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=2.609e^-9)
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	0.001217

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2R_NS	10.5339	0.0052

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2321 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
2R	10324237	2R_10324237_SNP [dm3] 2R_14436732_SNP [dm6]	G	A	3.623e^-7	0.189	INTRON Oaz
2R	10324673	2R_10324673_SNP [dm3] 2R_14437168_SNP [dm6]	A	G	7.784e^-7	0.189	INTRON Oaz	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	23158236	3R_23158236_SNP [dm3] 3R_27332514_SNP [dm6]	A	T	9.360e^-7	0.189	INTERGENIC
X	4585949	X_4585949_SNP [dm3] X_4691916_SNP [dm6]	C	T	1.041e^-6	0.189	INTRON ctp	TF binding site BDTNP1_TFBS_dl
X	4586105	X_4586105_SNP [dm3] X_4692072_SNP [dm6]	A	G	1.160e^-6	0.189	INTRON ctp	TF binding site BDTNP1_TFBS_dl
3L	7624737	3L_7624737_SNP [dm3] 3L_7631637_SNP [dm6]	C	A	1.336e^-6	0.189	INTRON CG33275
3R	17577684	3R_17577684_SNP [dm3] 3R_21751962_SNP [dm6]	C	G	1.375e^-6	0.189	SYNONYMOUS_CODING CG31233	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	13939139	3R_13939139_DEL [dm3] 3R_18113417_DEL [dm6]	TGT	T	1.566e^-6	0.189	INTRON sr
3L	11436134	3L_11436134_SNP [dm3] 3L_11443034_SNP [dm6]	A	T	1.601e^-6	0.189	INTERGENIC
3R	14161625	3R_14161625_SNP [dm3] 3R_18335903_SNP [dm6]	T	G	1.887e^-6	0.189	INTRON CG15803
3R	20123159	3R_20123159_SNP [dm3] 3R_24297437_SNP [dm6]	G	A	1.947e^-6	0.189	INTRON crb	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_kni BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_disco mE1_TFBS_HSA
X	4584155	X_4584155_SNP [dm3] X_4690122_SNP [dm6]	G	A	1.958e^-6	0.189	INTRON ctp	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3R	20122986	3R_20122986_SNP [dm3] 3R_24297264_SNP [dm6]	C	A	2.120e^-6	0.189	INTRON crb	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_HSA
3R	20122988	3R_20122988_SNP [dm3] 3R_24297266_SNP [dm6]	G	A	2.120e^-6	0.189	INTRON crb	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_HSA
3R	20123124	3R_20123124_SNP [dm3] 3R_24297402_SNP [dm6]	C	A	2.120e^-6	0.189	INTRON crb	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_kni BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_HSA
3R	20123126	3R_20123126_MNP [dm3] 3R_24297404_MNP [dm6]	CTA	AGG	2.120e^-6	0.189	INTRON crb	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_kni BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_HSA
3L	16533655	3L_16533655_SNP [dm3] 3L_16540555_SNP [dm6]	C	T	2.154e^-6	0.189	INTRON CG43373
2R	6631668	2R_6631668_SNP [dm3] 2R_10744163_SNP [dm6]	G	A	2.308e^-6	0.189	INTRON CG33144
3R	20123148	3R_20123148_SNP [dm3] 3R_24297426_SNP [dm6]	T	A	2.337e^-6	0.189	INTRON crb	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_kni BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_disco mE1_TFBS_HSA
3R	20123027	3R_20123027_INS [dm3] 3R_24297305_INS [dm6]	A	ACAAGAGTGCAAATGCATCG...	2.349e^-6	0.189	INTRON crb	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_HSA
X	4586084	X_4586084_DEL [dm3] X_4692051_DEL [dm6]	TT	T	2.505e^-6	0.189	INTRON ctp	TF binding site BDTNP1_TFBS_dl
3R	20123136	3R_20123136_SNP [dm3] 3R_24297414_SNP [dm6]	T	G	2.596e^-6	0.189	INTRON crb	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_kni BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_HSA
X	4586128	X_4586128_SNP [dm3] X_4692095_SNP [dm6]	C	T	2.610e^-6	0.189	INTRON ctp	TF binding site BDTNP1_TFBS_dl
X	4588150	X_4588150_SNP [dm3] X_4694117_SNP [dm6]	G	T	2.644e^-6	0.189	INTRON ctp	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3R	5313819	3R_5313819_SNP [dm3] 3R_9488097_SNP [dm6]	A	T	2.672e^-6	0.189	INTRON CG16779	TF binding site BDTNP1_TFBS_dl
3R	14161621	3R_14161621_SNP [dm3] 3R_18335899_SNP [dm6]	A	G	2.774e^-6	0.189	INTRON CG15803
X	4584320	X_4584320_DEL [dm3] X_4690287_DEL [dm6]	TAAAG	A	2.916e^-6	0.189	INTRON ctp	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3L	12860727	3L_12860727_SNP [dm3] 3L_12867627_SNP [dm6]	T	C	2.939e^-6	0.189	INTERGENIC	TF binding site BDTNP1_TFBS_dl
3L	11435993	3L_11435993_SNP [dm3] 3L_11442893_SNP [dm6]	T	A	3.007e^-6	0.189	INTERGENIC
X	4588388	X_4588388_SNP [dm3] X_4694355_SNP [dm6]	A	G	3.018e^-6	0.189	INTRON ctp	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3L	16533780	3L_16533780_SNP [dm3] 3L_16540680_SNP [dm6]	T	A	3.845e^-6	0.227	INTRON CG43373
3L	16533818	3L_16533818_SNP [dm3] 3L_16540718_SNP [dm6]	T	A	3.871e^-6	0.227	INTRON CG43373
2R	17001692	2R_17001692_SNP [dm3] 2R_21114187_SNP [dm6]	T	C	4.513e^-6	0.256	INTRON ktub
3R	23231713	3R_23231713_SNP [dm3] 3R_27405991_SNP [dm6]	C	T	4.765e^-6	0.263	INTRON side	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	23158230	3R_23158230_SNP [dm3] 3R_27332508_SNP [dm6]	T	C	4.959e^-6	0.266	INTERGENIC
3L	12860775	3L_12860775_SNP [dm3] 3L_12867675_SNP [dm6]	C	A	5.887e^-6	0.307	INTERGENIC	TF binding site BDTNP1_TFBS_dl
X	4585403	X_4585403_SNP [dm3] X_4691370_SNP [dm6]	T	C	6.342e^-6	0.321	INTRON ctp	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	10324567	2R_10324567_SNP [dm3] 2R_14437062_SNP [dm6]	T	C	7.364e^-6	0.346	INTRON Oaz	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	16759214	3L_16759214_SNP [dm3] 3L_16766114_SNP [dm6]	C	T	7.369e^-6	0.346	UTR_5_PRIME Nrt	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	13638708	3R_13638708_SNP [dm3] 3R_17812986_SNP [dm6]	A	G	7.373e^-6	0.346	INTRON tinc	TF binding site BDTNP1_TFBS_dl
3L	11436006	3L_11436006_SNP [dm3] 3L_11442906_SNP [dm6]	G	T	7.763e^-6	0.35	INTERGENIC
X	11854197	X_11854197_SNP [dm3] X_11960164_SNP [dm6]	T	C	7.988e^-6	0.35	INTRON cac	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	4584286	X_4584286_SNP [dm3] X_4690253_SNP [dm6]	A	G	8.172e^-6	0.35	INTRON ctp	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
2R	4624225	2R_4624225_SNP [dm3] 2R_8736720_SNP [dm6]	A	T	8.200e^-6	0.35	UPSTREAM CG42615 INTRON CG8740
X	15359253	X_15359253_SNP [dm3] X_15465220_SNP [dm6]	G	A	9.078e^-6	0.364	UPSTREAM CG6299 DOWNSTREAM CG6294 & 1 other INTRON CG6299 & 1 other
3R	22732520	3R_22732520_DEL [dm3] 3R_26906798_DEL [dm6]	AAT	TG	9.085e^-6	0.364	INTRON T48	regulatory region REDfly_CRMs
3R	24627526	3R_24627526_SNP [dm3] 3R_28801804_SNP [dm6]	G	A	9.112e^-6	0.364	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	4584414	X_4584414_SNP [dm3] X_4690381_SNP [dm6]	A	G	9.456e^-6	0.369	INTRON ctp	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
X	4584116	X_4584116_INS [dm3] X_4690083_INS [dm6]	A	AA	9.832e^-6	0.376	INTRON ctp	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
X	4583793	X_4583793_SNP [dm3] X_4689760_SNP [dm6]	A	T	1.022e^-5	0.382	INTRON ctp	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3R	14161626	3R_14161626_SNP [dm3] 3R_18335904_SNP [dm6]	A	T	1.039e^-5	0.382	INTRON CG15803
3R	20123111	3R_20123111_INS [dm3] 3R_24297389_INS [dm6]	A	GT	1.083e^-5	0.384	INTRON crb	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_kni BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_HSA
X	4585380	X_4585380_SNP [dm3] X_4691347_SNP [dm6]	C	G	1.215e^-5	0.384	INTRON ctp	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
X	8759585	X_8759585_SNP [dm3] X_8865552_SNP [dm6]	A	G	1.218e^-5	0.384	INTRON CG12075	TF binding site mE1_TFBS_kn mE1_TFBS_zfh1
3R	24627542	3R_24627542_SNP [dm3] 3R_28801820_SNP [dm6]	A	T	1.280e^-5	0.384	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	4583768	X_4583768_SNP [dm3] X_4689735_SNP [dm6]	C	T	1.288e^-5	0.384	INTRON ctp	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3L	14716610	3L_14716610_SNP [dm3] 3L_14723510_SNP [dm6]	T	C	1.311e^-5	0.384	INTRON ome
2R	10344248	2R_10344248_SNP [dm3] 2R_14456743_SNP [dm6]	T	C	1.331e^-5	0.384	INTRON Oaz	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	10348157	2R_10348157_SNP [dm3] 2R_14460652_SNP [dm6]	C	T	1.346e^-5	0.384	INTRON Oaz	TF binding site mE1_TFBS_cad
3L	12709135	3L_12709135_SNP [dm3] 3L_12716035_SNP [dm6]	G	A	1.351e^-5	0.384	INTERGENIC
3R	21876717	3R_21876717_SNP [dm3] 3R_26050995_SNP [dm6]	G	C	1.359e^-5	0.384	SYNONYMOUS_CODING Exo84	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	22732614	3R_22732614_SNP [dm3] 3R_26906892_SNP [dm6]	G	A	1.367e^-5	0.384	INTRON T48	regulatory region REDfly_CRMs
3R	20123180	3R_20123180_INS [dm3] 3R_24297458_INS [dm6]	T	TT	1.398e^-5	0.384	INTRON crb	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_kni BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_disco mE1_TFBS_HSA
3L	4681359	3L_4681359_DEL [dm3] 3L_4681359_DEL [dm6]	TT	T	1.401e^-5	0.384	UTR_5_PRIME axo INTRON axo
2R	10344260	2R_10344260_SNP [dm3] 2R_14456755_SNP [dm6]	A	G	1.413e^-5	0.384	INTRON Oaz	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
X	4583641	X_4583641_DEL [dm3] X_4689608_DEL [dm6]	TT	T	1.417e^-5	0.384	INTRON ctp	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
X	4587346	X_4587346_SNP [dm3] X_4693313_SNP [dm6]	A	G	1.443e^-5	0.384	INTRON ctp	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
3R	21503438	3R_21503438_SNP [dm3] 3R_25677716_SNP [dm6]	A	T	1.466e^-5	0.384	SYNONYMOUS_CODING CG4730 UPSTREAM CR45225 & 1 other DOWNSTREAM Lgr3	TF binding site mE1_TFBS_sens
3R	5305845	3R_5305845_SNP [dm3] 3R_9480123_SNP [dm6]	G	A	1.492e^-5	0.384	INTRON CG16779
3R	14161651	3R_14161651_SNP [dm3] 3R_18335929_SNP [dm6]	A	T	1.495e^-5	0.384	INTRON CG15803
3R	14161654	3R_14161654_INS [dm3] 3R_18335932_INS [dm6]	A	ATCCGTC	1.495e^-5	0.384	INTRON CG15803
2L	10298497	2L_10298497_SNP [dm3] 2L_10298497_SNP [dm6]	T	G	1.503e^-5	0.384	UPSTREAM CYLD DOWNSTREAM CR44968 INTRON CYLD	TF binding site BDTNP1_TFBS_dl mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_inv
3R	23315487	3R_23315487_SNP [dm3] 3R_27489765_SNP [dm6]	G	A	1.504e^-5	0.384	UTR_3_PRIME Gr98a
X	4583727	X_4583727_SNP [dm3] X_4689694_SNP [dm6]	C	G	1.520e^-5	0.384	INTRON ctp	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
2R	11884331	2R_11884331_INS [dm3] 2R_15996826_INS [dm6]	T	TT	1.534e^-5	0.384	INTRON ATPCL
X	4581219	X_4581219_DEL [dm3] X_4687186_DEL [dm6]	ATCTCA	A	1.604e^-5	0.384	UPSTREAM ctp & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_Ubx
2R	10344245	2R_10344245_SNP [dm3] 2R_14456740_SNP [dm6]	T	C	1.618e^-5	0.384	INTRON Oaz	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	14161660	3R_14161660_SNP [dm3] 3R_18335938_SNP [dm6]	T	G	1.631e^-5	0.384	INTRON CG15803
3R	15665485	3R_15665485_SNP [dm3] 3R_19839763_SNP [dm6]	G	A	1.643e^-5	0.384	INTERGENIC	TF binding site BDTNP1_TFBS_da
2R	19502894	2R_19502894_SNP [dm3] 2R_23615371_SNP [dm6]	G	A	1.648e^-5	0.384	UPSTREAM CG4019 INTRON CG17664	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	8833238	3L_8833238_SNP [dm3] 3L_8840138_SNP [dm6]	C	T	1.665e^-5	0.384	INTRON dally	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_jumu
2L	5665504	2L_5665504_SNP [dm3] 2L_5665504_SNP [dm6]	G	A	1.678e^-5	0.384	INTRON Hsp60C
X	4585460	X_4585460_SNP [dm3] X_4691427_SNP [dm6]	G	C	1.698e^-5	0.384	INTRON ctp	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	10313946	2L_10313946_SNP [dm3] 2L_10313946_SNP [dm6]	A	C	1.729e^-5	0.386	SYNONYMOUS_CODING CG5384 UPSTREAM CG4972	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med
X	4583177	X_4583177_SNP [dm3] X_4689144_SNP [dm6]	T	C	1.764e^-5	0.389	INTRON ctp	TF binding site BDTNP1_TFBS_dl
3R	14161606	3R_14161606_SNP [dm3] 3R_18335884_SNP [dm6]	T	G	1.817e^-5	0.396	INTRON CG15803
X	4587298	X_4587298_DEL [dm3] X_4693265_DEL [dm6]	AAGCCCTGA	A	1.892e^-5	0.404	INTRON ctp	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
3R	14161618	3R_14161618_SNP [dm3] 3R_18335896_SNP [dm6]	A	T	1.916e^-5	0.404	INTRON CG15803
3R	14161601	3R_14161601_SNP [dm3] 3R_18335879_SNP [dm6]	A	G	1.919e^-5	0.404	INTRON CG15803
3R	14161615	3R_14161615_SNP [dm3] 3R_18335893_SNP [dm6]	T	A	1.937e^-5	0.404	INTRON CG15803
X	19171471	X_19171471_SNP [dm3] X_19277438_SNP [dm6]	G	A	2.029e^-5	0.417	SYNONYMOUS_CODING CG8028 UPSTREAM CG32537 & 1 other
3R	21372361	3R_21372361_DEL [dm3] 3R_25546639_DEL [dm6]	TGGGC	T	2.046e^-5	0.417	INTRON msi
X	4583645	X_4583645_SNP [dm3] X_4689612_SNP [dm6]	A	G	2.069e^-5	0.417	INTRON ctp	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
X	4585531	X_4585531_INS [dm3] X_4691498_INS [dm6]	G	GAGTGTGTG	2.168e^-5	0.432	INTRON ctp	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	25552992	3R_25552992_SNP [dm3] 3R_29727270_SNP [dm6]	T	C	2.203e^-5	0.435	INTRON Kul	TF binding site BDTNP1_TFBS_dl mE1_TFBS_chinmo mE1_TFBS_HSA
3L	2981345	3L_2981345_SNP [dm3] 3L_2981345_SNP [dm6]	C	G	2.266e^-5	0.443	NON_SYNONYMOUS_CODING CG2107	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_sna mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Ubx
3L	10653187	3L_10653187_SNP [dm3] 3L_10660087_SNP [dm6]	T	A	2.299e^-5	0.444	UPSTREAM CG32066 INTRON CG32066	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	15608580	3R_15608580_SNP [dm3] 3R_19782858_SNP [dm6]	T	G	2.321e^-5	0.444	SYNONYMOUS_CODING CG11407 UPSTREAM CG11453
3R	14161593	3R_14161593_DEL [dm3] 3R_18335871_DEL [dm6]	AC	A	2.464e^-5	0.465	INTRON CG15803
3R	14161687	3R_14161687_DEL [dm3] 3R_18335965_DEL [dm6]	CATTATTCTGTC...	C	2.478e^-5	0.465	INTRON CG15803

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=1.140e^-6)
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	0.06692

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_3R_Mo	6.0222	0.0492

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1899 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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Chromosome	Position	ID	Reference	Variant	p-value	FDR_BH	Transcript annotation	Binding site annotation
3R	18159145	3R_18159145_SNP [dm3] 3R_22333423_SNP [dm6]	T	C	3.449e^-7	0.647	SYNONYMOUS_CODING CG5391 DOWNSTREAM CG13862 & 1 other
X	8475723	X_8475723_SNP [dm3] X_8581690_SNP [dm6]	C	T	3.772e^-6	0.957	INTRON CG12065
3R	18159373	3R_18159373_SNP [dm3] 3R_22333651_SNP [dm6]	T	C	4.318e^-6	0.957	SYNONYMOUS_CODING CG5391 DOWNSTREAM CG5388
3R	17223682	3R_17223682_SNP [dm3] 3R_21397960_SNP [dm6]	G	C	4.428e^-6	0.957	NON_SYNONYMOUS_CODING CG6475
3R	13782821	3R_13782821_MNP [dm3] 3R_17957099_MNP [dm6]	AGAT	TTTC	4.439e^-6	0.957	INTRON cpo
3R	13782826	3R_13782826_MNP [dm3] 3R_17957104_MNP [dm6]	AAC	TTT	4.439e^-6	0.957	INTRON cpo
3R	23774283	3R_23774283_SNP [dm3] 3R_27948561_SNP [dm6]	A	G	4.942e^-6	0.957	UPSTREAM Gp93 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Ubx
3L	9436098	3L_9436098_SNP [dm3] 3L_9442998_SNP [dm6]	T	A	5.020e^-6	0.957	UPSTREAM CG33926 & 2 others INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA transposable element FlyBase
3L	13215783	3L_13215783_SNP [dm3] 3L_13222683_SNP [dm6]	G	C	5.138e^-6	0.957	INTERGENIC
3R	25071074	3R_25071074_SNP [dm3] 3R_29245352_SNP [dm6]	G	A	5.538e^-6	0.957	UPSTREAM CG31445 INTRON SP1029	TF binding site mE1_TFBS_cad
X	8914959	X_8914959_SNP [dm3] X_9020926_SNP [dm6]	G	A	7.520e^-6	0.957	SYNONYMOUS_CODING rdgA INTRON CR43836
2L	4639993	2L_4639993_SNP [dm3] 2L_4639993_SNP [dm6]	A	T	8.226e^-6	0.957	INTERGENIC
3R	13782813	3R_13782813_DEL [dm3] 3R_17957091_DEL [dm6]	TACAAA	T	8.724e^-6	0.957	INTRON cpo
3L	11162963	3L_11162963_SNP [dm3] 3L_11169863_SNP [dm6]	T	C	9.662e^-6	0.957	UTR_5_PRIME CG7616 UPSTREAM CG7616 & 1 other	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_disco mE1_TFBS_GATAe mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Ubx
3R	27455309	3R_27455309_SNP [dm3] 3R_31629587_SNP [dm6]	A	G	9.924e^-6	0.957	INTRON kek6
3R	19914307	3R_19914307_SNP [dm3] 3R_24088585_SNP [dm6]	A	G	1.045e^-5	0.957	INTRON 4EHP
3R	27455308	3R_27455308_SNP [dm3] 3R_31629586_SNP [dm6]	A	G	1.219e^-5	0.957	INTRON kek6
3R	10058466	3R_10058466_SNP [dm3] 3R_14232744_SNP [dm6]	C	T	1.229e^-5	0.957	INTERGENIC
3R	14403879	3R_14403879_SNP [dm3] 3R_18578157_SNP [dm6]	A	G	1.261e^-5	0.957	INTRON fray & 1 other
3L	14223225	3L_14223225_SNP [dm3] 3L_14230125_SNP [dm6]	C	A	1.299e^-5	0.957	INTRON nuf
3R	19914305	3R_19914305_SNP [dm3] 3R_24088583_SNP [dm6]	A	G	1.369e^-5	0.957	INTRON 4EHP
X	15132716	X_15132716_SNP [dm3] X_15238683_SNP [dm6]	T	G	1.389e^-5	0.957	INTERGENIC
2R	18570712	2R_18570712_DEL [dm3] 2R_22683207_DEL [dm6]	GGCCCG	G	1.393e^-5	0.957	INTERGENIC	TF binding site BDTNP1_TFBS_da mE1_TFBS_cnc mE1_TFBS_sens
3R	23774318	3R_23774318_SNP [dm3] 3R_27948596_SNP [dm6]	A	G	1.427e^-5	0.957	UPSTREAM Gp93 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Ubx
2R	16562368	2R_16562368_SNP [dm3] 2R_20674863_SNP [dm6]	G	A	1.427e^-5	0.957	INTERGENIC	TF binding site mE1_TFBS_chinmo
3L	4979121	3L_4979121_SNP [dm3] 3L_4979121_SNP [dm6]	A	G	1.527e^-5	0.957	DOWNSTREAM CG17030 INTRON Con	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi
3R	23774290	3R_23774290_SNP [dm3] 3R_27948568_SNP [dm6]	C	A	1.559e^-5	0.957	UPSTREAM Gp93 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Ubx
2R	2131803	2R_2131803_SNP [dm3] 2R_6244298_SNP [dm6]	G	T	1.584e^-5	0.957	INTRON Pld
3R	23774274	3R_23774274_SNP [dm3] 3R_27948552_SNP [dm6]	T	C	1.733e^-5	0.957	UPSTREAM Gp93 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Ubx
2L	13260591	2L_13260591_SNP [dm3] 2L_13260591_SNP [dm6]	C	T	1.898e^-5	0.957	UPSTREAM CG31730 & 1 other INTERGENIC
3L	2315161	3L_2315161_SNP [dm3] 3L_2315161_SNP [dm6]	G	A	1.963e^-5	0.957	INTERGENIC
X	8079306	X_8079306_SNP [dm3] X_8185273_SNP [dm6]	T	C	2.008e^-5	0.957	INTRON sdt
2R	16467546	2R_16467546_SNP [dm3] 2R_20580041_SNP [dm6]	A	G	2.009e^-5	0.957	INTRON qsm
2R	13851502	2R_13851502_SNP [dm3] 2R_17963997_SNP [dm6]	T	C	2.035e^-5	0.957	INTERGENIC
3L	8325186	3L_8325186_SNP [dm3] 3L_8332086_SNP [dm6]	C	G	2.072e^-5	0.957	INTERGENIC
3L	22596983	3L_22596983_SNP [dm3] 3L_22603883_SNP [dm6]	C	T	2.110e^-5	0.957	INTRON CG14459
2L	4364814	2L_4364814_INS [dm3] 2L_4364814_INS [dm6]	C	CAGA	2.124e^-5	0.957	UPSTREAM CR45363 INTRON Traf4	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
X	19859377	X_19859377_SNP [dm3] X_19965344_SNP [dm6]	T	C	2.312e^-5	0.957	SYNONYMOUS_CODING Nep3	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
X	8475805	X_8475805_SNP [dm3] X_8581772_SNP [dm6]	T	C	2.368e^-5	0.957	INTRON CG12065
3R	14403880	3R_14403880_SNP [dm3] 3R_18578158_SNP [dm6]	C	T	2.385e^-5	0.957	INTRON fray & 1 other
2L	6145354	2L_6145354_SNP [dm3] 2L_6145354_SNP [dm6]	G	A	2.422e^-5	0.957	DOWNSTREAM CG13991 INTERGENIC
2R	10962634	2R_10962634_SNP [dm3] 2R_15075129_SNP [dm6]	G	T	2.587e^-5	0.957	INTERGENIC
3R	16956968	3R_16956968_SNP [dm3] 3R_21131246_SNP [dm6]	G	T	2.818e^-5	0.957	NON_SYNONYMOUS_CODING Ice2 START_GAINED Ice2 UTR_5_PRIME Ice2	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2R	16953230	2R_16953230_SNP [dm3] 2R_21065725_SNP [dm6]	G	T	2.872e^-5	0.957	SYNONYMOUS_CODING Cht4 UPSTREAM Cht12	TF binding site mE1_TFBS_cad
3R	19914279	3R_19914279_SNP [dm3] 3R_24088557_SNP [dm6]	T	G	2.905e^-5	0.957	INTRON 4EHP
3R	11206710	3R_11206710_SNP [dm3] 3R_15380988_SNP [dm6]	T	C	2.940e^-5	0.957	DOWNSTREAM h-cup INTRON Rbp
3L	8163511	3L_8163511_SNP [dm3] 3L_8170411_SNP [dm6]	C	G	3.026e^-5	0.957	DOWNSTREAM RecQ4 INTERGENIC	TF binding site mE1_TFBS_cnc
2L	4819005	2L_4819005_DEL [dm3] 2L_4819005_DEL [dm6]	CGTCGATTCC	C	3.207e^-5	0.957	UPSTREAM CG3225 INTERGENIC
X	768139	X_768139_SNP [dm3] X_874106_SNP [dm6]	T	A	3.238e^-5	0.957	INTRON CG43867	TF binding site mE1_TFBS_chinmo
3L	6089335	3L_6089335_SNP [dm3] 3L_6096235_SNP [dm6]	A	G	3.377e^-5	0.957	SYNONYMOUS_CODING loj
3R	23774301	3R_23774301_SNP [dm3] 3R_27948579_SNP [dm6]	T	A	3.389e^-5	0.957	UPSTREAM Gp93 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Ubx
3L	14552562	3L_14552562_SNP [dm3] 3L_14559462_SNP [dm6]	G	C	3.392e^-5	0.957	UPSTREAM CG34039 & 1 other DOWNSTREAM Lk INTERGENIC
3R	27456476	3R_27456476_DEL [dm3] 3R_31630754_DEL [dm6]	GCCCAGCGGTAGGG...	G	3.414e^-5	0.957	INTRON kek6
X	21007024	X_21007024_SNP [dm3] X_21135997_SNP [dm6]	A	C	3.436e^-5	0.957	INTRON CG34120
3R	3847255	3R_3847255_SNP [dm3] 3R_8021533_SNP [dm6]	A	T	3.530e^-5	0.957	SYNONYMOUS_CODING CG2747	TF binding site mE1_TFBS_cad
3L	17238518	3L_17238518_SNP [dm3] 3L_17245418_SNP [dm6]	A	C	3.627e^-5	0.957	UPSTREAM CR43870 DOWNSTREAM CG7707 INTERGENIC	transposable element FlyBase
3R	20367708	3R_20367708_SNP [dm3] 3R_24541986_SNP [dm6]	G	T	3.831e^-5	0.957	INTRON CG5789
3R	23774336	3R_23774336_SNP [dm3] 3R_27948614_SNP [dm6]	G	A	3.914e^-5	0.957	UPSTREAM Gp93 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_jumu mE1_TFBS_Ubx
2R	19055659	2R_19055659_SNP [dm3] 2R_23168136_SNP [dm6]	C	T	3.919e^-5	0.957	NON_SYNONYMOUS_CODING CG34371	TF binding site BDTNP1_TFBS_sna mE1_TFBS_chinmo mE1_TFBS_HSA
3R	17383770	3R_17383770_SNP [dm3] 3R_21558048_SNP [dm6]	G	A	4.025e^-5	0.957	UPSTREAM slou INTERGENIC	regulatory region FlyBase TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
3R	23774323	3R_23774323_SNP [dm3] 3R_27948601_SNP [dm6]	C	T	4.120e^-5	0.957	UPSTREAM Gp93 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Ubx
2R	16466867	2R_16466867_SNP [dm3] 2R_20579362_SNP [dm6]	A	C	4.145e^-5	0.957	INTRON qsm
2R	9574134	2R_9574134_SNP [dm3] 2R_13686629_SNP [dm6]	A	T	4.145e^-5	0.957	INTRON fas
2R	6994678	2R_6994678_SNP [dm3] 2R_11107173_SNP [dm6]	C	A	4.168e^-5	0.957	UPSTREAM luna INTRON luna	TF binding site BDTNP1_TFBS_dl
X	16004107	X_16004107_SNP [dm3] X_16110074_SNP [dm6]	C	A	4.235e^-5	0.957	INTERGENIC
3R	16026162	3R_16026162_SNP [dm3] 3R_20200440_SNP [dm6]	C	A	4.278e^-5	0.957	INTERGENIC
2R	9574132	2R_9574132_SNP [dm3] 2R_13686627_SNP [dm6]	C	A	4.395e^-5	0.957	INTRON fas
2L	11833795	2L_11833795_SNP [dm3] 2L_11833795_SNP [dm6]	T	G	4.422e^-5	0.957	UPSTREAM CG45011 & 1 other INTRON Pde1c
3L	7105603	3L_7105603_SNP [dm3] 3L_7112503_SNP [dm6]	A	G	4.491e^-5	0.957	INTRON form3
3L	7105606	3L_7105606_SNP [dm3] 3L_7112506_SNP [dm6]	G	T	4.491e^-5	0.957	INTRON form3
3L	7105607	3L_7105607_SNP [dm3] 3L_7112507_SNP [dm6]	G	T	4.491e^-5	0.957	INTRON form3
3L	7105609	3L_7105609_DEL [dm3] 3L_7112509_DEL [dm6]	GCACT	A	4.491e^-5	0.957	INTRON form3
3R	14403907	3R_14403907_SNP [dm3] 3R_18578185_SNP [dm6]	G	C	4.496e^-5	0.957	INTRON fray & 1 other
X	17654034	X_17654034_SNP [dm3] X_17760001_SNP [dm6]	A	C	4.559e^-5	0.957	INTERGENIC
2L	4179678	2L_4179678_SNP [dm3] 2L_4179678_SNP [dm6]	T	A	4.562e^-5	0.957	INTERGENIC	TF binding site mE1_TFBS_GATAe mE1_TFBS_HSA
3L	19386244	3L_19386244_SNP [dm3] 3L_19393144_SNP [dm6]	G	T	4.567e^-5	0.957	INTRON CG32206
3R	18163168	3R_18163168_SNP [dm3] 3R_22337446_SNP [dm6]	A	G	4.570e^-5	0.957	SYNONYMOUS_CODING CG5388
2R	3528133	2R_3528133_SNP [dm3] 2R_7640628_SNP [dm6]	T	A	4.600e^-5	0.957	INTRON CG43340	TF binding site mE1_TFBS_cad
3L	17238530	3L_17238530_SNP [dm3] 3L_17245430_SNP [dm6]	C	G	4.603e^-5	0.957	UPSTREAM CR43870 DOWNSTREAM CG7707 INTERGENIC	transposable element FlyBase
3L	17238199	3L_17238199_INS [dm3] 3L_17245099_INS [dm6]	A	AA	4.631e^-5	0.957	UPSTREAM CR43870 DOWNSTREAM CG7707 INTERGENIC	transposable element FlyBase
3L	7105615	3L_7105615_SNP [dm3] 3L_7112515_SNP [dm6]	A	G	4.758e^-5	0.957	INTRON form3
3R	26457392	3R_26457392_SNP [dm3] 3R_30631670_SNP [dm6]	C	A	4.759e^-5	0.957	INTERGENIC
2R	14151325	2R_14151325_SNP [dm3] 2R_18263820_SNP [dm6]	A	C	4.773e^-5	0.957	INTERGENIC
2R	12900312	2R_12900312_SNP [dm3] 2R_17012807_SNP [dm6]	T	A	4.796e^-5	0.957	INTRON Ehbp1
2R	3528129	2R_3528129_SNP [dm3] 2R_7640624_SNP [dm6]	T	C	4.832e^-5	0.957	SPLICE_SITE_REGION CG43340 INTRON CG43340	TF binding site mE1_TFBS_cad
2L	12158791	2L_12158791_DEL [dm3] 2L_12158791_DEL [dm6]	AA	A	4.844e^-5	0.957	INTRON CG31760	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
X	8475796	X_8475796_SNP [dm3] X_8581763_SNP [dm6]	T	A	4.864e^-5	0.957	INTRON CG12065
2R	3316120	2R_3316120_SNP [dm3] 2R_7428615_SNP [dm6]	G	T	4.914e^-5	0.957	UPSTREAM CG11145 DOWNSTREAM CR44203 INTRON so	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	3316132	2R_3316132_SNP [dm3] 2R_7428627_SNP [dm6]	T	G	4.922e^-5	0.957	UPSTREAM CG11145 DOWNSTREAM CR44203 INTRON so	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	3528266	2R_3528266_SNP [dm3] 2R_7640761_SNP [dm6]	A	C	5.037e^-5	0.957	INTRON CG43340	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2L	4691893	2L_4691893_SNP [dm3] 2L_4691893_SNP [dm6]	G	T	5.054e^-5	0.957	INTERGENIC
3L	535392	3L_535392_SNP [dm3] 3L_535392_SNP [dm6]	A	C	5.363e^-5	0.957	INTRON klar	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
3R	10179840	3R_10179840_SNP [dm3] 3R_14354118_SNP [dm6]	T	C	5.391e^-5	0.957	INTRON NK7.1
3R	5044833	3R_5044833_SNP [dm3] 3R_9219111_SNP [dm6]	T	G	5.483e^-5	0.957	INTRON pum
3L	18017184	3L_18017184_SNP [dm3] 3L_18024084_SNP [dm6]	C	T	5.561e^-5	0.957	INTRON Eip75B
3L	8607211	3L_8607211_SNP [dm3] 3L_8614111_SNP [dm6]	T	C	5.641e^-5	0.957	INTRON CG6282
2L	17800654	2L_17800654_SNP [dm3] 2L_17800654_SNP [dm6]	A	T	5.650e^-5	0.957	INTRON CadN2
2R	13851476	2R_13851476_SNP [dm3] 2R_17963971_SNP [dm6]	C	T	5.678e^-5	0.957	INTERGENIC
3L	2619417	3L_2619417_SNP [dm3] 3L_2619417_SNP [dm6]	G	A	5.716e^-5	0.957	INTRON Pxn
3R	2868311	3R_2868311_INS [dm3] 3R_7042589_INS [dm6]	C	CGGA	5.765e^-5	0.957	INTERGENIC	TF binding site BDTNP1_TFBS_da

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By genomic position
Variant impact
Gene name

cv_BoutLength_Day 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