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=4.704e^-5)
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_2L_t	3.252e-07
In_3R_K	0.0260

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	17.7496	0.0001
In_3R_K	6.1276	0.0467

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2334 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
2L	8521314	2L_8521314_SNP [dm3] 2L_8521314_SNP [dm6]	G	C	8.031e^-14	1.030e^-7	NON_SYNONYMOUS_CODING CG13091 UPSTREAM Acer	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_h mE1_TFBS_sens mE1_TFBS_Ubx
2L	8521447	2L_8521447_SNP [dm3] 2L_8521447_SNP [dm6]	C	T	1.099e^-13	1.030e^-7	UPSTREAM Acer INTRON CG13091	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_h mE1_TFBS_sens mE1_TFBS_Ubx
2L	8521332	2L_8521332_SNP [dm3] 2L_8521332_SNP [dm6]	A	C	2.299e^-13	1.437e^-7	SYNONYMOUS_CODING CG13091 UPSTREAM Acer	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_h mE1_TFBS_sens mE1_TFBS_Ubx
2L	8520050	2L_8520050_SNP [dm3] 2L_8520050_SNP [dm6]	T	C	6.294e^-13	2.951e^-7	DOWNSTREAM CG13090 INTRON CG13091	TF binding site mE1_TFBS_chinmo
2L	8520294	2L_8520294_SNP [dm3] 2L_8520294_SNP [dm6]	G	A	1.015e^-12	3.806e^-7	SYNONYMOUS_CODING CG13091	TF binding site mE1_TFBS_chinmo mE1_TFBS_sens
2L	8520129	2L_8520129_SNP [dm3] 2L_8520129_SNP [dm6]	C	G	2.590e^-12	8.097e^-7	SYNONYMOUS_CODING CG13091 DOWNSTREAM CG13090	TF binding site mE1_TFBS_chinmo
2L	8520273	2L_8520273_SNP [dm3] 2L_8520273_SNP [dm6]	T	C	5.520e^-12	1.479e^-6	SYNONYMOUS_CODING CG13091	TF binding site mE1_TFBS_chinmo mE1_TFBS_sens
2L	8524326	2L_8524326_SNP [dm3] 2L_8524326_SNP [dm6]	C	T	9.349e^-12	2.192e^-6	SYNONYMOUS_CODING Acer DOWNSTREAM lmgA & 1 other	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2L	8520157	2L_8520157_SNP [dm3] 2L_8520157_SNP [dm6]	C	A	1.318e^-11	2.746e^-6	NON_SYNONYMOUS_CODING CG13091 DOWNSTREAM CG13090	TF binding site mE1_TFBS_chinmo
2L	8528842	2L_8528842_SNP [dm3] 2L_8528842_SNP [dm6]	T	G	4.185e^-11	7.850e^-6	UPSTREAM lmgB & 2 others INTERGENIC	TF binding site BDTNP1_TFBS_dl
2L	8521633	2L_8521633_SNP [dm3] 2L_8521633_SNP [dm6]	G	A	6.987e^-11	1.129e^-5	UTR_3_PRIME CG13091 UPSTREAM Acer	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Ubx
2L	8524906	2L_8524906_SNP [dm3] 2L_8524906_SNP [dm6]	C	A	7.225e^-11	1.129e^-5	UTR_3_PRIME Acer DOWNSTREAM lmgA & 2 others
2L	8524323	2L_8524323_SNP [dm3] 2L_8524323_SNP [dm6]	T	C	1.019e^-10	1.471e^-5	SYNONYMOUS_CODING Acer DOWNSTREAM lmgA & 1 other	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2L	8528865	2L_8528865_SNP [dm3] 2L_8528865_SNP [dm6]	C	T	4.402e^-10	5.504e^-5	UPSTREAM lmgB & 2 others INTERGENIC	TF binding site BDTNP1_TFBS_dl
2L	8528881	2L_8528881_SNP [dm3] 2L_8528881_SNP [dm6]	A	G	4.402e^-10	5.504e^-5	UPSTREAM lmgB & 2 others INTERGENIC	TF binding site BDTNP1_TFBS_dl
2L	8528825	2L_8528825_SNP [dm3] 2L_8528825_SNP [dm6]	C	T	7.833e^-10	9.183e^-5	UPSTREAM lmgB & 2 others INTERGENIC	TF binding site BDTNP1_TFBS_dl
2L	8528818	2L_8528818_SNP [dm3] 2L_8528818_SNP [dm6]	A	C	9.523e^-10	1.051e^-4	UPSTREAM lmgB & 2 others INTERGENIC	TF binding site BDTNP1_TFBS_dl
2L	8523762	2L_8523762_SNP [dm3] 2L_8523762_SNP [dm6]	G	T	1.261e^-9	1.258e^-4	SYNONYMOUS_CODING Acer	TF binding site mE1_TFBS_cad
2L	8529077	2L_8529077_SNP [dm3] 2L_8529077_SNP [dm6]	G	C	1.349e^-9	1.258e^-4	UPSTREAM CG17834 & 2 others INTERGENIC	TF binding site BDTNP1_TFBS_dl
2L	8529069	2L_8529069_SNP [dm3] 2L_8529069_SNP [dm6]	T	C	1.399e^-9	1.258e^-4	UPSTREAM CG17834 & 2 others INTERGENIC	TF binding site BDTNP1_TFBS_dl
2L	8528846	2L_8528846_SNP [dm3] 2L_8528846_SNP [dm6]	T	A	1.408e^-9	1.258e^-4	UPSTREAM lmgB & 2 others INTERGENIC	TF binding site BDTNP1_TFBS_dl
2L	8529062	2L_8529062_SNP [dm3] 2L_8529062_SNP [dm6]	C	T	1.478e^-9	1.260e^-4	UPSTREAM lmgB & 2 others INTERGENIC	TF binding site BDTNP1_TFBS_dl
2L	8525014	2L_8525014_SNP [dm3] 2L_8525014_SNP [dm6]	A	T	1.746e^-9	1.424e^-4	UTR_3_PRIME Acer & 2 others DOWNSTREAM lmgA & 2 others
2L	8524455	2L_8524455_SNP [dm3] 2L_8524455_SNP [dm6]	T	C	7.974e^-9	6.232e^-4	SYNONYMOUS_CODING Acer DOWNSTREAM lmgA & 1 other	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2L	8528806	2L_8528806_SNP [dm3] 2L_8528806_SNP [dm6]	A	C	8.438e^-9	6.331e^-4	UPSTREAM lmgB & 2 others INTERGENIC	TF binding site BDTNP1_TFBS_dl
2L	8529111	2L_8529111_SNP [dm3] 2L_8529111_SNP [dm6]	A	G	1.136e^-8	7.943e^-4	UPSTREAM CG17834 & 2 others INTERGENIC	TF binding site BDTNP1_TFBS_dl
2R	5762919	2R_5762919_SNP [dm3] 2R_9875414_SNP [dm6]	G	A	1.169e^-8	7.943e^-4	UTR_5_PRIME CG12744 UPSTREAM cbx DOWNSTREAM Sec24AB INTRON CG12744	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2L	8528721	2L_8528721_SNP [dm3] 2L_8528721_SNP [dm6]	A	G	1.186e^-8	7.943e^-4	UPSTREAM lmgB & 2 others INTERGENIC	TF binding site BDTNP1_TFBS_dl
2L	8527696	2L_8527696_SNP [dm3] 2L_8527696_SNP [dm6]	C	T	1.274e^-8	8.243e^-4	SYNONYMOUS_CODING lmgB UTR_3_PRIME lmgA DOWNSTREAM lmgA	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	8523852	2L_8523852_SNP [dm3] 2L_8523852_SNP [dm6]	C	G	1.580e^-8	9.879e^-4	NON_SYNONYMOUS_CODING Acer	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2L	8517836	2L_8517836_SNP [dm3] 2L_8517836_SNP [dm6]	A	G	2.063e^-8	0.001	NON_SYNONYMOUS_CODING CG13090 UPSTREAM mRpL51	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Ubx
2R	5760716	2R_5760716_SNP [dm3] 2R_9873211_SNP [dm6]	C	T	2.656e^-8	0.002	INTRON cbx & 1 other	TF binding site BDTNP1_TFBS_hb mE1_TFBS_cad mE1_TFBS_sens
2L	8528886	2L_8528886_SNP [dm3] 2L_8528886_SNP [dm6]	T	C	2.992e^-8	0.002	UPSTREAM lmgB & 2 others INTERGENIC	TF binding site BDTNP1_TFBS_dl
2L	8524431	2L_8524431_SNP [dm3] 2L_8524431_SNP [dm6]	A	T	3.457e^-8	0.002	SYNONYMOUS_CODING Acer DOWNSTREAM lmgA & 1 other	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2R	5741733	2R_5741733_SNP [dm3] 2R_9854228_SNP [dm6]	A	G	5.940e^-8	0.003	INTRON CG1516	TF binding site mE1_TFBS_cad
2L	8522458	2L_8522458_SNP [dm3] 2L_8522458_SNP [dm6]	T	C	6.303e^-8	0.003	SYNONYMOUS_CODING Acer DOWNSTREAM CG13091	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2L	8524089	2L_8524089_SNP [dm3] 2L_8524089_SNP [dm6]	G	A	7.413e^-8	0.004	SYNONYMOUS_CODING Acer DOWNSTREAM lmgA & 1 other	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	5731332	2R_5731332_SNP [dm3] 2R_9843827_SNP [dm6]	C	T	7.576e^-8	0.004	SYNONYMOUS_CODING CG1667	TF binding site mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_ttk mE1_TFBS_Ubx
2L	8527621	2L_8527621_SNP [dm3] 2L_8527621_SNP [dm6]	T	C	8.205e^-8	0.004	SYNONYMOUS_CODING lmgB UTR_3_PRIME lmgA DOWNSTREAM lmgA	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	8523948	2L_8523948_SNP [dm3] 2L_8523948_SNP [dm6]	G	C	1.036e^-7	0.005	SYNONYMOUS_CODING Acer	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	8520815	2L_8520815_SNP [dm3] 2L_8520815_SNP [dm6]	T	C	1.064e^-7	0.005	NON_SYNONYMOUS_CODING CG13091	TF binding site BDTNP1_TFBS_dl mE1_TFBS_sens
2R	5735501	2R_5735501_SNP [dm3] 2R_9847996_SNP [dm6]	T	A	1.137e^-7	0.005	UPSTREAM CG1671 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cnc mE1_TFBS_HSA
2L	8522486	2L_8522486_SNP [dm3] 2L_8522486_SNP [dm6]	T	C	1.310e^-7	0.006	SYNONYMOUS_CODING Acer DOWNSTREAM CG13091	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2L	8525183	2L_8525183_SNP [dm3] 2L_8525183_SNP [dm6]	G	T	1.477e^-7	0.006	UTR_3_PRIME Acer & 2 others DOWNSTREAM lmgA & 2 others
2L	8529738	2L_8529738_SNP [dm3] 2L_8529738_SNP [dm6]	A	C	1.867e^-7	0.008	INTRON CG17834	TF binding site BDTNP1_TFBS_prd mE1_TFBS_HSA
2L	8521004	2L_8521004_SNP [dm3] 2L_8521004_SNP [dm6]	C	A	1.961e^-7	0.008	NON_SYNONYMOUS_CODING CG13091 UPSTREAM Acer	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_sens
2R	5777768	2R_5777768_DEL [dm3] 2R_9890263_DEL [dm6]	AGACCTTTAA	A	2.093e^-7	0.008	DOWNSTREAM CG12923 INTRON CG1513 & 1 other
2R	5762328	2R_5762328_SNP [dm3] 2R_9874823_SNP [dm6]	A	G	2.175e^-7	0.008	SPLICE_SITE_REGION cbx UTR_5_PRIME cbx UPSTREAM CG12744	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	8530229	2L_8530229_SNP [dm3] 2L_8530229_SNP [dm6]	G	A	2.333e^-7	0.009	INTRON CG17834	TF binding site BDTNP1_TFBS_prd mE1_TFBS_HSA
2R	5763531	2R_5763531_SNP [dm3] 2R_9876026_SNP [dm6]	C	T	2.508e^-7	0.009	SYNONYMOUS_CODING CG12744 UPSTREAM cbx DOWNSTREAM Sec24AB	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
2L	8513188	2L_8513188_SNP [dm3] 2L_8513188_SNP [dm6]	A	G	3.338e^-7	0.012	SYNONYMOUS_CODING CG13097	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_sens
2R	5762331	2R_5762331_SNP [dm3] 2R_9874826_SNP [dm6]	C	G	3.571e^-7	0.013	UTR_5_PRIME cbx UPSTREAM CG12744	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	5771199	2R_5771199_SNP [dm3] 2R_9883694_SNP [dm6]	C	T	3.585e^-7	0.013	UTR_3_PRIME CG1513
2L	8526126	2L_8526126_SNP [dm3] 2L_8526126_SNP [dm6]	T	G	4.008e^-7	0.014	UTR_3_PRIME lmgB & 1 other DOWNSTREAM lmgA & 2 others
2R	5735502	2R_5735502_SNP [dm3] 2R_9847997_SNP [dm6]	C	A	4.546e^-7	0.016	UPSTREAM CG1671 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cnc mE1_TFBS_HSA
2L	8530244	2L_8530244_SNP [dm3] 2L_8530244_SNP [dm6]	G	A	4.770e^-7	0.016	INTRON CG17834	TF binding site BDTNP1_TFBS_prd mE1_TFBS_HSA
2R	5735181	2R_5735181_SNP [dm3] 2R_9847676_SNP [dm6]	T	G	5.150e^-7	0.017	UPSTREAM CG1671 INTRON Prosalpha7	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 mE1_TFBS_cnc mE1_TFBS_HSA
2L	8517273	2L_8517273_SNP [dm3] 2L_8517273_SNP [dm6]	A	G	5.585e^-7	0.018	NON_SYNONYMOUS_CODING mRpL51 UPSTREAM CG13090 DOWNSTREAM PIG-U	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Ubx
2R	5734458	2R_5734458_SNP [dm3] 2R_9846953_SNP [dm6]	T	G	7.132e^-7	0.023	UPSTREAM Orc6 INTRON Prosalpha7	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
2R	5735512	2R_5735512_SNP [dm3] 2R_9848007_SNP [dm6]	C	T	8.266e^-7	0.026	UPSTREAM CG1671 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cnc mE1_TFBS_HSA
2R	5731874	2R_5731874_SNP [dm3] 2R_9844369_SNP [dm6]	C	A	8.420e^-7	0.026	SYNONYMOUS_CODING CG1667	TF binding site mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_ttk
2L	8524462	2L_8524462_SNP [dm3] 2L_8524462_SNP [dm6]	C	T	9.392e^-7	0.028	SYNONYMOUS_CODING Acer DOWNSTREAM lmgA & 1 other	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2L	8514811	2L_8514811_SNP [dm3] 2L_8514811_SNP [dm6]	C	T	9.458e^-7	0.028	UTR_5_PRIME CG13097 UPSTREAM PIG-U	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_Ubx
2L	8524383	2L_8524383_SNP [dm3] 2L_8524383_SNP [dm6]	C	T	1.014e^-6	0.029	SYNONYMOUS_CODING Acer DOWNSTREAM lmgA & 1 other	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2L	8515600	2L_8515600_SNP [dm3] 2L_8515600_SNP [dm6]	T	C	1.019e^-6	0.029	NON_SYNONYMOUS_CODING PIG-U UPSTREAM CG13097	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	8530270	2L_8530270_SNP [dm3] 2L_8530270_SNP [dm6]	C	A	1.116e^-6	0.032	INTRON CG17834	TF binding site BDTNP1_TFBS_prd mE1_TFBS_HSA
2L	8515461	2L_8515461_SNP [dm3] 2L_8515461_SNP [dm6]	T	C	1.160e^-6	0.032	SYNONYMOUS_CODING PIG-U UPSTREAM CG13097	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	5717075	2R_5717075_SNP [dm3] 2R_9829570_SNP [dm6]	G	A	1.682e^-6	0.046	SYNONYMOUS_CODING hebe	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2R	5738442	2R_5738442_SNP [dm3] 2R_9850937_SNP [dm6]	A	G	1.752e^-6	0.047	UTR_3_PRIME CG1516 DOWNSTREAM CG1671
2L	8514835	2L_8514835_SNP [dm3] 2L_8514835_SNP [dm6]	A	T	1.758e^-6	0.047	UTR_5_PRIME CG13097 UPSTREAM PIG-U	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_Ubx
2L	8515035	2L_8515035_SNP [dm3] 2L_8515035_SNP [dm6]	G	T	1.860e^-6	0.049	UPSTREAM PIG-U & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_eve mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_Ubx
2L	8515387	2L_8515387_SNP [dm3] 2L_8515387_SNP [dm6]	C	T	1.926e^-6	0.05	SYNONYMOUS_CODING PIG-U UPSTREAM CG13097	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	8515482	2L_8515482_SNP [dm3] 2L_8515482_SNP [dm6]	C	T	2.127e^-6	0.055	SYNONYMOUS_CODING PIG-U UPSTREAM CG13097	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	5714577	2R_5714577_INS [dm3] 2R_9827072_INS [dm6]	G	GTA	2.377e^-6	0.06	FRAME_SHIFT dila INTRON dila	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad
2L	8529262	2L_8529262_SNP [dm3] 2L_8529262_SNP [dm6]	T	C	2.475e^-6	0.061	UTR_5_PRIME CG17834 UPSTREAM lmgA & 1 other	TF binding site BDTNP1_TFBS_dl
2R	5710601	2R_5710601_SNP [dm3] 2R_9823096_SNP [dm6]	T	A	2.507e^-6	0.061	UTR_3_PRIME dila UPSTREAM CG30001	TF binding site mE1_TFBS_cad mE1_TFBS_hkb mE1_TFBS_HSA mE1_TFBS_ttk
2R	5790017	2R_5790017_SNP [dm3] 2R_9902512_SNP [dm6]	A	T	2.521e^-6	0.061	INTRON CG1441	TF binding site mE1_TFBS_cad
2R	5735690	2R_5735690_SNP [dm3] 2R_9848185_SNP [dm6]	A	G	2.727e^-6	0.066	UPSTREAM Prosalpha7 INTRON CG1671	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cnc mE1_TFBS_HSA
2R	5736012	2R_5736012_SNP [dm3] 2R_9848507_SNP [dm6]	G	A	3.131e^-6	0.074	SYNONYMOUS_CODING CG1671 UPSTREAM Prosalpha7	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
2L	8513479	2L_8513479_SNP [dm3] 2L_8513479_SNP [dm6]	G	A	3.465e^-6	0.081	SYNONYMOUS_CODING CG13097	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	5715403	2R_5715403_SNP [dm3] 2R_9827898_SNP [dm6]	G	A	4.111e^-6	0.095	UPSTREAM dila DOWNSTREAM hebe INTERGENIC
2R	13023236	2R_13023236_SNP [dm3] 2R_17135731_SNP [dm6]	T	G	4.164e^-6	0.095	UPSTREAM Gbp DOWNSTREAM CG11400 EXON CR44391
2L	8515658	2L_8515658_SNP [dm3] 2L_8515658_SNP [dm6]	G	A	4.185e^-6	0.095	NON_SYNONYMOUS_CODING PIG-U UPSTREAM CG13097	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_sens
2L	8525341	2L_8525341_SNP [dm3] 2L_8525341_SNP [dm6]	C	A	4.470e^-6	0.098	UTR_3_PRIME Acer & 2 others DOWNSTREAM lmgA & 2 others
2L	8523105	2L_8523105_SNP [dm3] 2L_8523105_SNP [dm6]	G	C	4.471e^-6	0.098	INTRON Acer	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad
2L	8523133	2L_8523133_SNP [dm3] 2L_8523133_SNP [dm6]	G	A	4.471e^-6	0.098	INTRON Acer	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad
2L	8527887	2L_8527887_SNP [dm3] 2L_8527887_SNP [dm6]	C	A	4.530e^-6	0.098	NON_SYNONYMOUS_CODING lmgB UTR_3_PRIME lmgA DOWNSTREAM lmgA	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2R	8467841	2R_8467841_SNP [dm3] 2R_12580336_SNP [dm6]	G	A	4.625e^-6	0.099	NON_SYNONYMOUS_CODING Sin3A
2L	8513770	2L_8513770_SNP [dm3] 2L_8513770_SNP [dm6]	G	A	4.786e^-6	0.1	SYNONYMOUS_CODING CG13097	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	8513779	2L_8513779_SNP [dm3] 2L_8513779_SNP [dm6]	T	C	4.786e^-6	0.1	SYNONYMOUS_CODING CG13097	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	5721479	2R_5721479_SNP [dm3] 2R_9833974_SNP [dm6]	G	C	4.831e^-6	0.1	UPSTREAM hebe INTRON hebe	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	8288353	3L_8288353_SNP [dm3] 3L_8295253_SNP [dm6]	T	A	4.897e^-6	0.1	UTR_5_PRIME CG7201
2R	5781559	2R_5781559_SNP [dm3] 2R_9894054_SNP [dm6]	C	T	4.949e^-6	0.1	NON_SYNONYMOUS_CODING CG30007
2R	5714614	2R_5714614_SNP [dm3] 2R_9827109_SNP [dm6]	T	C	5.187e^-6	0.102	NON_SYNONYMOUS_CODING dila DOWNSTREAM hebe	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad
2R	5779845	2R_5779845_SNP [dm3] 2R_9892340_SNP [dm6]	A	T	5.257e^-6	0.102	NON_SYNONYMOUS_CODING CG30007 UPSTREAM CG1513	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	5777267	2R_5777267_SNP [dm3] 2R_9889762_SNP [dm6]	G	A	5.280e^-6	0.102	UPSTREAM CG30008 DOWNSTREAM CG12923 INTRON CG1513
2R	5707119	2R_5707119_SNP [dm3] 2R_9819614_SNP [dm6]	C	T	5.287e^-6	0.102	UPSTREAM CG34033 INTRON CG1648	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_HSA
3R	19066093	3R_19066093_SNP [dm3] 3R_23240371_SNP [dm6]	T	G	5.691e^-6	0.108	UPSTREAM CG4467 INTRON CG4467
2R	5716533	2R_5716533_SNP [dm3] 2R_9829028_SNP [dm6]	C	G	5.694e^-6	0.108	NON_SYNONYMOUS_CODING hebe	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	8515377	2L_8515377_SNP [dm3] 2L_8515377_SNP [dm6]	T	C	5.843e^-6	0.11	SYNONYMOUS_CODING PIG-U UPSTREAM CG13097	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens

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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=1.075e^-21)
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_3R_K	7.9522	0.0188

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2253 significant hits at p-value < 0.001. The 1000 top results are displayed in the table below.

Variant impact HIGH MODERATE LOW MODIFIER

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Search:

Chromosome	Position	ID	Reference	Variant	p-value	FDR_BH	Transcript annotation	Binding site annotation
3L	11016619	3L_11016619_SNP [dm3] 3L_11023519_SNP [dm6]	T	A	4.241e^-8	0.08	UPSTREAM Fad2 INTERGENIC	TF binding site BDTNP1_TFBS_twi
3L	11021221	3L_11021221_SNP [dm3] 3L_11028121_SNP [dm6]	A	T	1.612e^-7	0.119	SYNONYMOUS_CODING CG32081 DOWNSTREAM CG32079
3L	11004879	3L_11004879_SNP [dm3] 3L_11011779_SNP [dm6]	A	G	2.529e^-7	0.119	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_inv
3R	15074808	3R_15074808_SNP [dm3] 3R_19249086_SNP [dm6]	T	C	2.536e^-7	0.119	UPSTREAM CG5217 INTERGENIC	TF binding site mE1_TFBS_inv
3R	7859559	3R_7859559_SNP [dm3] 3R_12033837_SNP [dm6]	T	C	5.209e^-7	0.195	SYNONYMOUS_CODING ssp5	TF binding site BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	11004941	3L_11004941_SNP [dm3] 3L_11011841_SNP [dm6]	T	G	7.931e^-7	0.215	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_inv
3R	24947353	3R_24947353_SNP [dm3] 3R_29121631_SNP [dm6]	G	T	8.079e^-7	0.215	INTRON yem	regulatory region FlyBase TF binding site BDTNP1_TFBS_dl mE1_TFBS_sens
3L	12184966	3L_12184966_SNP [dm3] 3L_12191866_SNP [dm6]	G	T	9.183e^-7	0.215	NON_SYNONYMOUS_CODING Est-P DOWNSTREAM thoc6
3R	13714805	3R_13714805_SNP [dm3] 3R_17889083_SNP [dm6]	T	G	1.614e^-6	0.336	INTRON Rim
3L	11005187	3L_11005187_INS [dm3] 3L_11012087_INS [dm6]	T	TT	1.802e^-6	0.338	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_inv
3L	12163798	3L_12163798_SNP [dm3] 3L_12170698_SNP [dm6]	A	G	2.192e^-6	0.374	INTRON Rh7
3L	12185525	3L_12185525_SNP [dm3] 3L_12192425_SNP [dm6]	C	T	2.526e^-6	0.395	SPLICE_SITE_ACCEPTOR thoc6 SYNONYMOUS_CODING Est-P DOWNSTREAM thoc6 INTRON thoc6
2L	15641089	2L_15641089_SNP [dm3] 2L_15641089_SNP [dm6]	A	C	3.196e^-6	0.441	INTERGENIC
3R	26260744	3R_26260744_SNP [dm3] 3R_30435022_SNP [dm6]	T	G	3.289e^-6	0.441	UTR_3_PRIME CG15534 DOWNSTREAM CG15537
3L	11017325	3L_11017325_SNP [dm3] 3L_11024225_SNP [dm6]	C	G	3.730e^-6	0.45	SYNONYMOUS_CODING Fad2	TF binding site BDTNP1_TFBS_twi mE1_TFBS_sens
2L	2389228	2L_2389228_SNP [dm3] 2L_2389228_SNP [dm6]	A	C	4.135e^-6	0.45	DOWNSTREAM CG43750 INTERGENIC	TF binding site BDTNP1_TFBS_twi
3L	11015542	3L_11015542_SNP [dm3] 3L_11022442_SNP [dm6]	A	C	4.159e^-6	0.45	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	8608143	3L_8608143_SNP [dm3] 3L_8615043_SNP [dm6]	C	T	4.314e^-6	0.45	SYNONYMOUS_CODING CG6282
3L	12458544	3L_12458544_SNP [dm3] 3L_12465444_SNP [dm6]	G	T	4.907e^-6	0.484	INTRON eyg	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo
3L	12464851	3L_12464851_INS [dm3] 3L_12471751_INS [dm6]	G	GG	5.460e^-6	0.512	UTR_5_PRIME CG10616	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_h mE1_TFBS_HSA
3L	11015320	3L_11015320_INS [dm3] 3L_11022220_INS [dm6]	T	TT	6.695e^-6	0.598	INTERGENIC	TF binding site mE1_TFBS_cad
3L	19378294	3L_19378294_SNP [dm3] 3L_19385194_SNP [dm6]	A	G	7.577e^-6	0.6	INTRON CG32206
3L	12163807	3L_12163807_SNP [dm3] 3L_12170707_SNP [dm6]	T	C	8.049e^-6	0.6	INTRON Rh7
3L	12185514	3L_12185514_SNP [dm3] 3L_12192414_SNP [dm6]	G	T	8.676e^-6	0.6	NON_SYNONYMOUS_CODING Est-P UTR_3_PRIME thoc6 DOWNSTREAM thoc6
3L	12186824	3L_12186824_SNP [dm3] 3L_12193724_SNP [dm6]	A	G	9.551e^-6	0.6	UPSTREAM thoc6 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 mE1_TFBS_HSA mE1_TFBS_jumu
3L	13466794	3L_13466794_SNP [dm3] 3L_13473694_SNP [dm6]	G	C	9.615e^-6	0.6	INTRON CG10089
3R	24700490	3R_24700490_SNP [dm3] 3R_28874768_SNP [dm6]	C	T	1.023e^-5	0.6	SYNONYMOUS_CODING CG14529 UPSTREAM CG14528 INTRON CG33203	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3R	27166882	3R_27166882_INS [dm3] 3R_31341160_INS [dm6]	C	CGC	1.028e^-5	0.6	INTRON CG34347
3R	9252601	3R_9252601_SNP [dm3] 3R_13426879_SNP [dm6]	T	C	1.073e^-5	0.6	SYNONYMOUS_CODING Act87E UPSTREAM CR45591	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2L	14463787	2L_14463787_SNP [dm3] 2L_14463787_SNP [dm6]	A	C	1.106e^-5	0.6	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_Kr
3R	26260569	3R_26260569_SNP [dm3] 3R_30434847_SNP [dm6]	G	C	1.129e^-5	0.6	DOWNSTREAM CG15537 INTRON CG15534
3L	9272066	3L_9272066_SNP [dm3] 3L_9278966_SNP [dm6]	G	A	1.161e^-5	0.6	INTRON GluRIB
3L	12186593	3L_12186593_SNP [dm3] 3L_12193493_SNP [dm6]	A	G	1.162e^-5	0.6	SPLICE_SITE_REGION thoc6 SYNONYMOUS_CODING thoc6 DOWNSTREAM Est-P	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 mE1_TFBS_HSA mE1_TFBS_jumu
X	15535875	X_15535875_SNP [dm3] X_15641842_SNP [dm6]	A	G	1.165e^-5	0.6	EXON CR44893
3L	11018550	3L_11018550_INS [dm3] 3L_11025450_INS [dm6]	G	GCT	1.190e^-5	0.6	UPSTREAM CG32079 DOWNSTREAM Fad2 INTERGENIC
2L	10730671	2L_10730671_SNP [dm3] 2L_10730671_SNP [dm6]	T	C	1.215e^-5	0.6	DOWNSTREAM CG6443 & 1 other INTRON CG17118	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3L	11017014	3L_11017014_SNP [dm3] 3L_11023914_SNP [dm6]	C	A	1.318e^-5	0.6	SYNONYMOUS_CODING Fad2	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3R	24821956	3R_24821956_SNP [dm3] 3R_28996234_SNP [dm6]	C	T	1.339e^-5	0.6	INTRON wat	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	11943429	2R_11943429_SNP [dm3] 2R_16055924_SNP [dm6]	C	G	1.344e^-5	0.6	INTRON CG8405
3L	12464869	3L_12464869_SNP [dm3] 3L_12471769_SNP [dm6]	A	T	1.387e^-5	0.6	UTR_5_PRIME CG10616	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_h mE1_TFBS_HSA
3R	26260564	3R_26260564_SNP [dm3] 3R_30434842_SNP [dm6]	G	A	1.393e^-5	0.6	DOWNSTREAM CG15537 INTRON CG15534
3R	25006176	3R_25006176_SNP [dm3] 3R_29180454_SNP [dm6]	C	A	1.416e^-5	0.6	INTRON CG14509
3L	11017214	3L_11017214_SNP [dm3] 3L_11024114_SNP [dm6]	A	G	1.424e^-5	0.6	SYNONYMOUS_CODING Fad2	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
2L	18256181	2L_18256181_SNP [dm3] 2L_18256181_SNP [dm6]	G	T	1.454e^-5	0.6	UPSTREAM CR43408 INTRON CG42750	TF binding site mE1_TFBS_HSA
3L	11017013	3L_11017013_SNP [dm3] 3L_11023913_SNP [dm6]	C	A	1.544e^-5	0.6	SYNONYMOUS_CODING Fad2	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3R	22322786	3R_22322786_SNP [dm3] 3R_26497064_SNP [dm6]	T	C	1.635e^-5	0.6	INTRON plum
3R	27207574	3R_27207574_SNP [dm3] 3R_31381852_SNP [dm6]	G	A	1.648e^-5	0.6	UPSTREAM CG1607 INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA
2L	16391341	2L_16391341_SNP [dm3] 2L_16391341_SNP [dm6]	A	C	1.652e^-5	0.6	INTERGENIC
2L	14478337	2L_14478337_SNP [dm3] 2L_14478337_SNP [dm6]	C	T	1.657e^-5	0.6	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Kr
3R	24947652	3R_24947652_SNP [dm3] 3R_29121930_SNP [dm6]	A	G	1.660e^-5	0.6	INTRON yem	regulatory region FlyBase TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
3L	11967156	3L_11967156_SNP [dm3] 3L_11974056_SNP [dm6]	T	C	1.742e^-5	0.6	UPSTREAM CG42397 & 1 other INTERGENIC
2L	15735651	2L_15735651_SNP [dm3] 2L_15735651_SNP [dm6]	C	T	1.759e^-5	0.6	INTRON CycE	regulatory region FlyBase REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3L	1847616	3L_1847616_SNP [dm3] 3L_1847616_SNP [dm6]	A	G	1.761e^-5	0.6	INTERGENIC
3L	12462225	3L_12462225_SNP [dm3] 3L_12469125_SNP [dm6]	C	A	1.840e^-5	0.6	UTR_3_PRIME CG32102	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_kn
X	17620747	X_17620747_SNP [dm3] X_17726714_SNP [dm6]	T	A	1.843e^-5	0.6	INTRON CG42684
2L	15735639	2L_15735639_SNP [dm3] 2L_15735639_SNP [dm6]	C	A	1.905e^-5	0.6	INTRON CycE	regulatory region FlyBase REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3R	16473291	3R_16473291_SNP [dm3] 3R_20647569_SNP [dm6]	A	G	1.961e^-5	0.6	SYNONYMOUS_CODING GluRIIE
2R	13531220	2R_13531220_SNP [dm3] 2R_17643715_SNP [dm6]	C	T	1.972e^-5	0.6	INTERGENIC
3R	9252571	3R_9252571_SNP [dm3] 3R_13426849_SNP [dm6]	T	C	1.978e^-5	0.6	SYNONYMOUS_CODING Act87E UPSTREAM CR45591	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	9459061	3R_9459061_SNP [dm3] 3R_13633339_SNP [dm6]	G	C	2.030e^-5	0.6	SYNONYMOUS_CODING CG10841
3R	17935131	3R_17935131_SNP [dm3] 3R_22109409_SNP [dm6]	C	T	2.045e^-5	0.6	INTRON CG5778	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
2R	8145393	2R_8145393_SNP [dm3] 2R_12257888_SNP [dm6]	A	T	2.058e^-5	0.6	INTRON Vha36-2	TF binding site mE1_TFBS_cad
3R	11885217	3R_11885217_SNP [dm3] 3R_16059495_SNP [dm6]	C	T	2.068e^-5	0.6	SYNONYMOUS_CODING msps
3L	12184935	3L_12184935_SNP [dm3] 3L_12191835_SNP [dm6]	T	A	2.114e^-5	0.6	NON_SYNONYMOUS_CODING Est-P DOWNSTREAM thoc6
X	10119522	X_10119522_SNP [dm3] X_10225489_SNP [dm6]	C	T	2.117e^-5	0.6	SYNONYMOUS_CODING CG34408	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	3735862	3L_3735862_SNP [dm3] 3L_3735862_SNP [dm6]	T	G	2.187e^-5	0.6	INTRON CG32264
2L	8989393	2L_8989393_SNP [dm3] 2L_8989393_SNP [dm6]	G	A	2.195e^-5	0.6	UTR_5_PRIME rost UPSTREAM rost
3L	12063199	3L_12063199_SNP [dm3] 3L_12070099_SNP [dm6]	G	C	2.253e^-5	0.6	NON_SYNONYMOUS_CODING Sema-5c	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	20704871	3R_20704871_INS [dm3] 3R_24879149_INS [dm6]	T	TGC	2.309e^-5	0.6	DOWNSTREAM CG31381 INTRON CG11089	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3L	11967139	3L_11967139_SNP [dm3] 3L_11974039_SNP [dm6]	A	T	2.353e^-5	0.6	UPSTREAM CG42397 & 1 other INTERGENIC
3L	12185838	3L_12185838_SNP [dm3] 3L_12192738_SNP [dm6]	G	A	2.363e^-5	0.6	SYNONYMOUS_CODING thoc6 DOWNSTREAM Est-P
3R	14361245	3R_14361245_SNP [dm3] 3R_18535523_SNP [dm6]	A	T	2.377e^-5	0.6	INTRON fru
3L	12185848	3L_12185848_SNP [dm3] 3L_12192748_SNP [dm6]	T	C	2.378e^-5	0.6	SYNONYMOUS_CODING thoc6 DOWNSTREAM Est-P	TF binding site mE1_TFBS_sens
2L	2767212	2L_2767212_SNP [dm3] 2L_2767212_SNP [dm6]	T	C	2.445e^-5	0.6	UTR_3_PRIME aph-1 UPSTREAM Taf10 DOWNSTREAM Taf10b & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_sens
3L	12069108	3L_12069108_INS [dm3] 3L_12076008_INS [dm6]	G	GCAGTTG	2.459e^-5	0.6	INTRON Sema-5c
3R	26260573	3R_26260573_SNP [dm3] 3R_30434851_SNP [dm6]	T	A	2.481e^-5	0.6	DOWNSTREAM CG15537 INTRON CG15534
3R	9251965	3R_9251965_SNP [dm3] 3R_13426243_SNP [dm6]	A	C	2.481e^-5	0.6	UPSTREAM Act87E & 1 other INTRON Act87E	TF binding site BDTNP1_TFBS_twi
3R	16473297	3R_16473297_SNP [dm3] 3R_20647575_SNP [dm6]	A	G	2.514e^-5	0.6	SYNONYMOUS_CODING GluRIIE
3R	11883481	3R_11883481_SNP [dm3] 3R_16057759_SNP [dm6]	T	C	2.527e^-5	0.6	SYNONYMOUS_CODING msps
3R	24954614	3R_24954614_SNP [dm3] 3R_29128892_SNP [dm6]	A	T	2.574e^-5	0.6	DOWNSTREAM CG11880 INTRON dgt6	TF binding site mE1_TFBS_cad
3R	24954655	3R_24954655_SNP [dm3] 3R_29128933_SNP [dm6]	T	A	2.614e^-5	0.6	DOWNSTREAM CG11880 INTRON dgt6	TF binding site mE1_TFBS_cad
2L	14478561	2L_14478561_SNP [dm3] 2L_14478561_SNP [dm6]	T	A	2.623e^-5	0.6	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Kr
2L	16025035	2L_16025035_SNP [dm3] 2L_16025035_SNP [dm6]	A	G	2.702e^-5	0.611	INTRON beat-Ic
3R	9748163	3R_9748163_SNP [dm3] 3R_13922441_SNP [dm6]	G	T	2.751e^-5	0.611	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	15641105	2L_15641105_DEL [dm3] 2L_15641105_DEL [dm6]	CTGCCATCTCCAATCT...	C	2.768e^-5	0.611	INTERGENIC
2L	14478322	2L_14478322_SNP [dm3] 2L_14478322_SNP [dm6]	G	C	2.801e^-5	0.611	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Kr
3R	6594384	3R_6594384_SNP [dm3] 3R_10768662_SNP [dm6]	T	G	2.915e^-5	0.621	NON_SYNONYMOUS_CODING CG45076 UPSTREAM TfIIFbeta DOWNSTREAM CG45076	TF binding site mE1_TFBS_chinmo
2L	6932879	2L_6932879_SNP [dm3] 2L_6932879_SNP [dm6]	A	G	2.941e^-5	0.621	SYNONYMOUS_CODING CG18304 DOWNSTREAM Hrb27C & 1 other	TF binding site mE1_TFBS_cad
3L	20660939	3L_20660939_SNP [dm3] 3L_20667839_SNP [dm6]	C	A	2.960e^-5	0.621	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	14618938	3R_14618938_DEL [dm3] 3R_18793216_DEL [dm6]	TG	T	3.006e^-5	0.621	UPSTREAM CG7720 INTRON CG7720
2L	434331	2L_434331_SNP [dm3] 2L_434331_SNP [dm6]	G	T	3.013e^-5	0.621	INTRON ex
3R	6628348	3R_6628348_SNP [dm3] 3R_10802626_SNP [dm6]	T	A	3.052e^-5	0.622	INTRON CG14692
3L	11020960	3L_11020960_SNP [dm3] 3L_11027860_SNP [dm6]	G	A	3.169e^-5	0.633	NON_SYNONYMOUS_CODING CG32081 DOWNSTREAM CG32079
3R	24954354	3R_24954354_SNP [dm3] 3R_29128632_SNP [dm6]	T	G	3.173e^-5	0.633	UTR_3_PRIME dgt6 DOWNSTREAM CG11880
2L	2767411	2L_2767411_SNP [dm3] 2L_2767411_SNP [dm6]	A	G	3.234e^-5	0.638	SYNONYMOUS_CODING Taf10b UPSTREAM Taf10 DOWNSTREAM aph-1	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_sens
3L	9054881	3L_9054881_DEL [dm3] 3L_9061781_DEL [dm6]	TAACAAAGTGC...	T	3.443e^-5	0.653	INTRON Argk
3L	11596613	3L_11596613_SNP [dm3] 3L_11603513_SNP [dm6]	A	G	3.456e^-5	0.653	INTRON CG7368	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	12185047	3L_12185047_SNP [dm3] 3L_12191947_SNP [dm6]	G	A	3.503e^-5	0.653	NON_SYNONYMOUS_CODING Est-P DOWNSTREAM thoc6
3R	16474292	3R_16474292_SNP [dm3] 3R_20648570_SNP [dm6]	C	G	3.510e^-5	0.653	NON_SYNONYMOUS_CODING GluRIIE DOWNSTREAM GluRIID
2L	16497795	2L_16497795_SNP [dm3] 2L_16497795_SNP [dm6]	A	G	3.512e^-5	0.653	INTRON Tpr2

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By genomic position
Variant impact
Gene name

Cuticul_7_C25_1 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results