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=7.896e^-3)
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_2R_NS	0.09594

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2R_NS	5.241	0.0728

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2131 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

Show entries

Search:

Chromosome	Position	ID	Reference	Variant	p-value	FDR_BH	Transcript annotation	Binding site annotation
3L	20930721	3L_20930721_SNP [dm3] 3L_20937621_SNP [dm6]	T	A	5.313e^-8	0.1	INTRON fng
3R	5014418	3R_5014418_INS [dm3] 3R_9188696_INS [dm6]	A	ATGTTTATGA	6.537e^-7	0.382	INTRON pum
3L	10225308	3L_10225308_SNP [dm3] 3L_10232208_SNP [dm6]	C	T	9.945e^-7	0.382	INTERGENIC
2R	11423994	2R_11423994_SNP [dm3] 2R_15536489_SNP [dm6]	G	T	1.805e^-6	0.382	SPLICE_SITE_REGION CG30471 INTRON CG30471
2L	16227584	2L_16227584_SNP [dm3] 2L_16227584_SNP [dm6]	T	C	2.070e^-6	0.382	INTERGENIC
3L	10225319	3L_10225319_INS [dm3] 3L_10232219_INS [dm6]	T	TT	2.265e^-6	0.382	INTERGENIC
3L	10225322	3L_10225322_SNP [dm3] 3L_10232222_SNP [dm6]	T	C	2.265e^-6	0.382	INTERGENIC
3L	10225329	3L_10225329_SNP [dm3] 3L_10232229_SNP [dm6]	A	T	2.265e^-6	0.382	INTERGENIC
2L	16227554	2L_16227554_SNP [dm3] 2L_16227554_SNP [dm6]	T	A	2.315e^-6	0.382	INTERGENIC
2R	18865921	2R_18865921_SNP [dm3] 2R_22978398_SNP [dm6]	A	T	2.563e^-6	0.382	INTERGENIC
3R	26168016	3R_26168016_SNP [dm3] 3R_30342294_SNP [dm6]	G	A	2.696e^-6	0.382	INTRON hdc
2L	16227572	2L_16227572_SNP [dm3] 2L_16227572_SNP [dm6]	T	C	2.762e^-6	0.382	INTERGENIC
2L	3665280	2L_3665280_SNP [dm3] 2L_3665280_SNP [dm6]	T	C	3.075e^-6	0.382	INTRON CG34340
3L	17147921	3L_17147921_SNP [dm3] 3L_17154821_SNP [dm6]	T	A	3.135e^-6	0.382	INTRON Rbp6	TF binding site BDTNP1_TFBS_prd mE1_TFBS_HSA
3R	25446875	3R_25446875_SNP [dm3] 3R_29621153_SNP [dm6]	G	A	3.251e^-6	0.382	DOWNSTREAM CG1907 INTERGENIC
3R	5008299	3R_5008299_SNP [dm3] 3R_9182577_SNP [dm6]	C	T	3.263e^-6	0.382	INTRON pum
3R	15062285	3R_15062285_SNP [dm3] 3R_19236563_SNP [dm6]	G	T	4.021e^-6	0.385	INTRON unc79
3L	10225290	3L_10225290_SNP [dm3] 3L_10232190_SNP [dm6]	C	G	4.024e^-6	0.385	INTERGENIC
3L	10225261	3L_10225261_SNP [dm3] 3L_10232161_SNP [dm6]	C	T	4.246e^-6	0.385	INTERGENIC
3L	10225269	3L_10225269_SNP [dm3] 3L_10232169_SNP [dm6]	G	T	4.246e^-6	0.385	INTERGENIC
2R	18865927	2R_18865927_SNP [dm3] 2R_22978404_SNP [dm6]	T	A	4.308e^-6	0.385	INTERGENIC
3R	15062288	3R_15062288_SNP [dm3] 3R_19236566_SNP [dm6]	A	G	4.840e^-6	0.413	INTRON unc79
3R	5008300	3R_5008300_SNP [dm3] 3R_9182578_SNP [dm6]	T	G	5.830e^-6	0.458	INTRON pum
2R	11423954	2R_11423954_SNP [dm3] 2R_15536449_SNP [dm6]	A	G	5.857e^-6	0.458	INTRON CG30471
2L	11506440	2L_11506440_SNP [dm3] 2L_11506440_SNP [dm6]	T	C	6.391e^-6	0.479	SYNONYMOUS_CODING spz4	TF binding site mE1_TFBS_cad
2L	16227582	2L_16227582_SNP [dm3] 2L_16227582_SNP [dm6]	T	G	7.133e^-6	0.483	INTERGENIC
3R	25446874	3R_25446874_SNP [dm3] 3R_29621152_SNP [dm6]	G	C	7.540e^-6	0.483	DOWNSTREAM CG1907 INTERGENIC
X	16950573	X_16950573_SNP [dm3] X_17056540_SNP [dm6]	C	A	7.570e^-6	0.483	INTRON CG45002
2L	16227593	2L_16227593_SNP [dm3] 2L_16227593_SNP [dm6]	A	T	7.702e^-6	0.483	INTERGENIC
3R	5008319	3R_5008319_SNP [dm3] 3R_9182597_SNP [dm6]	A	G	7.726e^-6	0.483	INTRON pum
3L	10225314	3L_10225314_SNP [dm3] 3L_10232214_SNP [dm6]	T	G	9.086e^-6	0.528	INTERGENIC
2L	16227566	2L_16227566_SNP [dm3] 2L_16227566_SNP [dm6]	A	G	9.245e^-6	0.528	INTERGENIC
3R	10544290	3R_10544290_SNP [dm3] 3R_14718568_SNP [dm6]	A	T	9.351e^-6	0.528	INTRON kibra	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	18703035	2R_18703035_SNP [dm3] 2R_22815530_SNP [dm6]	G	A	9.563e^-6	0.528	SYNONYMOUS_CODING stl UPSTREAM CG30271	TF binding site mE1_TFBS_chinmo mE1_TFBS_inv
2L	16226132	2L_16226132_SNP [dm3] 2L_16226132_SNP [dm6]	A	G	9.913e^-6	0.531	INTERGENIC
3L	20915635	3L_20915635_SNP [dm3] 3L_20922535_SNP [dm6]	C	G	1.030e^-5	0.537	UPSTREAM CR43929 INTERGENIC	enhancer mE1_CBP_Enhancers TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_eve mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2L	7640302	2L_7640302_SNP [dm3] 2L_7640302_SNP [dm6]	T	C	1.154e^-5	0.582	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	22246548	3R_22246548_SNP [dm3] 3R_26420826_SNP [dm6]	G	C	1.180e^-5	0.582	INTERGENIC
3R	4679157	3R_4679157_SNP [dm3] 3R_8853435_SNP [dm6]	T	G	1.306e^-5	0.608	INTRON pyd
X	18371844	X_18371844_INS [dm3] X_18477811_INS [dm6]	A	AGAGGATGCA	1.311e^-5	0.608	INTRON CG32547
X	16611256	X_16611256_SNP [dm3] X_16717223_SNP [dm6]	G	A	1.394e^-5	0.608	INTRON CG34325
X	16611259	X_16611259_SNP [dm3] X_16717226_SNP [dm6]	A	C	1.394e^-5	0.608	INTRON CG34325
X	16611273	X_16611273_SNP [dm3] X_16717240_SNP [dm6]	C	T	1.394e^-5	0.608	INTRON CG34325
2L	6920309	2L_6920309_SNP [dm3] 2L_6920309_SNP [dm6]	T	G	1.536e^-5	0.655	UPSTREAM Hrb27C & 1 other INTERGENIC	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_Ubx
2L	4206417	2L_4206417_SNP [dm3] 2L_4206417_SNP [dm6]	T	C	1.572e^-5	0.655	SYNONYMOUS_CODING ft	TF binding site mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens
3L	18243744	3L_18243744_DEL [dm3] 3L_18250644_DEL [dm6]	AC	G	1.647e^-5	0.672	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi
2L	9249854	2L_9249854_SNP [dm3] 2L_9249854_SNP [dm6]	C	G	1.718e^-5	0.676	UTR_3_PRIME tai DOWNSTREAM aust
2L	3402485	2L_3402485_SNP [dm3] 2L_3402485_SNP [dm6]	G	A	1.742e^-5	0.676	INTERGENIC
2L	3402468	2L_3402468_SNP [dm3] 2L_3402468_SNP [dm6]	T	C	1.815e^-5	0.676	INTERGENIC
2R	9006819	2R_9006819_SNP [dm3] 2R_13119314_SNP [dm6]	C	G	1.825e^-5	0.676	INTRON CG13325
2L	3402462	2L_3402462_SNP [dm3] 2L_3402462_SNP [dm6]	C	G	1.838e^-5	0.676	INTERGENIC
3L	1434809	3L_1434809_SNP [dm3] 3L_1434809_SNP [dm6]	C	T	1.900e^-5	0.682	SYNONYMOUS_CODING SA-2 INTRON Ptp61F	TF binding site mE1_TFBS_cad
2R	16415521	2R_16415521_SNP [dm3] 2R_20528016_SNP [dm6]	T	A	1.940e^-5	0.682	DOWNSTREAM CG30151 INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
3R	5014472	3R_5014472_SNP [dm3] 3R_9188750_SNP [dm6]	T	G	1.965e^-5	0.682	INTRON pum
2L	8303639	2L_8303639_SNP [dm3] 2L_8303639_SNP [dm6]	C	T	2.039e^-5	0.695	SYNONYMOUS_CODING Scgalpha UPSTREAM wol	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
3R	26809140	3R_26809140_SNP [dm3] 3R_30983418_SNP [dm6]	G	A	2.146e^-5	0.71	INTRON 5-HT7
3L	6281226	3L_6281226_SNP [dm3] 3L_6288126_SNP [dm6]	G	C	2.157e^-5	0.71	INTERGENIC
3L	19542604	3L_19542604_SNP [dm3] 3L_19549504_SNP [dm6]	T	C	2.229e^-5	0.721	SYNONYMOUS_CODING l_3_76BDr
3L	6439151	3L_6439151_SNP [dm3] 3L_6446051_SNP [dm6]	G	A	2.287e^-5	0.721	INTRON CG42747
2L	6698598	2L_6698598_SNP [dm3] 2L_6698598_SNP [dm6]	A	G	2.306e^-5	0.721	INTRON Tsp
2R	18865887	2R_18865887_DEL [dm3] 2R_22978364_DEL [dm6]	ATGAAACG	A	2.493e^-5	0.766	INTERGENIC
3R	5014336	3R_5014336_SNP [dm3] 3R_9188614_SNP [dm6]	C	A	2.772e^-5	0.772	INTRON pum
3R	13673851	3R_13673851_SNP [dm3] 3R_17848129_SNP [dm6]	T	C	2.778e^-5	0.772	INTRON tinc
3L	815344	3L_815344_SNP [dm3] 3L_815344_SNP [dm6]	C	G	2.820e^-5	0.772	DOWNSTREAM CR44537 INTERGENIC	TF binding site BDTNP1_TFBS_twi
2R	16102008	2R_16102008_SNP [dm3] 2R_20214503_SNP [dm6]	A	C	2.861e^-5	0.772	INTERGENIC
2L	16567044	2L_16567044_SNP [dm3] 2L_16567044_SNP [dm6]	G	A	2.898e^-5	0.772	INTRON CG42389
2L	14170308	2L_14170308_SNP [dm3] 2L_14170308_SNP [dm6]	C	T	2.921e^-5	0.772	INTRON CG43333
2R	11053200	2R_11053200_SNP [dm3] 2R_15165695_SNP [dm6]	T	C	3.078e^-5	0.772	INTRON igl
3R	18441262	3R_18441262_SNP [dm3] 3R_22615540_SNP [dm6]	G	A	3.262e^-5	0.772	SYNONYMOUS_CODING EF-G2 UPSTREAM CG31161
3R	22732730	3R_22732730_DEL [dm3] 3R_26907008_DEL [dm6]	GTACCGCG	G	3.330e^-5	0.772	INTRON T48	regulatory region REDfly_CRMs
2L	9474706	2L_9474706_SNP [dm3] 2L_9474706_SNP [dm6]	G	A	3.416e^-5	0.772	INTERGENIC
3L	14997665	3L_14997665_SNP [dm3] 3L_15004565_SNP [dm6]	T	A	3.489e^-5	0.772	INTRON Reck
2R	9646146	2R_9646146_SNP [dm3] 2R_13758641_SNP [dm6]	T	G	3.491e^-5	0.772	SYNONYMOUS_CODING CG6280	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2L	3402428	2L_3402428_SNP [dm3] 2L_3402428_SNP [dm6]	G	A	3.517e^-5	0.772	INTERGENIC
2L	12153869	2L_12153869_SNP [dm3] 2L_12153869_SNP [dm6]	T	A	3.523e^-5	0.772	SYNONYMOUS_CODING CG31760
3R	6276451	3R_6276451_SNP [dm3] 3R_10450729_SNP [dm6]	A	C	3.552e^-5	0.772	INTERGENIC
3R	4744528	3R_4744528_SNP [dm3] 3R_8918806_SNP [dm6]	G	A	3.580e^-5	0.772	INTRON pyd	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad
X	9630728	X_9630728_SNP [dm3] X_9736695_SNP [dm6]	C	T	3.584e^-5	0.772	INTRON Sp1	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_sens
3L	9970818	3L_9970818_SNP [dm3] 3L_9977718_SNP [dm6]	G	T	3.606e^-5	0.772	INTRON dpr6
3R	10543178	3R_10543178_SNP [dm3] 3R_14717456_SNP [dm6]	T	C	3.628e^-5	0.772	INTRON kibra	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
X	16611745	X_16611745_SNP [dm3] X_16717712_SNP [dm6]	C	T	3.707e^-5	0.772	INTRON CG34325
3L	18243601	3L_18243601_SNP [dm3] 3L_18250501_SNP [dm6]	G	T	3.780e^-5	0.772	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi
X	18371867	X_18371867_SNP [dm3] X_18477834_SNP [dm6]	T	A	3.804e^-5	0.772	INTRON CG32547
2L	6698602	2L_6698602_SNP [dm3] 2L_6698602_SNP [dm6]	A	C	3.816e^-5	0.772	INTRON Tsp
X	6638260	X_6638260_SNP [dm3] X_6744227_SNP [dm6]	G	C	3.835e^-5	0.772	UTR_5_PRIME RpL17 UPSTREAM snoRNA:Psi28S-1232 & 2 others DOWNSTREAM tRNA:CR32740	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_inv
3L	8910839	3L_8910839_SNP [dm3] 3L_8917739_SNP [dm6]	A	G	3.865e^-5	0.772	INTRON Tsp66E
3L	1582237	3L_1582237_SNP [dm3] 3L_1582237_SNP [dm6]	A	G	3.877e^-5	0.772	INTRON CG13917
2R	9886482	2R_9886482_SNP [dm3] 2R_13998977_SNP [dm6]	T	G	3.880e^-5	0.772	INTRON mam	TF binding site BDTNP1_TFBS_dl
3R	26808556	3R_26808556_SNP [dm3] 3R_30982834_SNP [dm6]	T	G	3.987e^-5	0.772	INTRON 5-HT7
2L	6515749	2L_6515749_SNP [dm3] 2L_6515749_SNP [dm6]	A	T	3.999e^-5	0.772	INTRON CG31637
3L	10816650	3L_10816650_SNP [dm3] 3L_10823550_SNP [dm6]	G	A	4.033e^-5	0.772	INTERGENIC
2L	9511459	2L_9511459_SNP [dm3] 2L_9511459_SNP [dm6]	G	A	4.074e^-5	0.772	INTRON CG33298	TF binding site mE1_TFBS_sens
2L	9511312	2L_9511312_SNP [dm3] 2L_9511312_SNP [dm6]	T	C	4.075e^-5	0.772	INTRON CG33298
2R	18286941	2R_18286941_SNP [dm3] 2R_22399436_SNP [dm6]	T	C	4.088e^-5	0.772	INTRON babos	TF binding site BDTNP1_TFBS_dl
3R	26168020	3R_26168020_SNP [dm3] 3R_30342298_SNP [dm6]	T	C	4.168e^-5	0.772	INTRON hdc
3L	9969042	3L_9969042_INS [dm3] 3L_9975942_INS [dm6]	A	AT	4.227e^-5	0.772	INTRON dpr6
3L	9969086	3L_9969086_SNP [dm3] 3L_9975986_SNP [dm6]	A	G	4.227e^-5	0.772	INTRON dpr6
3L	9969104	3L_9969104_DEL [dm3] 3L_9976004_DEL [dm6]	ACTGT	A	4.227e^-5	0.772	INTRON dpr6
3L	9969111	3L_9969111_SNP [dm3] 3L_9976011_SNP [dm6]	C	T	4.227e^-5	0.772	INTRON dpr6
3R	26814020	3R_26814020_SNP [dm3] 3R_30988298_SNP [dm6]	G	T	4.290e^-5	0.772	INTRON 5-HT7

Showing 1 to 100 of 1,000 entries

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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=2.102e^-3)
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
wolba	0.067831
In_2R_NS	0.001202
In_3R_Mo	0.048752

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2R_NS	10.2587	0.0059

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2118 significant hits at p-value < 0.001. The 1000 top results are displayed in the table below.

Variant impact HIGH MODERATE LOW MODIFIER

Show entries

Search:

Chromosome	Position	ID	Reference	Variant	p-value	FDR_BH	Transcript annotation	Binding site annotation
3L	15149090	3L_15149090_SNP [dm3] 3L_15155990_SNP [dm6]	T	C	3.415e^-8	0.064	SYNONYMOUS_CODING Msh6	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
X	16761643	X_16761643_SNP [dm3] X_16867610_SNP [dm6]	G	A	4.256e^-7	0.366	INTRON CG13003
X	11186504	X_11186504_SNP [dm3] X_11292471_SNP [dm6]	C	G	5.847e^-7	0.366	INTRON CG44422
3R	9401301	3R_9401301_SNP [dm3] 3R_13575579_SNP [dm6]	C	T	2.266e^-6	0.745	DOWNSTREAM CR43848 INTERGENIC
2L	12210735	2L_12210735_SNP [dm3] 2L_12210735_SNP [dm6]	T	A	2.579e^-6	0.745	DOWNSTREAM CG31759 INTRON aret
3R	21848182	3R_21848182_SNP [dm3] 3R_26022460_SNP [dm6]	A	G	2.623e^-6	0.745	SYNONYMOUS_CODING E_spl_m3-HLH	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2R	11878083	2R_11878083_SNP [dm3] 2R_15990578_SNP [dm6]	A	G	3.351e^-6	0.745	SYNONYMOUS_CODING CG8314 DOWNSTREAM Pex11	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	26649212	3R_26649212_SNP [dm3] 3R_30823490_SNP [dm6]	T	A	3.636e^-6	0.745	UPSTREAM cindr INTRON cindr
3L	9796288	3L_9796288_SNP [dm3] 3L_9803188_SNP [dm6]	C	T	4.010e^-6	0.745	DOWNSTREAM Ilp4 INTRON CG32052	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	20511208	3L_20511208_DEL [dm3] 3L_20518108_DEL [dm6]	TTT	T	4.236e^-6	0.745	UPSTREAM CG5059 INTRON CG5059	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_Trl mE1_TFBS_ttk
3R	20759813	3R_20759813_SNP [dm3] 3R_24934091_SNP [dm6]	A	T	5.213e^-6	0.745	SYNONYMOUS_CODING CG11771 DOWNSTREAM Osbp	TF binding site mE1_TFBS_chinmo
X	7204575	X_7204575_SNP [dm3] X_7310542_SNP [dm6]	T	C	5.378e^-6	0.745	SYNONYMOUS_CODING brk INTRON CR44357 & 1 other	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad
3R	16007340	3R_16007340_SNP [dm3] 3R_20181618_SNP [dm6]	T	C	5.639e^-6	0.745	INTERGENIC
3L	13937200	3L_13937200_SNP [dm3] 3L_13944100_SNP [dm6]	A	G	5.823e^-6	0.745	INTRON CG32137
3L	4233379	3L_4233379_SNP [dm3] 3L_4233379_SNP [dm6]	G	T	6.409e^-6	0.745	INTRON ImpL2	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
3L	4233392	3L_4233392_SNP [dm3] 3L_4233392_SNP [dm6]	G	A	6.599e^-6	0.745	INTRON ImpL2	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
2R	11878071	2R_11878071_SNP [dm3] 2R_15990566_SNP [dm6]	T	C	6.757e^-6	0.745	SYNONYMOUS_CODING CG8314 DOWNSTREAM Pex11	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	11103519	2L_11103519_SNP [dm3] 2L_11103519_SNP [dm6]	C	T	8.159e^-6	0.811	INTRON Reps
3L	15150176	3L_15150176_SNP [dm3] 3L_15157076_SNP [dm6]	A	G	8.526e^-6	0.811	INTRON Msh6
3R	26582579	3R_26582579_SNP [dm3] 3R_30756857_SNP [dm6]	T	A	8.652e^-6	0.811	INTERGENIC	TF binding site BDTNP1_TFBS_twi
X	13199489	X_13199489_SNP [dm3] X_13305456_SNP [dm6]	T	C	1.049e^-5	0.853	UPSTREAM CR45018 & 1 other INTRON IP3K2 EXON CR45018	TF binding site mE1_TFBS_cad
3L	17012528	3L_17012528_SNP [dm3] 3L_17019428_SNP [dm6]	T	C	1.105e^-5	0.853	SYNONYMOUS_CODING CG7728 DOWNSTREAM CG6652	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	14463362	3R_14463362_SNP [dm3] 3R_18637640_SNP [dm6]	T	C	1.132e^-5	0.853	INTRON qin & 1 other
X	8718530	X_8718530_SNP [dm3] X_8824497_SNP [dm6]	A	C	1.173e^-5	0.853	INTERGENIC
3L	19503628	3L_19503628_SNP [dm3] 3L_19510528_SNP [dm6]	G	A	1.180e^-5	0.853	INTERGENIC
2R	11091156	2R_11091156_SNP [dm3] 2R_15203651_SNP [dm6]	A	G	1.284e^-5	0.853	SYNONYMOUS_CODING CG11807 DOWNSTREAM CG42391	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	1969638	2R_1969638_SNP [dm3] 2R_6082133_SNP [dm6]	G	C	1.415e^-5	0.853	SYNONYMOUS_CODING Ars2 UTR_3_PRIME Ars2
3R	26649266	3R_26649266_SNP [dm3] 3R_30823544_SNP [dm6]	T	C	1.426e^-5	0.853	UPSTREAM cindr INTRON cindr
2R	11878125	2R_11878125_SNP [dm3] 2R_15990620_SNP [dm6]	G	A	1.441e^-5	0.853	SYNONYMOUS_CODING CG8314 DOWNSTREAM Pex11	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	4233402	3L_4233402_SNP [dm3] 3L_4233402_SNP [dm6]	A	T	1.466e^-5	0.853	INTRON ImpL2	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
3L	17013801	3L_17013801_SNP [dm3] 3L_17020701_SNP [dm6]	A	G	1.539e^-5	0.853	SYNONYMOUS_CODING CG6652 DOWNSTREAM CG7728	TF binding site mE1_TFBS_cad
3R	23394366	3R_23394366_SNP [dm3] 3R_27568644_SNP [dm6]	G	C	1.562e^-5	0.853	INTRON wdb
3R	25689954	3R_25689954_SNP [dm3] 3R_29864232_SNP [dm6]	C	T	1.612e^-5	0.853	SYNONYMOUS_CODING Zip99C DOWNSTREAM snoRNA:Me28S-A2564 & 1 other
2L	16136371	2L_16136371_SNP [dm3] 2L_16136371_SNP [dm6]	A	T	1.631e^-5	0.853	UPSTREAM CR44871 INTERGENIC
2R	10031949	2R_10031949_SNP [dm3] 2R_14144444_SNP [dm6]	G	T	1.694e^-5	0.853	DOWNSTREAM mir-989 INTERGENIC
3R	4371802	3R_4371802_SNP [dm3] 3R_8546080_SNP [dm6]	C	A	1.813e^-5	0.853	UPSTREAM CR45574 DOWNSTREAM CR45575 INTERGENIC
3L	13301136	3L_13301136_SNP [dm3] 3L_13308036_SNP [dm6]	G	T	1.889e^-5	0.853	INTERGENIC
3R	3050309	3R_3050309_SNP [dm3] 3R_7224587_SNP [dm6]	A	T	1.927e^-5	0.853	INTRON CG14608
2R	16279449	2R_16279449_SNP [dm3] 2R_20391944_SNP [dm6]	A	T	1.940e^-5	0.853	INTERGENIC
3R	23257914	3R_23257914_SNP [dm3] 3R_27432192_SNP [dm6]	G	A	1.942e^-5	0.853	INTRON side
X	7204570	X_7204570_SNP [dm3] X_7310537_SNP [dm6]	C	T	1.944e^-5	0.853	SYNONYMOUS_CODING brk INTRON CR44357 & 1 other	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad
3L	1350858	3L_1350858_SNP [dm3] 3L_1350858_SNP [dm6]	G	A	2.151e^-5	0.853	UPSTREAM 312 & 1 other INTRON Ptp61F	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_zfh1
3L	12366546	3L_12366546_SNP [dm3] 3L_12373446_SNP [dm6]	T	G	2.162e^-5	0.853	SYNONYMOUS_CODING Ncc69
3R	16597740	3R_16597740_SNP [dm3] 3R_20772018_SNP [dm6]	A	G	2.338e^-5	0.853	SYNONYMOUS_CODING Takl1 INTRON Syp
2L	9248038	2L_9248038_SNP [dm3] 2L_9248038_SNP [dm6]	A	T	2.477e^-5	0.853	UTR_3_PRIME tai DOWNSTREAM tai
2R	9603487	2R_9603487_SNP [dm3] 2R_13715982_SNP [dm6]	C	G	2.613e^-5	0.853	INTRON fas	TF binding site BDTNP1_TFBS_prd mE1_TFBS_HSA
3R	26086129	3R_26086129_SNP [dm3] 3R_30260407_SNP [dm6]	A	C	2.684e^-5	0.853	INTERGENIC
3L	839303	3L_839303_SNP [dm3] 3L_839303_SNP [dm6]	A	G	2.743e^-5	0.853	SYNONYMOUS_CODING CG13887 UTR_3_PRIME CG13887 DOWNSTREAM CG13902
2L	17554583	2L_17554583_SNP [dm3] 2L_17554583_SNP [dm6]	C	T	2.768e^-5	0.853	SYNONYMOUS_CODING CG7094
3L	14392123	3L_14392123_SNP [dm3] 3L_14399023_SNP [dm6]	T	A	2.842e^-5	0.853	INTERGENIC
2R	2942985	2R_2942985_SNP [dm3] 2R_7055480_SNP [dm6]	A	G	2.959e^-5	0.853	UTR_3_PRIME Tsp42Ep DOWNSTREAM Tsp42Ep INTRON Tsp42Eo
X	9343712	X_9343712_SNP [dm3] X_9449679_SNP [dm6]	T	C	3.066e^-5	0.853	INTRON mgl	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	18363341	3R_18363341_SNP [dm3] 3R_22537619_SNP [dm6]	G	T	3.117e^-5	0.853	INTRON CG5326
3R	23257894	3R_23257894_SNP [dm3] 3R_27432172_SNP [dm6]	A	C	3.123e^-5	0.853	INTRON side
2R	13892698	2R_13892698_SNP [dm3] 2R_18005193_SNP [dm6]	G	T	3.128e^-5	0.853	UPSTREAM CR44419 INTRON dpr13	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
X	13198920	X_13198920_SNP [dm3] X_13304887_SNP [dm6]	A	T	3.270e^-5	0.853	UPSTREAM CR45018 & 1 other INTRON IP3K2 EXON CR45018	TF binding site mE1_TFBS_HSA
2L	4279046	2L_4279046_MNP [dm3] 2L_4279046_MNP [dm6]	AAA	TGG	3.315e^-5	0.853	INTRON Art2	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	26611380	3R_26611380_SNP [dm3] 3R_30785658_SNP [dm6]	C	T	3.365e^-5	0.853	SYNONYMOUS_CODING zfh1	TF binding site BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	15150234	3L_15150234_SNP [dm3] 3L_15157134_SNP [dm6]	G	T	3.413e^-5	0.853	SYNONYMOUS_CODING Msh6
3R	26809250	3R_26809250_INS [dm3] 3R_30983528_INS [dm6]	A	AGAA	3.470e^-5	0.853	INTRON 5-HT7
3R	25628244	3R_25628244_SNP [dm3] 3R_29802522_SNP [dm6]	G	A	3.529e^-5	0.853	SYNONYMOUS_CODING CG7834 UPSTREAM CG7789 DOWNSTREAM Ice	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA
3R	25807429	3R_25807429_SNP [dm3] 3R_29981707_SNP [dm6]	T	A	3.552e^-5	0.853	INTERGENIC
3R	23398457	3R_23398457_SNP [dm3] 3R_27572735_SNP [dm6]	C	A	3.612e^-5	0.853	INTRON wdb
2R	18158195	2R_18158195_SNP [dm3] 2R_22270690_SNP [dm6]	G	A	3.630e^-5	0.853	UPSTREAM dve INTRON dve	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl mE1_TFBS_zfh1
2L	7227353	2L_7227353_SNP [dm3] 2L_7227353_SNP [dm6]	T	C	3.631e^-5	0.853	SPLICE_SITE_REGION Ndae1 UPSTREAM CG43799 INTRON Ndae1	TF binding site BDTNP1_TFBS_dl mE1_TFBS_inv
3L	4233383	3L_4233383_SNP [dm3] 3L_4233383_SNP [dm6]	T	C	3.662e^-5	0.853	INTRON ImpL2	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
3R	21853454	3R_21853454_SNP [dm3] 3R_26027732_SNP [dm6]	G	A	3.686e^-5	0.853	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Stat92E
2L	12879895	2L_12879895_SNP [dm3] 2L_12879895_SNP [dm6]	T	A	3.753e^-5	0.853	INTERGENIC
2L	3101146	2L_3101146_SNP [dm3] 2L_3101146_SNP [dm6]	A	C	3.758e^-5	0.853	INTRON toc
X	13199020	X_13199020_SNP [dm3] X_13304987_SNP [dm6]	A	T	3.830e^-5	0.853	UPSTREAM CR45018 & 1 other INTRON IP3K2 EXON CR45018
3R	24808035	3R_24808035_SNP [dm3] 3R_28982313_SNP [dm6]	C	T	3.834e^-5	0.853	INTERGENIC
3R	20965420	3R_20965420_SNP [dm3] 3R_25139698_SNP [dm6]	A	G	3.912e^-5	0.853	UTR_3_PRIME danr
3R	26482702	3R_26482702_SNP [dm3] 3R_30656980_SNP [dm6]	A	C	3.923e^-5	0.853	INTERGENIC
3R	15074955	3R_15074955_SNP [dm3] 3R_19249233_SNP [dm6]	T	C	3.948e^-5	0.853	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_inv
3R	24807977	3R_24807977_SNP [dm3] 3R_28982255_SNP [dm6]	C	A	3.978e^-5	0.853	INTERGENIC
3L	834130	3L_834130_SNP [dm3] 3L_834130_SNP [dm6]	A	G	3.997e^-5	0.853	START_GAINED CG42553 UTR_5_PRIME CG42553 UPSTREAM snoRNA:Psi18S-1086 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_Ubx
2L	19633105	2L_19633105_SNP [dm3] 2L_19633105_SNP [dm6]	C	G	4.082e^-5	0.853	INTRON Lar
3R	19367947	3R_19367947_SNP [dm3] 3R_23542225_SNP [dm6]	G	C	4.150e^-5	0.853	INTERGENIC
3R	16812356	3R_16812356_SNP [dm3] 3R_20986634_SNP [dm6]	A	T	4.209e^-5	0.853	UTR_3_PRIME CG43446 INTRON Calx
3L	14392121	3L_14392121_SNP [dm3] 3L_14399021_SNP [dm6]	A	G	4.274e^-5	0.853	INTERGENIC
2R	10021224	2R_10021224_SNP [dm3] 2R_14133719_SNP [dm6]	T	G	4.331e^-5	0.853	INTRON Prosap
3L	3447899	3L_3447899_SNP [dm3] 3L_3447899_SNP [dm6]	G	T	4.421e^-5	0.853	INTRON eIF5B
2R	10020532	2R_10020532_SNP [dm3] 2R_14133027_SNP [dm6]	C	T	4.440e^-5	0.853	INTRON Prosap	TF binding site mE1_TFBS_inv
X	16764148	X_16764148_DEL [dm3] X_16870115_DEL [dm6]	ATGATCAAA	A	4.451e^-5	0.853	INTRON CG13003
3L	5312731	3L_5312731_SNP [dm3] 3L_5319631_SNP [dm6]	C	A	4.577e^-5	0.853	INTERGENIC
X	8935093	X_8935093_SNP [dm3] X_9041060_SNP [dm6]	A	C	4.578e^-5	0.853	INTRON CR43836 & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_Trl
X	13199030	X_13199030_SNP [dm3] X_13304997_SNP [dm6]	C	T	4.638e^-5	0.853	UPSTREAM CR45018 & 1 other INTRON IP3K2 EXON CR45018
3R	14085313	3R_14085313_SNP [dm3] 3R_18259591_SNP [dm6]	C	T	4.730e^-5	0.853	INTERGENIC
3R	23257263	3R_23257263_SNP [dm3] 3R_27431541_SNP [dm6]	C	T	4.771e^-5	0.853	INTRON side
2R	1965761	2R_1965761_SNP [dm3] 2R_6078256_SNP [dm6]	G	A	4.819e^-5	0.853	DOWNSTREAM CG14590 & 1 other INTERGENIC
3R	22558397	3R_22558397_SNP [dm3] 3R_26732675_SNP [dm6]	C	T	4.918e^-5	0.853	INTERGENIC
3L	15150183	3L_15150183_SNP [dm3] 3L_15157083_SNP [dm6]	A	T	4.975e^-5	0.853	INTRON Msh6
3R	21851944	3R_21851944_SNP [dm3] 3R_26026222_SNP [dm6]	T	C	5.021e^-5	0.853	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi
3L	17013798	3L_17013798_SNP [dm3] 3L_17020698_SNP [dm6]	A	G	5.035e^-5	0.853	SYNONYMOUS_CODING CG6652 DOWNSTREAM CG7728	TF binding site mE1_TFBS_cad
X	7317279	X_7317279_SNP [dm3] X_7423246_SNP [dm6]	T	A	5.060e^-5	0.853	INTERGENIC
3L	4233366	3L_4233366_SNP [dm3] 3L_4233366_SNP [dm6]	T	A	5.081e^-5	0.853	INTRON ImpL2	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
3R	18874267	3R_18874267_SNP [dm3] 3R_23048545_SNP [dm6]	G	A	5.129e^-5	0.853	UPSTREAM CG17121 INTERGENIC	TF binding site BDTNP1_TFBS_z
3L	5314572	3L_5314572_SNP [dm3] 3L_5321472_SNP [dm6]	G	A	5.131e^-5	0.853	INTERGENIC
2R	12601968	2R_12601968_SNP [dm3] 2R_16714463_SNP [dm6]	A	G	5.163e^-5	0.853	INTRON CG30463
3L	7833000	3L_7833000_SNP [dm3] 3L_7839900_SNP [dm6]	G	A	5.173e^-5	0.853	INTRON Pdp1	regulatory region REDfly_CRMs

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Rhythmicity_Index phenotype

Phenotype distribution and association to known covariates

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Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results