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=5.244e^-1)
Null hypothesis is not rejected (p>0.05).
Interpretation: NORMAL distribution of this phenotype

We tested for association of this phenotype with 6 known covariates Huang et al., 2014 using both ANOVA and Kruskal-Wallis association tests.

ANOVA test

Covariate	p-value	Significance
In_3R_K	0.03847
In_3R_Mo	0.02435

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_3R_K	4.9377	0.0847
In_3R_Mo	9.6999	0.0078

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1943 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
3R	19232134	3R_19232134_SNP [dm3] 3R_23406412_SNP [dm6]	T	A	3.208e^-6	0.945	SYNONYMOUS_CODING Ir94e	TF binding site mE1_TFBS_sens
3L	8207850	3L_8207850_SNP [dm3] 3L_8214750_SNP [dm6]	T	C	6.041e^-6	0.945	UPSTREAM CG8012 INTERGENIC
3R	24741850	3R_24741850_SNP [dm3] 3R_28916128_SNP [dm6]	G	T	6.457e^-6	0.945	INTRON Doa
2R	16522079	2R_16522079_SNP [dm3] 2R_20634574_SNP [dm6]	C	A	7.699e^-6	0.945	SYNONYMOUS_CODING rig	TF binding site mE1_TFBS_cad
X	17863857	X_17863857_SNP [dm3] X_17969824_SNP [dm6]	A	C	8.333e^-6	0.945	INTRON Sh
2R	16522034	2R_16522034_SNP [dm3] 2R_20634529_SNP [dm6]	A	G	8.480e^-6	0.945	SYNONYMOUS_CODING rig	TF binding site mE1_TFBS_cad
2R	16522052	2R_16522052_SNP [dm3] 2R_20634547_SNP [dm6]	C	T	8.480e^-6	0.945	SYNONYMOUS_CODING rig	TF binding site mE1_TFBS_cad
2R	10807748	2R_10807748_SNP [dm3] 2R_14920243_SNP [dm6]	T	C	8.862e^-6	0.945	INTRON CG10249	TF binding site mE1_TFBS_cnc
2R	12419991	2R_12419991_SNP [dm3] 2R_16532486_SNP [dm6]	A	G	9.432e^-6	0.945	UTR_3_PRIME Sema-2a
3R	15166169	3R_15166169_SNP [dm3] 3R_19340447_SNP [dm6]	G	T	1.018e^-5	0.945	INTERGENIC	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 mE1_TFBS_Kr mE1_TFBS_Trl
3L	16698650	3L_16698650_SNP [dm3] 3L_16705550_SNP [dm6]	T	C	1.049e^-5	0.945	SYNONYMOUS_CODING CG9692 INTRON Lasp & 1 other	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	11798043	3L_11798043_SNP [dm3] 3L_11804943_SNP [dm6]	A	G	1.201e^-5	0.945	SYNONYMOUS_CODING CG42255	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3R	19356813	3R_19356813_SNP [dm3] 3R_23531091_SNP [dm6]	A	T	1.365e^-5	0.945	UPSTREAM CG10175 INTERGENIC
3L	13927092	3L_13927092_SNP [dm3] 3L_13933992_SNP [dm6]	G	T	1.457e^-5	0.945	SYNONYMOUS_CODING Gl	TF binding site BDTNP1_TFBS_prd mE1_TFBS_cad mE1_TFBS_HSA
2R	11467370	2R_11467370_INS [dm3] 2R_15579865_INS [dm6]	A	AAGTGAA	1.459e^-5	0.945	INTERGENIC
2L	20319073	2L_20319073_SNP [dm3] 2L_20319073_SNP [dm6]	C	G	1.555e^-5	0.945	INTRON spir
3R	22515522	3R_22515522_SNP [dm3] 3R_26689800_SNP [dm6]	A	T	1.574e^-5	0.945	INTERGENIC
3R	6489509	3R_6489509_SNP [dm3] 3R_10663787_SNP [dm6]	T	C	1.577e^-5	0.945	INTERGENIC	TF binding site mE1_TFBS_sens
3R	25437389	3R_25437389_SNP [dm3] 3R_29611667_SNP [dm6]	T	G	1.592e^-5	0.945	INTRON alph
3R	4426920	3R_4426920_SNP [dm3] 3R_8601198_SNP [dm6]	C	A	1.634e^-5	0.945	INTRON 5-HT2B
3R	15166309	3R_15166309_INS [dm3] 3R_19340587_INS [dm6]	A	AA	1.712e^-5	0.945	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_Trl
2R	11467404	2R_11467404_SNP [dm3] 2R_15579899_SNP [dm6]	C	G	1.719e^-5	0.945	INTERGENIC
2R	11467386	2R_11467386_SNP [dm3] 2R_15579881_SNP [dm6]	G	A	1.755e^-5	0.945	INTERGENIC
2R	7792376	2R_7792376_SNP [dm3] 2R_11904871_SNP [dm6]	C	A	1.923e^-5	0.945	UPSTREAM MCPH1 INTRON CG13183	TF binding site mE1_TFBS_inv
3R	15166312	3R_15166312_SNP [dm3] 3R_19340590_SNP [dm6]	A	T	1.941e^-5	0.945	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_Trl
3R	16387040	3R_16387040_SNP [dm3] 3R_20561318_SNP [dm6]	A	T	1.942e^-5	0.945	START_GAINED CG5191 UTR_5_PRIME CG5191 INTRON CG5191	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
X	4289569	X_4289569_SNP [dm3] X_4395536_SNP [dm6]	C	T	1.998e^-5	0.945	INTRON CR32773	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2R	11467342	2R_11467342_SNP [dm3] 2R_15579837_SNP [dm6]	T	A	2.041e^-5	0.945	INTERGENIC
X	3184892	X_3184892_SNP [dm3] X_3290859_SNP [dm6]	G	A	2.043e^-5	0.945	UPSTREAM dnc INTRON dnc
X	13656452	X_13656452_SNP [dm3] X_13762419_SNP [dm6]	C	A	2.100e^-5	0.945	UPSTREAM rdgB DOWNSTREAM Yp3 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_jumu mE1_TFBS_Trl
2L	10310614	2L_10310614_SNP [dm3] 2L_10310614_SNP [dm6]	G	T	2.163e^-5	0.945	UTR_5_PRIME Cdk5alpha DOWNSTREAM CG5385	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb
2R	12420001	2R_12420001_SNP [dm3] 2R_16532496_SNP [dm6]	A	G	2.182e^-5	0.945	UTR_3_PRIME Sema-2a
3R	18740523	3R_18740523_SNP [dm3] 3R_22914801_SNP [dm6]	G	A	2.194e^-5	0.945	INTRON klg
2R	11467331	2R_11467331_SNP [dm3] 2R_15579826_SNP [dm6]	G	T	2.343e^-5	0.945	INTERGENIC
2R	17504251	2R_17504251_SNP [dm3] 2R_21616746_SNP [dm6]	G	C	2.419e^-5	0.945	UTR_5_PRIME CG18870 DOWNSTREAM clt	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA
X	17863833	X_17863833_SNP [dm3] X_17969800_SNP [dm6]	C	G	2.518e^-5	0.945	INTRON Sh
2R	20355319	2R_20355319_SNP [dm3] 2R_24467796_SNP [dm6]	T	C	2.546e^-5	0.945	INTRON CG13579
3R	18740517	3R_18740517_SNP [dm3] 3R_22914795_SNP [dm6]	A	G	2.611e^-5	0.945	INTRON klg
X	5045284	X_5045284_SNP [dm3] X_5151251_SNP [dm6]	C	A	2.720e^-5	0.945	INTRON rg & 1 other
2L	5563305	2L_5563305_SNP [dm3] 2L_5563305_SNP [dm6]	A	G	2.805e^-5	0.945	SYNONYMOUS_CODING GluRIIB	TF binding site mE1_TFBS_cad
2R	18887422	2R_18887422_SNP [dm3] 2R_22999899_SNP [dm6]	G	C	2.809e^-5	0.945	INTRON twi
3L	1122497	3L_1122497_SNP [dm3] 3L_1122497_SNP [dm6]	G	T	2.832e^-5	0.945	INTERGENIC
3L	7722633	3L_7722633_SNP [dm3] 3L_7729533_SNP [dm6]	G	A	2.957e^-5	0.945	NON_SYNONYMOUS_CODING CG8492 INTRON CG32373	TF binding site mE1_TFBS_sens
2L	1954687	2L_1954687_SNP [dm3] 2L_1954687_SNP [dm6]	G	A	3.022e^-5	0.945	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	7722478	3L_7722478_SNP [dm3] 3L_7729378_SNP [dm6]	G	A	3.067e^-5	0.945	SYNONYMOUS_CODING CG8492 INTRON CG32373	TF binding site mE1_TFBS_sens
3R	15166328	3R_15166328_SNP [dm3] 3R_19340606_SNP [dm6]	G	A	3.085e^-5	0.945	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Kr
2R	7792377	2R_7792377_SNP [dm3] 2R_11904872_SNP [dm6]	T	A	3.104e^-5	0.945	UPSTREAM MCPH1 INTRON CG13183	TF binding site mE1_TFBS_inv
3R	15166554	3R_15166554_SNP [dm3] 3R_19340832_SNP [dm6]	G	A	3.126e^-5	0.945	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Kr
2L	2061144	2L_2061144_SNP [dm3] 2L_2061144_SNP [dm6]	C	A	3.127e^-5	0.945	INTRON dpr3
3R	23873095	3R_23873095_SNP [dm3] 3R_28047373_SNP [dm6]	T	C	3.129e^-5	0.945	UPSTREAM CG34362 INTRON CG34362
3L	7722600	3L_7722600_SNP [dm3] 3L_7729500_SNP [dm6]	T	G	3.195e^-5	0.945	NON_SYNONYMOUS_CODING CG8492 INTRON CG32373	TF binding site mE1_TFBS_sens
3R	22515651	3R_22515651_SNP [dm3] 3R_26689929_SNP [dm6]	G	C	3.267e^-5	0.945	INTERGENIC
2L	2060601	2L_2060601_SNP [dm3] 2L_2060601_SNP [dm6]	G	A	3.312e^-5	0.945	INTRON dpr3
3R	26719975	3R_26719975_SNP [dm3] 3R_30894253_SNP [dm6]	C	A	3.340e^-5	0.945	NON_SYNONYMOUS_CODING Cyp4c3	TF binding site BDTNP1_TFBS_hb mE1_TFBS_HSA
3R	25437387	3R_25437387_SNP [dm3] 3R_29611665_SNP [dm6]	A	T	3.373e^-5	0.945	INTRON alph
3R	15166259	3R_15166259_SNP [dm3] 3R_19340537_SNP [dm6]	C	G	3.505e^-5	0.945	INTERGENIC	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 mE1_TFBS_Kr mE1_TFBS_Trl
3R	19356833	3R_19356833_SNP [dm3] 3R_23531111_SNP [dm6]	T	G	3.508e^-5	0.945	UPSTREAM CG10175 INTERGENIC
2L	15370895	2L_15370895_SNP [dm3] 2L_15370895_SNP [dm6]	T	G	3.625e^-5	0.945	INTERGENIC	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad
3R	24924570	3R_24924570_SNP [dm3] 3R_29098848_SNP [dm6]	G	A	3.709e^-5	0.945	SYNONYMOUS_CODING CG11873	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2R	7751483	2R_7751483_SNP [dm3] 2R_11863978_SNP [dm6]	G	C	3.807e^-5	0.945	UPSTREAM CG42531 & 1 other INTERGENIC
X	19726924	X_19726924_INS [dm3] X_19832891_INS [dm6]	G	GG	3.814e^-5	0.945	UTR_3_PRIME pico
2R	19645317	2R_19645317_SNP [dm3] 2R_23757794_SNP [dm6]	A	G	3.838e^-5	0.945	SYNONYMOUS_CODING CG9850
2L	7848509	2L_7848509_SNP [dm3] 2L_7848509_SNP [dm6]	T	G	3.875e^-5	0.945	SYNONYMOUS_CODING CG14535	TF binding site mE1_TFBS_cad
2L	14788646	2L_14788646_SNP [dm3] 2L_14788646_SNP [dm6]	T	C	3.964e^-5	0.945	INTERGENIC
X	19726949	X_19726949_SNP [dm3] X_19832916_SNP [dm6]	A	T	4.023e^-5	0.945	UTR_3_PRIME pico
3L	7720516	3L_7720516_SNP [dm3] 3L_7727416_SNP [dm6]	T	C	4.081e^-5	0.945	UPSTREAM CG7457 DOWNSTREAM CG8492 INTRON CG32373	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2R	9886112	2R_9886112_SNP [dm3] 2R_13998607_SNP [dm6]	G	A	4.095e^-5	0.945	INTRON mam	TF binding site BDTNP1_TFBS_dl
2R	9886432	2R_9886432_SNP [dm3] 2R_13998927_SNP [dm6]	T	C	4.095e^-5	0.945	INTRON mam	TF binding site BDTNP1_TFBS_dl
2R	16294534	2R_16294534_SNP [dm3] 2R_20407029_SNP [dm6]	A	C	4.141e^-5	0.945	INTERGENIC
2R	11409462	2R_11409462_SNP [dm3] 2R_15521957_SNP [dm6]	G	A	4.251e^-5	0.945	INTRON Khc-73
2L	8412283	2L_8412283_SNP [dm3] 2L_8412283_SNP [dm6]	T	C	4.257e^-5	0.945	UTR_3_PRIME CG13398 UPSTREAM CG13397 DOWNSTREAM CG13398
2R	17769771	2R_17769771_SNP [dm3] 2R_21882266_SNP [dm6]	T	C	4.285e^-5	0.945	SYNONYMOUS_CODING PpN58A INTRON Fili	TF binding site mE1_TFBS_sens
2L	16214563	2L_16214563_SNP [dm3] 2L_16214563_SNP [dm6]	A	T	4.339e^-5	0.945	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	2833210	2L_2833210_SNP [dm3] 2L_2833210_SNP [dm6]	G	A	4.368e^-5	0.945	INTERGENIC
2R	12291285	2R_12291285_SNP [dm3] 2R_16403780_SNP [dm6]	T	C	4.374e^-5	0.945	INTRON Sema-2b
2L	713145	2L_713145_SNP [dm3] 2L_713145_SNP [dm6]	T	C	4.421e^-5	0.945	INTRON ds & 1 other	TF binding site 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_sens mE1_TFBS_Stat92E
2R	17042676	2R_17042676_SNP [dm3] 2R_21155171_SNP [dm6]	G	C	4.441e^-5	0.945	NON_SYNONYMOUS_CODING CG30389	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	5752313	2L_5752313_SNP [dm3] 2L_5752313_SNP [dm6]	T	A	4.459e^-5	0.945	INTRON CG11030
2L	13138840	2L_13138840_SNP [dm3] 2L_13138840_SNP [dm6]	A	G	4.465e^-5	0.945	INTERGENIC
3R	24201927	3R_24201927_SNP [dm3] 3R_28376205_SNP [dm6]	C	T	4.516e^-5	0.945	INTERGENIC	TF binding site mE1_TFBS_sbb
2L	12376443	2L_12376443_SNP [dm3] 2L_12376443_SNP [dm6]	G	A	4.537e^-5	0.945	INTRON bru-2
3R	22091412	3R_22091412_SNP [dm3] 3R_26265690_SNP [dm6]	A	G	4.572e^-5	0.945	INTRON CG6154
3R	15166285	3R_15166285_INS [dm3] 3R_19340563_INS [dm6]	T	TAGC	4.593e^-5	0.945	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_Trl
X	13656637	X_13656637_SNP [dm3] X_13762604_SNP [dm6]	T	G	4.613e^-5	0.945	UPSTREAM rdgB INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3R	26011590	3R_26011590_SNP [dm3] 3R_30185868_SNP [dm6]	C	T	4.617e^-5	0.945	SYNONYMOUS_CODING CG9747
2L	5752045	2L_5752045_SNP [dm3] 2L_5752045_SNP [dm6]	G	A	4.704e^-5	0.945	INTRON CG11030
2L	16214551	2L_16214551_SNP [dm3] 2L_16214551_SNP [dm6]	T	A	4.777e^-5	0.945	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
X	6495564	X_6495564_SNP [dm3] X_6601531_SNP [dm6]	T	C	4.831e^-5	0.945	UPSTREAM pigs INTRON pigs	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_sens mE1_TFBS_Trl
2L	18145615	2L_18145615_SNP [dm3] 2L_18145615_SNP [dm6]	A	G	4.970e^-5	0.945	DOWNSTREAM CR44478 INTRON Socs36E	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_Med BDTNP1_TFBS_shn BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA
2R	6786077	2R_6786077_SNP [dm3] 2R_10898572_SNP [dm6]	G	A	5.002e^-5	0.945	SYNONYMOUS_CODING Rpb5 UPSTREAM CG7712	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	15372445	2L_15372445_SNP [dm3] 2L_15372445_SNP [dm6]	T	C	5.040e^-5	0.945	INTERGENIC
3R	24936038	3R_24936038_SNP [dm3] 3R_29110316_SNP [dm6]	G	A	5.094e^-5	0.945	SYNONYMOUS_CODING alpha-Man-Ib
2R	8929285	2R_8929285_SNP [dm3] 2R_13041780_SNP [dm6]	C	G	5.131e^-5	0.945	INTERGENIC	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_inv mE1_TFBS_Trl
2L	4213719	2L_4213719_SNP [dm3] 2L_4213719_SNP [dm6]	A	C	5.148e^-5	0.945	SYNONYMOUS_CODING ft	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2L	1947694	2L_1947694_SNP [dm3] 2L_1947694_SNP [dm6]	T	A	5.169e^-5	0.945	UPSTREAM CG33673 INTERGENIC	regulatory region REDfly_CRMs TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3R	19625870	3R_19625870_SNP [dm3] 3R_23800148_SNP [dm6]	G	A	5.225e^-5	0.945	NON_SYNONYMOUS_CODING mbc
3R	26619006	3R_26619006_SNP [dm3] 3R_30793284_SNP [dm6]	G	T	5.227e^-5	0.945	SYNONYMOUS_CODING wts	TF binding site mE1_TFBS_chinmo
3R	26005517	3R_26005517_SNP [dm3] 3R_30179795_SNP [dm6]	G	A	5.229e^-5	0.945	UTR_3_PRIME CG15530 UPSTREAM Bet5	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_run mE1_TFBS_Ubx
2R	7398509	2R_7398509_SNP [dm3] 2R_11511004_SNP [dm6]	T	C	5.254e^-5	0.945	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_prd mE1_TFBS_HSA
2L	5824641	2L_5824641_SNP [dm3] 2L_5824641_SNP [dm6]	A	C	5.299e^-5	0.945	UTR_5_PRIME TrissinR UPSTREAM TrissinR

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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=1.585e^-1)
Null hypothesis is not rejected (p>0.05).
Interpretation: NORMAL distribution of this phenotype

We tested for association of this phenotype with 6 known covariates Huang et al., 2014 using both ANOVA and Kruskal-Wallis association tests.

ANOVA test

Covariate	p-value	Significance
In_3R_Mo	0.004521

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_3R_Mo	12.7328	0.0017

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1885 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
2R	17769771	2R_17769771_SNP [dm3] 2R_21882266_SNP [dm6]	T	C	2.554e^-7	0.479	SYNONYMOUS_CODING PpN58A INTRON Fili	TF binding site mE1_TFBS_sens
2L	2899342	2L_2899342_SNP [dm3] 2L_2899342_SNP [dm6]	A	T	1.534e^-6	0.968	INTRON lilli	TF binding site mE1_TFBS_Trl
2R	9523811	2R_9523811_SNP [dm3] 2R_13636306_SNP [dm6]	G	A	2.282e^-6	0.968	INTRON fas
3R	10530682	3R_10530682_SNP [dm3] 3R_14704960_SNP [dm6]	G	A	6.543e^-6	0.968	INTRON kibra
2R	9774945	2R_9774945_SNP [dm3] 2R_13887440_SNP [dm6]	G	T	8.140e^-6	0.968	SYNONYMOUS_CODING shot INTRON shot	TF binding site mE1_TFBS_cad
3L	11854273	3L_11854273_SNP [dm3] 3L_11861173_SNP [dm6]	C	T	9.687e^-6	0.968	INTRON CG44837
2L	19305247	2L_19305247_SNP [dm3] 2L_19305247_SNP [dm6]	T	A	1.106e^-5	0.968	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	18159836	2L_18159836_SNP [dm3] 2L_18159836_SNP [dm6]	C	T	1.129e^-5	0.968	UTR_3_PRIME CG42750 UPSTREAM CG7200 DOWNSTREAM CG42750
2L	4864962	2L_4864962_SNP [dm3] 2L_4864962_SNP [dm6]	A	T	1.159e^-5	0.968	INTRON pog
X	12146696	X_12146696_SNP [dm3] X_12252663_SNP [dm6]	T	C	1.213e^-5	0.968	INTRON Ten-a
2R	9774963	2R_9774963_SNP [dm3] 2R_13887458_SNP [dm6]	A	G	1.242e^-5	0.968	SYNONYMOUS_CODING shot INTRON shot	TF binding site mE1_TFBS_cad
2L	9561278	2L_9561278_SNP [dm3] 2L_9561278_SNP [dm6]	C	T	1.292e^-5	0.968	UPSTREAM jp INTRON jp
2L	13851785	2L_13851785_SNP [dm3] 2L_13851785_SNP [dm6]	G	A	1.323e^-5	0.968	INTRON CenG1A	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad
2L	2833210	2L_2833210_SNP [dm3] 2L_2833210_SNP [dm6]	G	A	1.449e^-5	0.968	INTERGENIC
2L	2899341	2L_2899341_SNP [dm3] 2L_2899341_SNP [dm6]	A	G	1.538e^-5	0.968	INTRON lilli	TF binding site mE1_TFBS_Trl
2R	6556000	2R_6556000_SNP [dm3] 2R_10668495_SNP [dm6]	A	C	1.575e^-5	0.968	INTERGENIC
2R	9502337	2R_9502337_SNP [dm3] 2R_13614832_SNP [dm6]	T	C	1.604e^-5	0.968	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	9560973	2L_9560973_SNP [dm3] 2L_9560973_SNP [dm6]	T	C	1.649e^-5	0.968	UPSTREAM jp INTRON jp
2L	2899331	2L_2899331_SNP [dm3] 2L_2899331_SNP [dm6]	C	G	1.682e^-5	0.968	INTRON lilli
2L	8246765	2L_8246765_SNP [dm3] 2L_8246765_SNP [dm6]	G	A	1.734e^-5	0.968	SPLICE_SITE_REGION CG8086 SYNONYMOUS_CODING CG8086 INTRON CG8086
2R	17042676	2R_17042676_SNP [dm3] 2R_21155171_SNP [dm6]	G	C	1.803e^-5	0.968	NON_SYNONYMOUS_CODING CG30389	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
X	16108180	X_16108180_SNP [dm3] X_16214147_SNP [dm6]	T	A	1.876e^-5	0.968	INTRON disco	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
X	18363771	X_18363771_SNP [dm3] X_18469738_SNP [dm6]	C	T	1.922e^-5	0.968	INTRON CG32547
2R	7200219	2R_7200219_SNP [dm3] 2R_11312714_SNP [dm6]	G	A	2.074e^-5	0.968	SYNONYMOUS_CODING nompA	TF binding site mE1_TFBS_cad
2R	18887422	2R_18887422_SNP [dm3] 2R_22999899_SNP [dm6]	G	C	2.077e^-5	0.968	INTRON twi
2L	4624624	2L_4624624_SNP [dm3] 2L_4624624_SNP [dm6]	G	A	2.145e^-5	0.968	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2L	18159829	2L_18159829_SNP [dm3] 2L_18159829_SNP [dm6]	T	A	2.153e^-5	0.968	UTR_3_PRIME CG42750 UPSTREAM CG7200 DOWNSTREAM CG42750
3R	26755944	3R_26755944_SNP [dm3] 3R_30930222_SNP [dm6]	G	T	2.228e^-5	0.968	UTR_3_PRIME Ptx1 DOWNSTREAM Ptx1
2R	20355730	2R_20355730_SNP [dm3] 2R_24468207_SNP [dm6]	C	T	2.452e^-5	0.968	INTRON CG13579
3R	12725010	3R_12725010_SNP [dm3] 3R_16899288_SNP [dm6]	A	C	2.553e^-5	0.968	INTRON iab-8	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3L	19009769	3L_19009769_SNP [dm3] 3L_19016669_SNP [dm6]	C	T	2.585e^-5	0.968	INTRON nkd	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	18159798	2L_18159798_SNP [dm3] 2L_18159798_SNP [dm6]	T	C	2.613e^-5	0.968	UPSTREAM CG7200 DOWNSTREAM CG42750 INTERGENIC
3L	16698650	3L_16698650_SNP [dm3] 3L_16705550_SNP [dm6]	T	C	2.777e^-5	0.968	SYNONYMOUS_CODING CG9692 INTRON Lasp & 1 other	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	12723450	3R_12723450_SNP [dm3] 3R_16897728_SNP [dm6]	C	T	2.779e^-5	0.968	INTRON iab-8 EXON CR43617	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
X	16559448	X_16559448_SNP [dm3] X_16665415_SNP [dm6]	T	A	2.789e^-5	0.968	UPSTREAM CG15865 INTRON r
3R	12993292	3R_12993292_SNP [dm3] 3R_17167570_SNP [dm6]	T	A	2.790e^-5	0.968	INTRON Mur89F
3L	3525107	3L_3525107_SNP [dm3] 3L_3525107_SNP [dm6]	G	A	2.883e^-5	0.968	INTRON Eip63E
2R	17477719	2R_17477719_SNP [dm3] 2R_21590214_SNP [dm6]	A	G	2.894e^-5	0.968	UPSTREAM CG33225 INTERGENIC
3R	24938524	3R_24938524_SNP [dm3] 3R_29112802_SNP [dm6]	C	T	3.119e^-5	0.968	UTR_5_PRIME alpha-Man-Ib UPSTREAM CG11876	TF binding site BDTNP1_TFBS_dl
3R	26719975	3R_26719975_SNP [dm3] 3R_30894253_SNP [dm6]	C	A	3.148e^-5	0.968	NON_SYNONYMOUS_CODING Cyp4c3	TF binding site BDTNP1_TFBS_hb mE1_TFBS_HSA
2R	10301917	2R_10301917_SNP [dm3] 2R_14414412_SNP [dm6]	C	T	3.204e^-5	0.968	DOWNSTREAM Sin1 INTERGENIC	TF binding site mE1_TFBS_cad
X	16108185	X_16108185_SNP [dm3] X_16214152_SNP [dm6]	T	C	3.296e^-5	0.968	INTRON disco	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
X	17076891	X_17076891_SNP [dm3] X_17182858_SNP [dm6]	A	G	3.390e^-5	0.968	DOWNSTREAM CR44026 INTRON baz
2L	9570077	2L_9570077_DEL [dm3] 2L_9570077_DEL [dm6]	ATTAATAGTTGA...	A	3.445e^-5	0.968	UPSTREAM CG3838 INTRON CG3838	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
X	4584663	X_4584663_SNP [dm3] X_4690630_SNP [dm6]	G	T	3.519e^-5	0.968	INTRON ctp	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
2L	5993439	2L_5993439_SNP [dm3] 2L_5993439_SNP [dm6]	C	A	3.585e^-5	0.968	INTRON lid	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
X	16710183	X_16710183_SNP [dm3] X_16816150_SNP [dm6]	C	A	3.633e^-5	0.968	UPSTREAM CG4829 & 1 other INTRON CG4829
2R	11333214	2R_11333214_SNP [dm3] 2R_15445709_SNP [dm6]	G	A	3.643e^-5	0.968	INTRON CG43729
2L	10985975	2L_10985975_SNP [dm3] 2L_10985975_SNP [dm6]	T	C	3.775e^-5	0.968	NON_SYNONYMOUS_CODING piwi	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA
3R	19625870	3R_19625870_SNP [dm3] 3R_23800148_SNP [dm6]	G	A	3.804e^-5	0.968	NON_SYNONYMOUS_CODING mbc
2L	2899376	2L_2899376_SNP [dm3] 2L_2899376_SNP [dm6]	G	T	3.810e^-5	0.968	INTRON lilli	TF binding site mE1_TFBS_Trl
2R	8275209	2R_8275209_SNP [dm3] 2R_12387704_SNP [dm6]	C	T	3.901e^-5	0.968	INTRON Cpr49Ac
2R	1504828	2R_1504828_SNP [dm3] 2R_5617323_SNP [dm6]	C	G	4.326e^-5	0.968	INTERGENIC
3R	24938744	3R_24938744_SNP [dm3] 3R_29113022_SNP [dm6]	C	T	4.336e^-5	0.968	UPSTREAM CG11876 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl
X	9222879	X_9222879_SNP [dm3] X_9328846_SNP [dm6]	G	A	4.339e^-5	0.968	DOWNSTREAM CG34450 INTRON CG34449
X	17863857	X_17863857_SNP [dm3] X_17969824_SNP [dm6]	A	C	4.431e^-5	0.968	INTRON Sh
3L	3886745	3L_3886745_SNP [dm3] 3L_3886745_SNP [dm6]	C	T	4.468e^-5	0.968	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_sens
2L	10450397	2L_10450397_SNP [dm3] 2L_10450397_SNP [dm6]	T	C	4.483e^-5	0.968	SYNONYMOUS_CODING ppk10 DOWNSTREAM loh
X	5440005	X_5440005_SNP [dm3] X_5545972_SNP [dm6]	G	A	4.518e^-5	0.968	INTRON Vsx2	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_slp1 mE1_TFBS_HSA
2L	9561128	2L_9561128_SNP [dm3] 2L_9561128_SNP [dm6]	T	C	4.518e^-5	0.968	UPSTREAM jp INTRON jp
2L	9563147	2L_9563147_SNP [dm3] 2L_9563147_SNP [dm6]	C	G	4.565e^-5	0.968	INTRON jp
2R	7398017	2R_7398017_SNP [dm3] 2R_11510512_SNP [dm6]	G	T	4.669e^-5	0.968	DOWNSTREAM inv INTERGENIC
3L	888405	3L_888405_SNP [dm3] 3L_888405_SNP [dm6]	A	T	4.681e^-5	0.968	NON_SYNONYMOUS_CODING CG32479 START_GAINED CG32479 UTR_5_PRIME CG32479
2L	9561194	2L_9561194_DEL [dm3] 2L_9561194_DEL [dm6]	TCGCAAAGT	T	4.767e^-5	0.968	UPSTREAM jp INTRON jp
2L	9561223	2L_9561223_SNP [dm3] 2L_9561223_SNP [dm6]	C	A	4.767e^-5	0.968	UPSTREAM jp INTRON jp
3L	1897452	3L_1897452_SNP [dm3] 3L_1897452_SNP [dm6]	T	C	4.773e^-5	0.968	INTRON CG1887	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_prd
2L	9561442	2L_9561442_SNP [dm3] 2L_9561442_SNP [dm6]	C	A	4.829e^-5	0.968	INTRON jp
3L	5752965	3L_5752965_SNP [dm3] 3L_5759865_SNP [dm6]	C	T	4.889e^-5	0.968	SYNONYMOUS_CODING Ubp64E	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
X	6790363	X_6790363_SNP [dm3] X_6896330_SNP [dm6]	C	T	4.970e^-5	0.968	INTERGENIC
2R	10301914	2R_10301914_SNP [dm3] 2R_14414409_SNP [dm6]	A	G	5.028e^-5	0.968	DOWNSTREAM Sin1 INTERGENIC	TF binding site mE1_TFBS_cad
3R	23867938	3R_23867938_SNP [dm3] 3R_28042216_SNP [dm6]	T	C	5.083e^-5	0.968	INTRON CG34362
X	16559445	X_16559445_SNP [dm3] X_16665412_SNP [dm6]	A	T	5.281e^-5	0.968	UPSTREAM CG15865 INTRON r
X	2326589	X_2326589_SNP [dm3] X_2432556_SNP [dm6]	G	C	5.281e^-5	0.968	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd mE1_TFBS_HSA mE1_TFBS_sens
2L	8243896	2L_8243896_SNP [dm3] 2L_8243896_SNP [dm6]	T	C	5.305e^-5	0.968	DOWNSTREAM CG8086 & 1 other INTRON CG43057
X	12146582	X_12146582_SNP [dm3] X_12252549_SNP [dm6]	G	A	5.329e^-5	0.968	INTRON Ten-a
X	2326700	X_2326700_SNP [dm3] X_2432667_SNP [dm6]	T	C	5.330e^-5	0.968	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_prd mE1_TFBS_HSA mE1_TFBS_sens
X	16178110	X_16178110_SNP [dm3] X_16284077_SNP [dm6]	A	G	5.378e^-5	0.968	SYNONYMOUS_CODING eas UTR_3_PRIME eas	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_sens
3R	14976110	3R_14976110_SNP [dm3] 3R_19150388_SNP [dm6]	G	A	5.387e^-5	0.968	DOWNSTREAM CR44107 INTRON CG5835
2R	9204972	2R_9204972_SNP [dm3] 2R_13317467_SNP [dm6]	T	G	5.390e^-5	0.968	INTERGENIC
2R	3288141	2R_3288141_INS [dm3] 2R_7400636_INS [dm6]	A	AT	5.454e^-5	0.968	UPSTREAM CG11112 INTRON Eaf
X	4584155	X_4584155_SNP [dm3] X_4690122_SNP [dm6]	G	A	5.494e^-5	0.968	INTRON ctp	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
2R	20316757	2R_20316757_SNP [dm3] 2R_24429234_SNP [dm6]	A	G	5.680e^-5	0.968	UPSTREAM prom DOWNSTREAM CG15873 INTERGENIC
X	6790350	X_6790350_INS [dm3] X_6896317_INS [dm6]	A	TCGTTGTG	5.896e^-5	0.968	INTERGENIC
2L	13832476	2L_13832476_SNP [dm3] 2L_13832476_SNP [dm6]	G	A	6.003e^-5	0.968	SYNONYMOUS_CODING DNApol-gamma35 UTR_3_PRIME CG33649 UPSTREAM RpII33 DOWNSTREAM Orc5	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
X	21923107	X_21923107_SNP [dm3] X_22521271_SNP [dm6]	A	C	6.147e^-5	0.968	INTRON CG17600
2R	9204973	2R_9204973_SNP [dm3] 2R_13317468_SNP [dm6]	G	C	6.168e^-5	0.968	INTERGENIC
X	12146740	X_12146740_SNP [dm3] X_12252707_SNP [dm6]	G	A	6.221e^-5	0.968	INTRON Ten-a
2L	9706602	2L_9706602_SNP [dm3] 2L_9706602_SNP [dm6]	G	T	6.284e^-5	0.968	UPSTREAM CG31710 INTRON pelo	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_Trl
X	16559447	X_16559447_SNP [dm3] X_16665414_SNP [dm6]	G	C	6.383e^-5	0.968	UPSTREAM CG15865 INTRON r
2L	7236073	2L_7236073_SNP [dm3] 2L_7236073_SNP [dm6]	G	A	6.387e^-5	0.968	INTRON Ndae1	TF binding site mE1_TFBS_cad mE1_TFBS_eve mE1_TFBS_HSA
3L	14417513	3L_14417513_SNP [dm3] 3L_14424413_SNP [dm6]	T	C	6.461e^-5	0.968	INTRON bbg
X	14156611	X_14156611_SNP [dm3] X_14262578_SNP [dm6]	T	A	6.483e^-5	0.968	INTRON CG1461
X	2088787	X_2088787_SNP [dm3] X_2194754_SNP [dm6]	G	A	6.495e^-5	0.968	UTR_5_PRIME Mct1 UPSTREAM CG14053 INTRON Mct1	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
2R	17769504	2R_17769504_SNP [dm3] 2R_21881999_SNP [dm6]	G	A	6.611e^-5	0.968	SYNONYMOUS_CODING PpN58A INTRON Fili	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	3525033	3L_3525033_SNP [dm3] 3L_3525033_SNP [dm6]	G	T	6.627e^-5	0.968	INTRON Eip63E
X	16559459	X_16559459_SNP [dm3] X_16665426_SNP [dm6]	G	A	6.730e^-5	0.968	UPSTREAM CG15865 INTRON r
2R	7813063	2R_7813063_SNP [dm3] 2R_11925558_SNP [dm6]	A	C	6.737e^-5	0.968	INTERGENIC	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA mE1_TFBS_run
2L	13846146	2L_13846146_SNP [dm3] 2L_13846146_SNP [dm6]	T	C	6.741e^-5	0.968	UPSTREAM CG8997 & 1 other INTRON CenG1A
3R	12993250	3R_12993250_SNP [dm3] 3R_17167528_SNP [dm6]	A	G	6.759e^-5	0.968	INTRON Mur89F
X	3862928	X_3862928_SNP [dm3] X_3968895_SNP [dm6]	T	G	6.832e^-5	0.968	UPSTREAM CR45481 & 1 other DOWNSTREAM CG6414 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_slp1

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By genomic position
Variant impact
Gene name

Femur_Length_T2 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