dm6]	G	C	7.844e^-5	0.846	INTRON sgg
3L	485585	3L_485585_SNP [dm3] 3L_485585_SNP [dm6]	T	C	7.881e^-5	0.846	INTRON klar	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	485591	3L_485591_SNP [dm3] 3L_485591_SNP [dm6]	T	C	7.881e^-5	0.846	INTRON klar	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	485597	3L_485597_SNP [dm3] 3L_485597_SNP [dm6]	A	C	7.881e^-5	0.846	INTRON klar	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	485628	3L_485628_SNP [dm3] 3L_485628_SNP [dm6]	C	A	7.881e^-5	0.846	INTRON klar	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	18551761	3L_18551761_SNP [dm3] 3L_18558661_SNP [dm6]	T	A	8.003e^-5	0.846	INTERGENIC
2R	11068421	2R_11068421_SNP [dm3] 2R_15180916_SNP [dm6]	C	A	8.274e^-5	0.846	INTRON igl
3R	6960180	3R_6960180_SNP [dm3] 3R_11134458_SNP [dm6]	C	A	8.274e^-5	0.846	INTERGENIC
3L	9867885	3L_9867885_SNP [dm3] 3L_9874785_SNP [dm6]	T	C	8.344e^-5	0.846	UPSTREAM CR45406 INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3R	19809547	3R_19809547_SNP [dm3] 3R_23983825_SNP [dm6]	A	G	8.344e^-5	0.846	DOWNSTREAM CG31140 EXON CR31451
3R	26279792	3R_26279792_SNP [dm3] 3R_30454070_SNP [dm6]	C	G	8.711e^-5	0.846	UPSTREAM aralar1 INTRON aralar1
X	8989142	X_8989142_SNP [dm3] X_9095109_SNP [dm6]	T	G	8.807e^-5	0.846	SYNONYMOUS_CODING CG7766	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3R	21675754	3R_21675754_SNP [dm3] 3R_25850032_SNP [dm6]	A	C	9.273e^-5	0.846	DOWNSTREAM CG14545 INTERGENIC
2R	18248965	2R_18248965_SNP [dm3] 2R_22361460_SNP [dm6]	C	A	9.451e^-5	0.846	INTRON Liprin-gamma
2R	17347287	2R_17347287_SNP [dm3] 2R_21459782_SNP [dm6]	C	T	9.782e^-5	0.846	INTRON Sdc
2R	17347371	2R_17347371_SNP [dm3] 2R_21459866_SNP [dm6]	A	G	9.782e^-5	0.846	INTRON Sdc
3L	5689555	3L_5689555_SNP [dm3] 3L_5696455_SNP [dm6]	G	C	9.875e^-5	0.846	UTR_5_PRIME sif INTRON sif	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	3135190	2L_3135190_SNP [dm3] 2L_3135190_SNP [dm6]	G	T	9.922e^-5	0.846	INTRON toc
2R	12491011	2R_12491011_SNP [dm3] 2R_16603506_SNP [dm6]	G	C	9.929e^-5	0.846	INTRON CG8303	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2L	16001587	2L_16001587_SNP [dm3] 2L_16001587_SNP [dm6]	A	T	9.936e^-5	0.846	UPSTREAM CR43825 INTRON beat-Ic
2R	19548138	2R_19548138_SNP [dm3] 2R_23660615_SNP [dm6]	A	G	1.006e^-4	0.846	INTRON Pde8	TF binding site BDTNP1_TFBS_dl mE1_TFBS_chinmo
2L	15508400	2L_15508400_SNP [dm3] 2L_15508400_SNP [dm6]	C	T	1.008e^-4	0.846	INTERGENIC
2R	18647404	2R_18647404_SNP [dm3] 2R_22759899_SNP [dm6]	C	T	1.016e^-4	0.846	NON_SYNONYMOUS_CODING CG42260 DOWNSTREAM CR30267 INTRON CG42260	TF binding site mE1_TFBS_cad
3L	486221	3L_486221_SNP [dm3] 3L_486221_SNP [dm6]	T	C	1.064e^-4	0.846	INTRON klar	TF binding site BDTNP1_TFBS_dl
2R	8410694	2R_8410694_SNP [dm3] 2R_12523189_SNP [dm6]	A	T	1.097e^-4	0.846	DOWNSTREAM CG33632 INTERGENIC
3L	7719704	3L_7719704_SNP [dm3] 3L_7726604_SNP [dm6]	G	A	1.097e^-4	0.846	UPSTREAM CG7457 INTRON CG32373	insulator Insulator_Class_I.mE01 TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	7719709	3L_7719709_SNP [dm3] 3L_7726609_SNP [dm6]	T	G	1.097e^-4	0.846	UPSTREAM CG7457 INTRON CG32373	insulator Insulator_Class_I.mE01 TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	7719725	3L_7719725_SNP [dm3] 3L_7726625_SNP [dm6]	C	T	1.097e^-4	0.846	UPSTREAM CG7457 INTRON CG32373	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	25228600	3R_25228600_SNP [dm3] 3R_29402878_SNP [dm6]	C	T	1.098e^-4	0.846	INTRON Ptp99A
3L	1251883	3L_1251883_SNP [dm3] 3L_1251883_SNP [dm6]	G	T	1.163e^-4	0.846	UPSTREAM CG9130 & 1 other DOWNSTREAM CG9129 INTERGENIC
3L	18552766	3L_18552766_SNP [dm3] 3L_18559666_SNP [dm6]	A	T	1.186e^-4	0.846	UPSTREAM AstC-R1 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	18552768	3L_18552768_SNP [dm3] 3L_18559668_SNP [dm6]	T	A	1.186e^-4	0.846	UPSTREAM AstC-R1 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	15817326	2R_15817326_SNP [dm3] 2R_19929821_SNP [dm6]	T	G	1.234e^-4	0.846	INTERGENIC
2L	17118024	2L_17118024_SNP [dm3] 2L_17118024_SNP [dm6]	C	T	1.250e^-4	0.846	INTERGENIC
3L	10454900	3L_10454900_SNP [dm3] 3L_10461800_SNP [dm6]	T	G	1.250e^-4	0.846	NON_SYNONYMOUS_CODING Gem3
3L	485649	3L_485649_SNP [dm3] 3L_485649_SNP [dm6]	C	T	1.260e^-4	0.846	INTRON klar	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	5055592	X_5055592_SNP [dm3] X_5161559_SNP [dm6]	A	T	1.279e^-4	0.846	INTRON rg & 1 other
2L	17342909	2L_17342909_SNP [dm3] 2L_17342909_SNP [dm6]	T	C	1.308e^-4	0.846	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3R	21675747	3R_21675747_SNP [dm3] 3R_25850025_SNP [dm6]	A	C	1.320e^-4	0.846	DOWNSTREAM CG14545 INTERGENIC
2L	20861770	2L_20861770_SNP [dm3] 2L_20861770_SNP [dm6]	A	G	1.325e^-4	0.846	DOWNSTREAM CG9336 & 1 other INTERGENIC	TF binding site mE1_TFBS_inv
3L	10322824	3L_10322824_SNP [dm3] 3L_10329724_SNP [dm6]	A	G	1.348e^-4	0.846	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_inv mE1_TFBS_Kr
3L	520406	3L_520406_INS [dm3] 3L_520406_INS [dm6]	T	TAAGGT	1.393e^-4	0.846	INTRON klar	TF binding site mE1_TFBS_HSA
3R	16199082	3R_16199082_SNP [dm3] 3R_20373360_SNP [dm6]	T	C	1.495e^-4	0.846	INTERGENIC
X	5672866	X_5672866_SNP [dm3] X_5778833_SNP [dm6]	G	T	1.495e^-4	0.846	INTRON CG42699 & 1 other
2R	11178065	2R_11178065_SNP [dm3] 2R_15290560_SNP [dm6]	T	A	1.515e^-4	0.846	INTRON Trpm
2L	2092051	2L_2092051_SNP [dm3] 2L_2092051_SNP [dm6]	G	A	1.557e^-4	0.846	INTRON dpr3
2L	19723182	2L_19723182_SNP [dm3] 2L_19723182_SNP [dm6]	G	A	1.573e^-4	0.846	INTRON Lar
2R	18670585	2R_18670585_SNP [dm3] 2R_22783080_SNP [dm6]	G	T	1.612e^-4	0.846	INTRON CG42260
3L	7752392	3L_7752392_SNP [dm3] 3L_7759292_SNP [dm6]	G	A	1.612e^-4	0.846	DOWNSTREAM CG32373 INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_ttk
2R	7461568	2R_7461568_SNP [dm3] 2R_11574063_SNP [dm6]	G	A	1.666e^-4	0.846	INTERGENIC
2R	7461574	2R_7461574_SNP [dm3] 2R_11574069_SNP [dm6]	A	C	1.666e^-4	0.846	INTERGENIC
2R	7461591	2R_7461591_SNP [dm3] 2R_11574086_SNP [dm6]	A	T	1.666e^-4	0.846	INTERGENIC
2R	7461607	2R_7461607_SNP [dm3] 2R_11574102_SNP [dm6]	G	A	1.666e^-4	0.846	INTERGENIC
3L	6816156	3L_6816156_SNP [dm3] 3L_6823056_SNP [dm6]	C	A	1.718e^-4	0.846	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA

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By genomic position
Variant impact
Gene name

RepOutput_Day08 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results