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=2.014e^-4)
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_3R_Mo	0.08949

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	6.269	0.0435
In_3R_Mo	5.3132	0.0702

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2021 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

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Chromosome	Position	ID	Reference	Variant	p-value	FDR_BH	Transcript annotation	Binding site annotation
X	8394094	X_8394094_SNP [dm3] X_8500061_SNP [dm6]	A	G	5.714e^-7	0.919	INTRON CG33181
2L	5393422	2L_5393422_SNP [dm3] 2L_5393422_SNP [dm6]	T	C	1.332e^-6	0.919	INTERGENIC	TF binding site BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	6860355	2L_6860355_SNP [dm3] 2L_6860355_SNP [dm6]	G	A	4.529e^-6	0.919	SYNONYMOUS_CODING l_2_k09022 DOWNSTREAM Nha1	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
X	16665748	X_16665748_SNP [dm3] X_16771715_SNP [dm6]	T	G	4.748e^-6	0.919	INTRON if
X	4457446	X_4457446_SNP [dm3] X_4563413_SNP [dm6]	T	A	7.295e^-6	0.919	INTRON CR32773	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	19192902	2R_19192902_SNP [dm3] 2R_23305379_SNP [dm6]	C	A	7.714e^-6	0.919	INTERGENIC
2R	4200078	2R_4200078_DEL [dm3] 2R_8312573_DEL [dm6]	CTCTT	AA	8.077e^-6	0.919	DOWNSTREAM CR44450 INTERGENIC
2R	19284821	2R_19284821_SNP [dm3] 2R_23397298_SNP [dm6]	G	T	8.167e^-6	0.919	SYNONYMOUS_CODING CG3520 UPSTREAM CG3530	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	16460862	3L_16460862_SNP [dm3] 3L_16467762_SNP [dm6]	A	G	8.698e^-6	0.919	INTRON CG33158
2R	7150271	2R_7150271_SNP [dm3] 2R_11262766_SNP [dm6]	T	C	9.902e^-6	0.919	UPSTREAM Cpr47Ed INTERGENIC
2R	16562368	2R_16562368_SNP [dm3] 2R_20674863_SNP [dm6]	G	A	9.971e^-6	0.919	INTERGENIC	TF binding site mE1_TFBS_chinmo
3R	10242258	3R_10242258_SNP [dm3] 3R_14416536_SNP [dm6]	G	A	1.027e^-5	0.919	SYNONYMOUS_CODING cv-c	TF binding site BDTNP1_TFBS_twi mE1_TFBS_chinmo mE1_TFBS_HSA
3L	13651481	3L_13651481_SNP [dm3] 3L_13658381_SNP [dm6]	T	A	1.027e^-5	0.919	INTRON bru-3	TF binding site mE1_TFBS_chinmo
X	4457545	X_4457545_SNP [dm3] X_4563512_SNP [dm6]	A	G	1.214e^-5	0.919	INTRON CR32773	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	9315610	3L_9315610_SNP [dm3] 3L_9322510_SNP [dm6]	A	G	1.311e^-5	0.919	INTERGENIC
2R	20031864	2R_20031864_SNP [dm3] 2R_24144341_SNP [dm6]	A	G	1.429e^-5	0.919	INTRON Dat
X	12198795	X_12198795_SNP [dm3] X_12304762_SNP [dm6]	G	A	1.476e^-5	0.919	INTRON Ten-a
3R	8031059	3R_8031059_SNP [dm3] 3R_12205337_SNP [dm6]	G	A	1.480e^-5	0.919	INTERGENIC
3L	6088856	3L_6088856_SNP [dm3] 3L_6095756_SNP [dm6]	A	T	1.558e^-5	0.919	SYNONYMOUS_CODING loj	TF binding site mE1_TFBS_sens
2L	8743608	2L_8743608_SNP [dm3] 2L_8743608_SNP [dm6]	A	G	1.572e^-5	0.919	INTERGENIC
3R	10242056	3R_10242056_SNP [dm3] 3R_14416334_SNP [dm6]	G	T	1.650e^-5	0.919	INTRON cv-c	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
X	18993114	X_18993114_SNP [dm3] X_19099081_SNP [dm6]	A	G	1.673e^-5	0.919	INTERGENIC
3L	13308708	3L_13308708_SNP [dm3] 3L_13315608_SNP [dm6]	T	C	1.768e^-5	0.919	INTERGENIC
3L	2137193	3L_2137193_SNP [dm3] 3L_2137193_SNP [dm6]	A	T	1.965e^-5	0.919	INTRON zormin
3L	13163006	3L_13163006_SNP [dm3] 3L_13169906_SNP [dm6]	C	T	2.074e^-5	0.919	INTERGENIC	TF binding site mE1_TFBS_Kr
X	4457491	X_4457491_INS [dm3] X_4563458_INS [dm6]	T	TGGGCGGTT	2.110e^-5	0.919	INTRON CR32773	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA
X	4457494	X_4457494_INS [dm3] X_4563461_INS [dm6]	A	AAATGCC	2.110e^-5	0.919	INTRON CR32773	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA
X	4457497	X_4457497_INS [dm3] X_4563464_INS [dm6]	T	TGGTG	2.110e^-5	0.919	INTRON CR32773	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA
X	4457558	X_4457558_SNP [dm3] X_4563525_SNP [dm6]	T	C	2.110e^-5	0.919	INTRON CR32773	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	6468370	3L_6468370_SNP [dm3] 3L_6475270_SNP [dm6]	A	C	2.174e^-5	0.919	INTRON CG42747
2L	11225773	2L_11225773_SNP [dm3] 2L_11225773_SNP [dm6]	G	A	2.199e^-5	0.919	UTR_5_PRIME ab	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	8318360	2R_8318360_SNP [dm3] 2R_12430855_SNP [dm6]	C	A	2.242e^-5	0.919	NON_SYNONYMOUS_CODING CG43204 DOWNSTREAM DUBAI INTRON Nup54	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_D mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_sens
3L	9507480	3L_9507480_SNP [dm3] 3L_9514380_SNP [dm6]	T	C	2.310e^-5	0.919	SYNONYMOUS_CODING CG33700 UPSTREAM CG33702 & 1 other
X	4457501	X_4457501_SNP [dm3] X_4563468_SNP [dm6]	T	C	2.324e^-5	0.919	INTRON CR32773	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA
X	4457594	X_4457594_DEL [dm3] X_4563561_DEL [dm6]	ACCATGTAAGTCAACCCA...	A	2.332e^-5	0.919	INTRON CR32773	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	11886948	2R_11886948_SNP [dm3] 2R_15999443_SNP [dm6]	A	T	2.367e^-5	0.919	INTRON ATPCL
3L	14734317	3L_14734317_SNP [dm3] 3L_14741217_SNP [dm6]	T	G	2.493e^-5	0.919	INTRON ome
3L	8441742	3L_8441742_SNP [dm3] 3L_8448642_SNP [dm6]	T	G	2.532e^-5	0.919	INTRON CG6983	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_hkb mE1_TFBS_HSA mE1_TFBS_inv
2L	7881118	2L_7881118_SNP [dm3] 2L_7881118_SNP [dm6]	A	G	2.557e^-5	0.919	INTERGENIC	TF binding site mE1_TFBS_Trl
2L	2355460	2L_2355460_SNP [dm3] 2L_2355460_SNP [dm6]	A	T	2.624e^-5	0.919	INTRON CG9967 & 1 other
2L	6854075	2L_6854075_SNP [dm3] 2L_6854075_SNP [dm6]	G	A	2.656e^-5	0.919	UPSTREAM l_2_k09022 DOWNSTREAM Rca1 INTERGENIC	insulator Insulator_Class_I.mE01 TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
X	4457499	X_4457499_INS [dm3] X_4563466_INS [dm6]	A	AAGT	2.735e^-5	0.919	INTRON CR32773	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	15004294	3R_15004294_SNP [dm3] 3R_19178572_SNP [dm6]	G	A	2.904e^-5	0.919	DOWNSTREAM CG14282 INTRON CG5555
3L	1583784	3L_1583784_SNP [dm3] 3L_1583784_SNP [dm6]	C	A	3.168e^-5	0.919	INTRON CG13917	TF binding site BDTNP1_TFBS_z mE1_TFBS_HSA
3R	9682445	3R_9682445_SNP [dm3] 3R_13856723_SNP [dm6]	G	A	3.199e^-5	0.919	INTERGENIC
3L	9140044	3L_9140044_SNP [dm3] 3L_9146944_SNP [dm6]	A	T	3.225e^-5	0.919	UTR_3_PRIME Rdl	TF binding site BDTNP1_TFBS_twi mE1_TFBS_kn
2R	7150254	2R_7150254_SNP [dm3] 2R_11262749_SNP [dm6]	G	A	3.457e^-5	0.919	UPSTREAM Cpr47Ed INTERGENIC
2R	12472142	2R_12472142_SNP [dm3] 2R_16584637_SNP [dm6]	C	T	3.730e^-5	0.919	SYNONYMOUS_CODING Cdk4	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3L	10701916	3L_10701916_SNP [dm3] 3L_10708816_SNP [dm6]	T	G	3.849e^-5	0.919	INTERGENIC
X	13920806	X_13920806_SNP [dm3] X_14026773_SNP [dm6]	T	C	3.851e^-5	0.919	INTERGENIC
3L	7639739	3L_7639739_SNP [dm3] 3L_7646639_SNP [dm6]	A	G	4.012e^-5	0.919	INTERGENIC
3L	6052401	3L_6052401_SNP [dm3] 3L_6059301_SNP [dm6]	G	T	4.013e^-5	0.919	UPSTREAM CG6592 EXON CR45441	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_run
3L	13308723	3L_13308723_SNP [dm3] 3L_13315623_SNP [dm6]	A	T	4.082e^-5	0.919	INTERGENIC
2R	17656577	2R_17656577_SNP [dm3] 2R_21769072_SNP [dm6]	T	C	4.140e^-5	0.919	NON_SYNONYMOUS_CODING CG30395
2L	6860082	2L_6860082_SNP [dm3] 2L_6860082_SNP [dm6]	G	A	4.184e^-5	0.919	SYNONYMOUS_CODING l_2_k09022 DOWNSTREAM Nha1	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3R	15004313	3R_15004313_SNP [dm3] 3R_19178591_SNP [dm6]	G	A	4.195e^-5	0.919	DOWNSTREAM CG14282 INTRON CG5555	TF binding site mE1_TFBS_sens
3L	6791730	3L_6791730_SNP [dm3] 3L_6798630_SNP [dm6]	A	G	4.375e^-5	0.919	INTERGENIC
3L	6088886	3L_6088886_SNP [dm3] 3L_6095786_SNP [dm6]	T	A	4.380e^-5	0.919	SYNONYMOUS_CODING loj	TF binding site mE1_TFBS_sens
3L	9583446	3L_9583446_INS [dm3] 3L_9590346_INS [dm6]	A	ACTTA	4.391e^-5	0.919	INTRON CG42673
3R	15004303	3R_15004303_DEL [dm3] 3R_19178581_DEL [dm6]	TGGTTA	C	4.485e^-5	0.919	DOWNSTREAM CG14282 INTRON CG5555
3R	15004314	3R_15004314_SNP [dm3] 3R_19178592_SNP [dm6]	G	C	4.485e^-5	0.919	DOWNSTREAM CG14282 INTRON CG5555	TF binding site mE1_TFBS_sens
3L	16112536	3L_16112536_DEL [dm3] 3L_16119436_DEL [dm6]	ATTGA	A	4.494e^-5	0.919	INTRON Taf4	TF binding site mE1_TFBS_cad
2R	9839886	2R_9839886_INS [dm3] 2R_13952381_INS [dm6]	A	AA	4.503e^-5	0.919	INTRON AGO1	TF binding site BDTNP1_TFBS_dl
3L	10521307	3L_10521307_SNP [dm3] 3L_10528207_SNP [dm6]	G	A	4.544e^-5	0.919	INTRON A2bp1
X	17445092	X_17445092_SNP [dm3] X_17551059_SNP [dm6]	T	C	4.574e^-5	0.919	INTRON CG43658
2L	1954687	2L_1954687_SNP [dm3] 2L_1954687_SNP [dm6]	G	A	4.601e^-5	0.919	UPSTREAM erm INTRON erm	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
3L	10741595	3L_10741595_SNP [dm3] 3L_10748495_SNP [dm6]	C	T	4.681e^-5	0.919	INTERGENIC
2R	3650404	2R_3650404_SNP [dm3] 2R_7762899_SNP [dm6]	A	G	4.734e^-5	0.919	INTRON CG30497 & 1 other
3L	9507191	3L_9507191_SNP [dm3] 3L_9514091_SNP [dm6]	A	G	4.745e^-5	0.919	UPSTREAM CG33702 & 1 other DOWNSTREAM CG33700 INTERGENIC
3L	16744830	3L_16744830_SNP [dm3] 3L_16751730_SNP [dm6]	C	G	4.776e^-5	0.919	INTERGENIC
X	9186904	X_9186904_SNP [dm3] X_9292871_SNP [dm6]	T	C	4.840e^-5	0.919	INTRON lz	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	4123984	3L_4123984_SNP [dm3] 3L_4123984_SNP [dm6]	A	T	4.861e^-5	0.919	UTR_3_PRIME ens
2R	18488998	2R_18488998_SNP [dm3] 2R_22601493_SNP [dm6]	T	A	4.902e^-5	0.919	DOWNSTREAM CG4269 INTRON CG4294	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	6850382	2L_6850382_SNP [dm3] 2L_6850382_SNP [dm6]	C	T	4.904e^-5	0.919	INTERGENIC	TF binding site BDTNP1_TFBS_twi
2L	15328274	2L_15328274_SNP [dm3] 2L_15328274_SNP [dm6]	C	T	4.970e^-5	0.919	INTERGENIC	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad mE1_TFBS_HSA
2R	15090423	2R_15090423_SNP [dm3] 2R_19202918_SNP [dm6]	T	G	5.104e^-5	0.919	INTRON hppy
2R	12880251	2R_12880251_DEL [dm3] 2R_16992746_DEL [dm6]	CTC	C	5.106e^-5	0.919	INTRON Cbp53E
3L	16460864	3L_16460864_SNP [dm3] 3L_16467764_SNP [dm6]	C	T	5.121e^-5	0.919	INTRON CG33158
3L	16744832	3L_16744832_SNP [dm3] 3L_16751732_SNP [dm6]	C	G	5.126e^-5	0.919	INTERGENIC
X	16909925	X_16909925_SNP [dm3] X_17015892_SNP [dm6]	C	G	5.143e^-5	0.919	INTRON CG45002
2R	7150261	2R_7150261_DEL [dm3] 2R_11262756_DEL [dm6]	TGACTGTAA	T	5.251e^-5	0.919	UPSTREAM Cpr47Ed INTERGENIC
2L	3420720	2L_3420720_SNP [dm3] 2L_3420720_SNP [dm6]	T	C	5.255e^-5	0.919	INTRON pgant2
2L	11226037	2L_11226037_SNP [dm3] 2L_11226037_SNP [dm6]	G	T	5.322e^-5	0.919	INTRON ab	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
3L	9140046	3L_9140046_SNP [dm3] 3L_9146946_SNP [dm6]	T	C	5.350e^-5	0.919	UTR_3_PRIME Rdl	TF binding site BDTNP1_TFBS_twi mE1_TFBS_kn
3L	12604028	3L_12604028_SNP [dm3] 3L_12610928_SNP [dm6]	C	A	5.424e^-5	0.919	INTRON caup	TF binding site mE1_TFBS_HSA
2L	5405578	2L_5405578_SNP [dm3] 2L_5405578_SNP [dm6]	G	A	5.429e^-5	0.919	INTRON H15
2R	18494413	2R_18494413_SNP [dm3] 2R_22606908_SNP [dm6]	T	C	5.430e^-5	0.919	UPSTREAM snoRNA:Psi28S-1175a & 3 others DOWNSTREAM snoRNA:Me28S-G2173 INTRON RpS16	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_sens
2R	14052697	2R_14052697_SNP [dm3] 2R_18165192_SNP [dm6]	C	A	5.452e^-5	0.919	SYNONYMOUS_CODING Nup75 DOWNSTREAM CG10915
X	5972530	X_5972530_SNP [dm3] X_6078497_SNP [dm6]	T	C	5.456e^-5	0.919	UPSTREAM CG4666 DOWNSTREAM CG4660 INTERGENIC
2L	1953926	2L_1953926_SNP [dm3] 2L_1953926_SNP [dm6]	G	A	5.514e^-5	0.919	INTRON erm	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	3969662	3L_3969662_SNP [dm3] 3L_3969662_SNP [dm6]	T	C	5.577e^-5	0.919	INTERGENIC
3L	6758469	3L_6758469_SNP [dm3] 3L_6765369_SNP [dm6]	A	T	5.618e^-5	0.919	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	13916030	2R_13916030_SNP [dm3] 2R_18028525_SNP [dm6]	C	T	5.671e^-5	0.919	INTERGENIC
3L	9140053	3L_9140053_SNP [dm3] 3L_9146953_SNP [dm6]	T	A	5.680e^-5	0.919	UTR_3_PRIME Rdl	TF binding site BDTNP1_TFBS_twi mE1_TFBS_kn
2R	17063339	2R_17063339_INS [dm3] 2R_21175834_INS [dm6]	C	AAGCTGAACAAATGAATCCC...	5.711e^-5	0.919	INTRON Pu
3L	1583967	3L_1583967_SNP [dm3] 3L_1583967_SNP [dm6]	C	T	5.751e^-5	0.919	INTRON CG13917	TF binding site mE1_TFBS_HSA
X	6600895	X_6600895_INS [dm3] X_6706862_INS [dm6]	G	GAG	5.755e^-5	0.919	INTRON CG14441	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	5663677	3L_5663677_INS [dm3] 3L_5670577_INS [dm6]	T	TCACAGATAAAGTGT...	5.880e^-5	0.919	INTRON sif
2R	7150224	2R_7150224_SNP [dm3] 2R_11262719_SNP [dm6]	A	T	5.895e^-5	0.919	UPSTREAM Cpr47Ed INTERGENIC
3L	6791758	3L_6791758_SNP [dm3] 3L_6798658_SNP [dm6]	T	G	5.995e^-5	0.919	INTERGENIC

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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=8.740e^-10)
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	0.07834

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	6.404	0.0407

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1871 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
2L	1954145	2L_1954145_SNP [dm3] 2L_1954145_SNP [dm6]	G	A	2.184e^-7	0.41	INTRON erm	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	7289685	2R_7289685_SNP [dm3] 2R_11402180_SNP [dm6]	A	T	2.345e^-6	0.722	INTERGENIC
2R	1548708	2R_1548708_SNP [dm3] 2R_5661203_SNP [dm6]	A	T	2.450e^-6	0.722	INTRON Not3	TF binding site BDTNP1_TFBS_dl mE1_TFBS_sens
3R	22363870	3R_22363870_INS [dm3] 3R_26538148_INS [dm6]	A	AAAATTGGTTAAGAAA...	2.660e^-6	0.722	INTRON scrib
2R	7289662	2R_7289662_SNP [dm3] 2R_11402157_SNP [dm6]	G	A	2.712e^-6	0.722	INTERGENIC
3L	3787061	3L_3787061_SNP [dm3] 3L_3787061_SNP [dm6]	T	A	3.238e^-6	0.722	INTRON CG32264	TF binding site BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Ubx
2R	7289661	2R_7289661_SNP [dm3] 2R_11402156_SNP [dm6]	G	A	3.355e^-6	0.722	INTERGENIC
2L	10196817	2L_10196817_SNP [dm3] 2L_10196817_SNP [dm6]	G	A	3.552e^-6	0.722	NON_SYNONYMOUS_CODING Sur
X	490193	X_490193_SNP [dm3] X_596160_SNP [dm6]	G	T	3.698e^-6	0.722	INTRON CG13366 & 1 other	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	7289795	2R_7289795_SNP [dm3] 2R_11402290_SNP [dm6]	T	G	3.848e^-6	0.722	INTERGENIC
3R	22363877	3R_22363877_SNP [dm3] 3R_26538155_SNP [dm6]	T	A	6.336e^-6	0.902	INTRON scrib
X	19597353	X_19597353_SNP [dm3] X_19703320_SNP [dm6]	C	T	6.413e^-6	0.902	UPSTREAM CG14230 INTRON CG14232	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2R	7289789	2R_7289789_SNP [dm3] 2R_11402284_SNP [dm6]	A	T	7.272e^-6	0.902	INTERGENIC
2R	7289819	2R_7289819_SNP [dm3] 2R_11402314_SNP [dm6]	T	A	7.972e^-6	0.902	INTERGENIC
3R	26617078	3R_26617078_SNP [dm3] 3R_30791356_SNP [dm6]	G	C	8.012e^-6	0.902	SYNONYMOUS_CODING wts DOWNSTREAM mir-1013
3L	12395009	3L_12395009_SNP [dm3] 3L_12401909_SNP [dm6]	C	T	8.184e^-6	0.902	START_GAINED Smyd4 UTR_5_PRIME Smyd4 DOWNSTREAM CG32103	TF binding site mE1_TFBS_cad
3R	9633006	3R_9633006_SNP [dm3] 3R_13807284_SNP [dm6]	C	T	8.839e^-6	0.902	INTERGENIC
3R	8545701	3R_8545701_SNP [dm3] 3R_12719979_SNP [dm6]	A	G	8.952e^-6	0.902	SYNONYMOUS_CODING Men UPSTREAM Men	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
3R	14672986	3R_14672986_SNP [dm3] 3R_18847264_SNP [dm6]	G	T	9.141e^-6	0.902	INTRON CG18208
2R	10133755	2R_10133755_SNP [dm3] 2R_14246250_SNP [dm6]	C	A	9.880e^-6	0.927	UPSTREAM Mdr50 DOWNSTREAM CG8503 INTERGENIC
3R	26617138	3R_26617138_SNP [dm3] 3R_30791416_SNP [dm6]	T	C	1.235e^-5	0.979	DOWNSTREAM mir-1013 INTRON wts
3L	13575701	3L_13575701_SNP [dm3] 3L_13582601_SNP [dm6]	G	T	1.247e^-5	0.979	INTRON bru-3
2L	21918567	2L_21918567_SNP [dm3] 2L_21918567_SNP [dm6]	C	T	1.265e^-5	0.979	INTRON CG11634
3L	3787077	3L_3787077_SNP [dm3] 3L_3787077_SNP [dm6]	C	T	1.322e^-5	0.979	INTRON CG32264	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Ubx
X	11734928	X_11734928_SNP [dm3] X_11840895_SNP [dm6]	C	T	1.409e^-5	0.979	INTRON Cyp28c1	TF binding site mE1_TFBS_chinmo
3R	8407296	3R_8407296_DEL [dm3] 3R_12581574_DEL [dm6]	TC	T	1.480e^-5	0.979	INTRON Octbeta2R
3R	26617141	3R_26617141_SNP [dm3] 3R_30791419_SNP [dm6]	T	A	1.570e^-5	0.979	DOWNSTREAM mir-1013 INTRON wts
3R	26617154	3R_26617154_SNP [dm3] 3R_30791432_SNP [dm6]	G	A	1.643e^-5	0.979	SPLICE_SITE_REGION wts DOWNSTREAM mir-1013 INTRON wts
2R	7605864	2R_7605864_SNP [dm3] 2R_11718359_SNP [dm6]	T	C	1.664e^-5	0.979	INTRON pyr	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	22363597	3R_22363597_SNP [dm3] 3R_26537875_SNP [dm6]	T	A	1.801e^-5	0.979	INTRON scrib	TF binding site BDTNP1_TFBS_dl
3R	22363878	3R_22363878_SNP [dm3] 3R_26538156_SNP [dm6]	T	G	1.838e^-5	0.979	INTRON scrib
3R	4669439	3R_4669439_SNP [dm3] 3R_8843717_SNP [dm6]	A	T	1.848e^-5	0.979	INTRON pyd	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_prd BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_HSA
2R	7289815	2R_7289815_SNP [dm3] 2R_11402310_SNP [dm6]	C	G	1.855e^-5	0.979	INTERGENIC
2L	15650884	2L_15650884_SNP [dm3] 2L_15650884_SNP [dm6]	A	C	1.988e^-5	0.979	NON_SYNONYMOUS_CODING CG4587	TF binding site mE1_TFBS_inv
3R	21610922	3R_21610922_SNP [dm3] 3R_25785200_SNP [dm6]	T	G	1.991e^-5	0.979	INTERGENIC
2L	16571140	2L_16571140_SNP [dm3] 2L_16571140_SNP [dm6]	C	T	2.040e^-5	0.979	INTRON CG42389
2R	11315704	2R_11315704_SNP [dm3] 2R_15428199_SNP [dm6]	T	G	2.138e^-5	0.979	UPSTREAM CG34188 INTRON CG43729
3R	9909155	3R_9909155_SNP [dm3] 3R_14083433_SNP [dm6]	C	A	2.157e^-5	0.979	INTRON foxo
X	5684287	X_5684287_SNP [dm3] X_5790254_SNP [dm6]	T	G	2.190e^-5	0.979	SYNONYMOUS_CODING CG15767 UPSTREAM mir-4963 DOWNSTREAM CG42699 & 1 other	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	26617149	3R_26617149_SNP [dm3] 3R_30791427_SNP [dm6]	C	T	2.245e^-5	0.979	DOWNSTREAM mir-1013 INTRON wts
X	11735046	X_11735046_SNP [dm3] X_11841013_SNP [dm6]	T	C	2.398e^-5	0.979	SYNONYMOUS_CODING Cyp28c1	TF binding site mE1_TFBS_chinmo
3R	22363568	3R_22363568_SNP [dm3] 3R_26537846_SNP [dm6]	A	T	2.428e^-5	0.979	INTRON scrib	TF binding site BDTNP1_TFBS_dl
3L	15448628	3L_15448628_SNP [dm3] 3L_15455528_SNP [dm6]	T	C	2.430e^-5	0.979	INTERGENIC
3R	19272078	3R_19272078_SNP [dm3] 3R_23446356_SNP [dm6]	C	T	2.612e^-5	0.979	INTRON CG4374	TF binding site mE1_TFBS_chinmo
3R	15045582	3R_15045582_SNP [dm3] 3R_19219860_SNP [dm6]	T	A	2.884e^-5	0.979	INTRON vib
3R	21610796	3R_21610796_SNP [dm3] 3R_25785074_SNP [dm6]	C	T	2.894e^-5	0.979	INTERGENIC
3R	16949507	3R_16949507_SNP [dm3] 3R_21123785_SNP [dm6]	T	C	2.930e^-5	0.979	INTRON slmb	TF binding site mE1_TFBS_HSA
2R	14043358	2R_14043358_SNP [dm3] 2R_18155853_SNP [dm6]	T	C	3.023e^-5	0.979	INTRON lolal	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_GATAe mE1_TFBS_HSA mE1_TFBS_sens
X	22155423	X_22155423_SNP [dm3] X_22753587_SNP [dm6]	T	C	3.058e^-5	0.979	INTRON CR44997	transposable element FlyBase
3R	22376817	3R_22376817_SNP [dm3] 3R_26551095_SNP [dm6]	C	T	3.139e^-5	0.979	INTRON scrib	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	7605831	2R_7605831_SNP [dm3] 2R_11718326_SNP [dm6]	T	C	3.165e^-5	0.979	INTRON pyr	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
X	11734924	X_11734924_SNP [dm3] X_11840891_SNP [dm6]	T	C	3.165e^-5	0.979	INTRON Cyp28c1	TF binding site mE1_TFBS_chinmo
X	11735019	X_11735019_SNP [dm3] X_11840986_SNP [dm6]	T	C	3.181e^-5	0.979	SYNONYMOUS_CODING Cyp28c1	TF binding site mE1_TFBS_chinmo
3R	19078967	3R_19078967_SNP [dm3] 3R_23253245_SNP [dm6]	A	G	3.262e^-5	0.979	SYNONYMOUS_CODING EloA
2L	10648575	2L_10648575_SNP [dm3] 2L_10648575_SNP [dm6]	C	A	3.365e^-5	0.979	NON_SYNONYMOUS_CODING CG17097	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_inv mE1_TFBS_run mE1_TFBS_sens
3R	8363723	3R_8363723_SNP [dm3] 3R_12538001_SNP [dm6]	T	G	3.479e^-5	0.979	INTRON Octbeta3R
2L	22114877	2L_22114877_SNP [dm3] 2L_22114877_SNP [dm6]	G	T	3.554e^-5	0.979	INTERGENIC
X	6711495	X_6711495_SNP [dm3] X_6817462_SNP [dm6]	G	A	3.574e^-5	0.979	SYNONYMOUS_CODING iav DOWNSTREAM Nf-YC	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	13398446	3R_13398446_SNP [dm3] 3R_17572724_SNP [dm6]	G	T	3.637e^-5	0.979	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
3R	22984706	3R_22984706_SNP [dm3] 3R_27158984_SNP [dm6]	G	T	3.665e^-5	0.979	INTRON grass	TF binding site mE1_TFBS_cad
2R	8536720	2R_8536720_SNP [dm3] 2R_12649215_SNP [dm6]	T	G	3.685e^-5	0.979	UPSTREAM CG8785 INTERGENIC
2R	19306398	2R_19306398_SNP [dm3] 2R_23418875_SNP [dm6]	A	G	3.707e^-5	0.979	INTRON CG9812
3R	14683680	3R_14683680_SNP [dm3] 3R_18857958_SNP [dm6]	T	C	3.789e^-5	0.979	INTERGENIC
3R	22363675	3R_22363675_SNP [dm3] 3R_26537953_SNP [dm6]	C	A	3.898e^-5	0.979	INTRON scrib
3L	13321297	3L_13321297_SNP [dm3] 3L_13328197_SNP [dm6]	G	A	3.899e^-5	0.979	UPSTREAM CG14113 INTERGENIC
3R	23549304	3R_23549304_SNP [dm3] 3R_27723582_SNP [dm6]	T	C	3.989e^-5	0.979	INTERGENIC
2L	12855134	2L_12855134_SNP [dm3] 2L_12855134_SNP [dm6]	T	C	4.100e^-5	0.979	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	24028078	3R_24028078_INS [dm3] 3R_28202356_INS [dm6]	T	TTACT	4.234e^-5	0.979	INTRON CG34354
3R	8363754	3R_8363754_SNP [dm3] 3R_12538032_SNP [dm6]	T	A	4.242e^-5	0.979	INTRON Octbeta3R
2L	439086	2L_439086_SNP [dm3] 2L_439086_SNP [dm6]	G	A	4.362e^-5	0.979	UPSTREAM CR43717 INTRON ex
X	19597298	X_19597298_SNP [dm3] X_19703265_SNP [dm6]	A	G	4.414e^-5	0.979	UPSTREAM CG14230 INTRON CG14232	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2R	14585924	2R_14585924_SNP [dm3] 2R_18698419_SNP [dm6]	C	T	4.527e^-5	0.979	INTRON Sik3
3R	26496217	3R_26496217_SNP [dm3] 3R_30670495_SNP [dm6]	C	A	4.544e^-5	0.979	INTERGENIC
2L	12643663	2L_12643663_SNP [dm3] 2L_12643663_SNP [dm6]	A	C	4.592e^-5	0.979	INTRON Ref2
2R	8567640	2R_8567640_SNP [dm3] 2R_12680135_SNP [dm6]	C	A	4.601e^-5	0.979	SYNONYMOUS_CODING CG8771 UPSTREAM CG42708
2L	1948750	2L_1948750_SNP [dm3] 2L_1948750_SNP [dm6]	T	A	4.668e^-5	0.979	INTERGENIC	regulatory region REDfly_CRMs
3L	13358275	3L_13358275_SNP [dm3] 3L_13365175_SNP [dm6]	G	A	4.745e^-5	0.979	INTERGENIC
X	19597283	X_19597283_SNP [dm3] X_19703250_SNP [dm6]	G	T	4.913e^-5	0.979	UPSTREAM CG14230 INTRON CG14232	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3R	8545974	3R_8545974_SNP [dm3] 3R_12720252_SNP [dm6]	T	A	5.068e^-5	0.979	UPSTREAM Men INTRON Men	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	8529996	3L_8529996_SNP [dm3] 3L_8536896_SNP [dm6]	C	G	5.251e^-5	0.979	NON_SYNONYMOUS_CODING ergic53
3R	8363828	3R_8363828_SNP [dm3] 3R_12538106_SNP [dm6]	C	G	5.285e^-5	0.979	INTRON Octbeta3R
3L	2663223	3L_2663223_SNP [dm3] 3L_2663223_SNP [dm6]	T	C	5.300e^-5	0.979	SYNONYMOUS_CODING CG33234 INTRON Fife
2L	10933703	2L_10933703_SNP [dm3] 2L_10933703_SNP [dm6]	T	A	5.415e^-5	0.979	INTRON dpr2
2R	17797699	2R_17797699_SNP [dm3] 2R_21910194_SNP [dm6]	A	G	5.459e^-5	0.979	INTRON Fili
3R	22376014	3R_22376014_SNP [dm3] 3R_26550292_SNP [dm6]	A	G	5.477e^-5	0.979	INTRON scrib	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	7289694	2R_7289694_SNP [dm3] 2R_11402189_SNP [dm6]	T	C	5.699e^-5	0.979	INTERGENIC
3R	8364009	3R_8364009_SNP [dm3] 3R_12538287_SNP [dm6]	T	G	5.717e^-5	0.979	INTRON Octbeta3R
3R	8525744	3R_8525744_SNP [dm3] 3R_12700022_SNP [dm6]	C	T	5.755e^-5	0.979	INTRON Past1
2L	7358793	2L_7358793_SNP [dm3] 2L_7358793_SNP [dm6]	C	T	5.845e^-5	0.979	INTERGENIC
X	490285	X_490285_SNP [dm3] X_596252_SNP [dm6]	A	C	5.850e^-5	0.979	INTRON CG13366 & 1 other	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3L	18032140	3L_18032140_SNP [dm3] 3L_18039040_SNP [dm6]	A	G	5.857e^-5	0.979	INTRON Eip75B
2L	12256688	2L_12256688_SNP [dm3] 2L_12256688_SNP [dm6]	G	C	6.074e^-5	0.979	INTRON aret
2R	7284662	2R_7284662_DEL [dm3] 2R_11397157_DEL [dm6]	TT	A	6.114e^-5	0.979	UTR_5_PRIME sprt	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3R	8407397	3R_8407397_SNP [dm3] 3R_12581675_SNP [dm6]	A	T	6.118e^-5	0.979	INTRON Octbeta2R
3L	9622447	3L_9622447_SNP [dm3] 3L_9629347_SNP [dm6]	A	G	6.301e^-5	0.979	UPSTREAM CG8336 & 1 other INTRON CG8336
2L	17297799	2L_17297799_SNP [dm3] 2L_17297799_SNP [dm6]	T	C	6.327e^-5	0.979	INTERGENIC
2L	17293208	2L_17293208_SNP [dm3] 2L_17293208_SNP [dm6]	C	T	6.343e^-5	0.979	INTERGENIC
2L	3303545	2L_3303545_SNP [dm3] 2L_3303545_SNP [dm6]	G	A	6.579e^-5	0.979	UPSTREAM CG3277 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
2L	3303550	2L_3303550_SNP [dm3] 2L_3303550_SNP [dm6]	C	T	6.579e^-5	0.979	UPSTREAM CG3277 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
3R	26895751	3R_26895751_INS [dm3] 3R_31070029_INS [dm6]	C	CT	6.621e^-5	0.979	INTRON Sox100B	TF binding site BDTNP1_TFBS_twi

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cv_BoutNumber_Day phenotype

Phenotype distribution and association to known covariates

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Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results