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=6.580e^-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
No significant result.

Kruskal-Wallis test

Covariate	χ²	p-value
In_2L_t	4.6579	0.0974
In_2R_NS	5.2075	0.074
In_3R_Mo	4.9854	0.0827

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2041 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	10652408	3R_10652408_SNP [dm3] 3R_14826686_SNP [dm6]	C	T	2.543e^-7	0.477	SYNONYMOUS_CODING btsz	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
X	5877626	X_5877626_SNP [dm3] X_5983593_SNP [dm6]	C	T	1.324e^-6	0.71	INTRON Grip
3L	4692539	3L_4692539_SNP [dm3] 3L_4692539_SNP [dm6]	T	C	2.118e^-6	0.71	UPSTREAM RhoGEF64C INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Trl
3L	11357121	3L_11357121_SNP [dm3] 3L_11364021_SNP [dm6]	G	T	2.120e^-6	0.71	UPSTREAM CR45036 INTRON CG6163	TF binding site mE1_TFBS_cad
X	16220389	X_16220389_SNP [dm3] X_16326356_SNP [dm6]	A	G	2.271e^-6	0.71	SYNONYMOUS_CODING CalpC DOWNSTREAM CG32579	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens
2R	9965586	2R_9965586_SNP [dm3] 2R_14078081_SNP [dm6]	T	C	3.124e^-6	0.71	INTRON Prosap
3R	25953010	3R_25953010_SNP [dm3] 3R_30127288_SNP [dm6]	A	G	3.720e^-6	0.71	NON_SYNONYMOUS_CODING Ppi1	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3L	4692512	3L_4692512_SNP [dm3] 3L_4692512_SNP [dm6]	T	C	3.804e^-6	0.71	UPSTREAM RhoGEF64C INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Trl
2R	18704014	2R_18704014_SNP [dm3] 2R_22816509_SNP [dm6]	C	G	3.828e^-6	0.71	UTR_5_PRIME CG30271 UPSTREAM CG30271 DOWNSTREAM stl
3R	10658898	3R_10658898_SNP [dm3] 3R_14833176_SNP [dm6]	C	T	4.025e^-6	0.71	INTRON btsz
3R	13180985	3R_13180985_DEL [dm3] 3R_17355263_DEL [dm6]	TTGT	T	4.755e^-6	0.71	INTRON beat-IIa	TF binding site mE1_TFBS_inv
3R	11217493	3R_11217493_SNP [dm3] 3R_15391771_SNP [dm6]	C	T	4.815e^-6	0.71	INTRON Rbp	TF binding site mE1_TFBS_cad
3R	25953104	3R_25953104_SNP [dm3] 3R_30127382_SNP [dm6]	A	T	5.390e^-6	0.71	SYNONYMOUS_CODING Ppi1	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3L	1139878	3L_1139878_SNP [dm3] 3L_1139878_SNP [dm6]	T	G	5.425e^-6	0.71	DOWNSTREAM bab2 INTERGENIC	TF binding site mE1_TFBS_HSA
3L	1139881	3L_1139881_SNP [dm3] 3L_1139881_SNP [dm6]	G	C	6.329e^-6	0.71	DOWNSTREAM bab2 INTERGENIC	TF binding site mE1_TFBS_HSA
3R	17965732	3R_17965732_SNP [dm3] 3R_22140010_SNP [dm6]	C	A	6.665e^-6	0.71	INTRON SKIP	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
3R	23268180	3R_23268180_SNP [dm3] 3R_27442458_SNP [dm6]	T	A	6.880e^-6	0.71	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_eve mE1_TFBS_HSA mE1_TFBS_sens
3L	11357109	3L_11357109_INS [dm3] 3L_11364009_INS [dm6]	A	ACAA	7.067e^-6	0.71	UPSTREAM CR45036 INTRON CG6163	TF binding site mE1_TFBS_cad
3R	25953203	3R_25953203_SNP [dm3] 3R_30127481_SNP [dm6]	A	G	7.198e^-6	0.71	SYNONYMOUS_CODING Ppi1	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3L	4692547	3L_4692547_INS [dm3] 3L_4692547_INS [dm6]	G	GC	7.895e^-6	0.74	UPSTREAM RhoGEF64C INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Trl
3R	25952830	3R_25952830_SNP [dm3] 3R_30127108_SNP [dm6]	T	C	8.587e^-6	0.766	NON_SYNONYMOUS_CODING Ppi1	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	23268228	3R_23268228_SNP [dm3] 3R_27442506_SNP [dm6]	G	A	9.205e^-6	0.768	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_eve mE1_TFBS_HSA mE1_TFBS_sens
3R	13722301	3R_13722301_SNP [dm3] 3R_17896579_SNP [dm6]	T	A	9.426e^-6	0.768	INTRON Rim
3R	10359904	3R_10359904_SNP [dm3] 3R_14534182_SNP [dm6]	G	A	1.065e^-5	0.818	INTRON Pde6
3R	25952966	3R_25952966_SNP [dm3] 3R_30127244_SNP [dm6]	T	C	1.172e^-5	0.818	SYNONYMOUS_CODING Ppi1	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	17683579	3R_17683579_SNP [dm3] 3R_21857857_SNP [dm6]	A	G	1.178e^-5	0.818	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_cnc mE1_TFBS_HSA
3R	14175484	3R_14175484_SNP [dm3] 3R_18349762_SNP [dm6]	T	C	1.278e^-5	0.818	INTRON CG15803
X	19206708	X_19206708_SNP [dm3] X_19312675_SNP [dm6]	C	A	1.324e^-5	0.818	NON_SYNONYMOUS_CODING out	TF binding site mE1_TFBS_cad
3R	13418710	3R_13418710_SNP [dm3] 3R_17592988_SNP [dm6]	C	T	1.337e^-5	0.818	INTERGENIC
3R	22311997	3R_22311997_SNP [dm3] 3R_26486275_SNP [dm6]	T	A	1.365e^-5	0.818	INTRON plum
X	16289127	X_16289127_SNP [dm3] X_16395094_SNP [dm6]	T	G	1.381e^-5	0.818	SYNONYMOUS_CODING mei-41
3R	11443794	3R_11443794_INS [dm3] 3R_15618072_INS [dm6]	A	AA	1.453e^-5	0.818	INTERGENIC
3R	13722160	3R_13722160_SNP [dm3] 3R_17896438_SNP [dm6]	T	A	1.471e^-5	0.818	INTRON Rim
2L	13874312	2L_13874312_SNP [dm3] 2L_13874312_SNP [dm6]	C	T	1.589e^-5	0.818	INTRON CenG1A
3R	13187998	3R_13187998_SNP [dm3] 3R_17362276_SNP [dm6]	A	C	1.637e^-5	0.818	INTRON beat-IIa
3R	14987341	3R_14987341_SNP [dm3] 3R_19161619_SNP [dm6]	G	C	1.675e^-5	0.818	SYNONYMOUS_CODING CG42359 INTRON CG42358	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb mE1_TFBS_HSA mE1_TFBS_sens
3R	10649336	3R_10649336_SNP [dm3] 3R_14823614_SNP [dm6]	G	T	1.765e^-5	0.818	INTRON btsz	TF binding site mE1_TFBS_bab1
X	5877627	X_5877627_SNP [dm3] X_5983594_SNP [dm6]	G	A	1.852e^-5	0.818	INTRON Grip
X	9754921	X_9754921_SNP [dm3] X_9860888_SNP [dm6]	T	C	1.875e^-5	0.818	INTERGENIC
3R	18435193	3R_18435193_SNP [dm3] 3R_22609471_SNP [dm6]	C	T	1.985e^-5	0.818	NON_SYNONYMOUS_CODING CG31156 UPSTREAM CG13843 DOWNSTREAM Efa6	TF binding site mE1_TFBS_inv
3L	17403244	3L_17403244_SNP [dm3] 3L_17410144_SNP [dm6]	A	T	1.993e^-5	0.818	INTRON blot
3R	23268536	3R_23268536_SNP [dm3] 3R_27442814_SNP [dm6]	C	T	2.110e^-5	0.818	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_eve mE1_TFBS_HSA mE1_TFBS_sens
3R	5443035	3R_5443035_SNP [dm3] 3R_9617313_SNP [dm6]	A	G	2.132e^-5	0.818	INTRON CG8312
3R	20949949	3R_20949949_INS [dm3] 3R_25124227_INS [dm6]	A	ATA	2.158e^-5	0.818	INTRON vig2	TF binding site BDTNP1_TFBS_Med mE1_TFBS_HSA
2R	18598851	2R_18598851_SNP [dm3] 2R_22711346_SNP [dm6]	A	T	2.159e^-5	0.818	SYNONYMOUS_CODING CG30275 UTR_3_PRIME CG30275
2R	17209052	2R_17209052_SNP [dm3] 2R_21321547_SNP [dm6]	A	G	2.184e^-5	0.818	SYNONYMOUS_CODING CG30394
3R	11465272	3R_11465272_SNP [dm3] 3R_15639550_SNP [dm6]	C	T	2.226e^-5	0.818	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_Med BDTNP1_TFBS_twi
3R	10360251	3R_10360251_SNP [dm3] 3R_14534529_SNP [dm6]	T	C	2.355e^-5	0.818	INTRON Pde6
3R	22312347	3R_22312347_SNP [dm3] 3R_26486625_SNP [dm6]	T	C	2.440e^-5	0.818	INTRON plum
2R	19881715	2R_19881715_SNP [dm3] 2R_23994192_SNP [dm6]	G	A	2.446e^-5	0.818	INTRON CG3860
3L	9900731	3L_9900731_SNP [dm3] 3L_9907631_SNP [dm6]	A	G	2.481e^-5	0.818	UPSTREAM CG34356 INTERGENIC
X	16289076	X_16289076_SNP [dm3] X_16395043_SNP [dm6]	G	A	2.494e^-5	0.818	SYNONYMOUS_CODING mei-41
X	5877675	X_5877675_INS [dm3] X_5983642_INS [dm6]	T	TCTTGGTCTG	2.516e^-5	0.818	INTRON Grip
2L	6015395	2L_6015395_SNP [dm3] 2L_6015395_SNP [dm6]	C	A	2.534e^-5	0.818	INTRON H2.0
X	5877660	X_5877660_SNP [dm3] X_5983627_SNP [dm6]	C	A	2.614e^-5	0.818	INTRON Grip
X	5877684	X_5877684_SNP [dm3] X_5983651_SNP [dm6]	A	T	2.618e^-5	0.818	INTRON Grip
2L	7102226	2L_7102226_SNP [dm3] 2L_7102226_SNP [dm6]	T	C	2.624e^-5	0.818	INTRON Pvf3
2R	17462108	2R_17462108_SNP [dm3] 2R_21574603_SNP [dm6]	C	T	2.648e^-5	0.818	INTRON CG10440
2L	2247949	2L_2247949_DEL [dm3] 2L_2247949_DEL [dm6]	GC	G	2.690e^-5	0.818	DOWNSTREAM CR42859 INTERGENIC
3R	10650757	3R_10650757_SNP [dm3] 3R_14825035_SNP [dm6]	A	G	2.699e^-5	0.818	SPLICE_SITE_DONOR btsz INTRON btsz
3R	9153967	3R_9153967_SNP [dm3] 3R_13328245_SNP [dm6]	A	G	2.717e^-5	0.818	DOWNSTREAM PK2-R2 INTERGENIC
2R	18495783	2R_18495783_SNP [dm3] 2R_22608278_SNP [dm6]	A	T	2.739e^-5	0.818	UPSTREAM Vps20 DOWNSTREAM snoRNA:Psi28S-1175b & 3 others INTERGENIC	TF binding site BDTNP1_TFBS_dl
2R	18455202	2R_18455202_SNP [dm3] 2R_22567697_SNP [dm6]	C	T	2.750e^-5	0.818	INTRON dnr1
2R	14092184	2R_14092184_SNP [dm3] 2R_18204679_SNP [dm6]	A	C	2.856e^-5	0.831	INTERGENIC
3L	1145625	3L_1145625_SNP [dm3] 3L_1145625_SNP [dm6]	A	G	2.882e^-5	0.831	INTRON bab2
3L	16738356	3L_16738356_SNP [dm3] 3L_16745256_SNP [dm6]	G	A	3.123e^-5	0.849	INTERGENIC	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad mE1_TFBS_HSA
2R	7497535	2R_7497535_SNP [dm3] 2R_11610030_SNP [dm6]	C	A	3.142e^-5	0.849	INTRON tou	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	2866986	3L_2866986_SNP [dm3] 3L_2866986_SNP [dm6]	C	T	3.185e^-5	0.849	INTRON CG43444	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	10530682	3R_10530682_SNP [dm3] 3R_14704960_SNP [dm6]	G	A	3.200e^-5	0.849	INTRON kibra
2L	7127119	2L_7127119_SNP [dm3] 2L_7127119_SNP [dm6]	G	T	3.249e^-5	0.849	INTRON Pvf3
3R	18496052	3R_18496052_SNP [dm3] 3R_22670330_SNP [dm6]	C	T	3.422e^-5	0.849	INTRON CG45058
3R	10657083	3R_10657083_SNP [dm3] 3R_14831361_SNP [dm6]	G	T	3.426e^-5	0.849	INTRON btsz
2L	6310982	2L_6310982_SNP [dm3] 2L_6310982_SNP [dm6]	T	C	3.493e^-5	0.849	INTRON Ddr
3L	12103556	3L_12103556_SNP [dm3] 3L_12110456_SNP [dm6]	C	T	3.507e^-5	0.849	INTERGENIC
3R	14175470	3R_14175470_SNP [dm3] 3R_18349748_SNP [dm6]	C	T	3.590e^-5	0.849	INTRON CG15803
2L	2738238	2L_2738238_SNP [dm3] 2L_2738238_SNP [dm6]	G	C	3.592e^-5	0.849	SYNONYMOUS_CODING CG31689 DOWNSTREAM mir-4914	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	10652723	3R_10652723_SNP [dm3] 3R_14827001_SNP [dm6]	G	A	3.648e^-5	0.849	SYNONYMOUS_CODING btsz UTR_5_PRIME btsz	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	13116080	3L_13116080_SNP [dm3] 3L_13122980_SNP [dm6]	A	T	3.649e^-5	0.849	INTERGENIC
3L	20995071	3L_20995071_DEL [dm3] 3L_21001971_DEL [dm6]	GACTTGGGG	G	3.669e^-5	0.849	INTRON skd	TF binding site mE1_TFBS_cad
X	5877665	X_5877665_SNP [dm3] X_5983632_SNP [dm6]	C	A	3.697e^-5	0.849	INTRON Grip
2R	12464260	2R_12464260_SNP [dm3] 2R_16576755_SNP [dm6]	A	T	3.701e^-5	0.849	UPSTREAM CG8317 INTERGENIC
3R	23253202	3R_23253202_SNP [dm3] 3R_27427480_SNP [dm6]	C	T	3.739e^-5	0.849	INTRON side
2L	3271697	2L_3271697_SNP [dm3] 2L_3271697_SNP [dm6]	A	T	3.773e^-5	0.849	UTR_3_PRIME CG3347
2R	18455229	2R_18455229_SNP [dm3] 2R_22567724_SNP [dm6]	C	A	3.805e^-5	0.849	INTRON dnr1
2R	15268200	2R_15268200_SNP [dm3] 2R_19380695_SNP [dm6]	C	A	3.998e^-5	0.852	UPSTREAM CG10073 DOWNSTREAM CG10062 INTRON CG10073
3R	13166212	3R_13166212_SNP [dm3] 3R_17340490_SNP [dm6]	C	G	4.168e^-5	0.852	INTRON beat-IIa
2R	15322942	2R_15322942_SNP [dm3] 2R_19435437_SNP [dm6]	C	G	4.172e^-5	0.852	SYNONYMOUS_CODING Fak
2R	7504304	2R_7504304_SNP [dm3] 2R_11616799_SNP [dm6]	C	G	4.218e^-5	0.852	UPSTREAM tou DOWNSTREAM Egm & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sbb mE1_TFBS_Trl
3L	1085457	3L_1085457_SNP [dm3] 3L_1085457_SNP [dm6]	C	G	4.231e^-5	0.852	INTRON bab1	regulatory region REDfly_CRMs TF binding site mE1_TFBS_cad
3L	14556127	3L_14556127_SNP [dm3] 3L_14563027_SNP [dm6]	G	T	4.336e^-5	0.852	DOWNSTREAM CG34039 INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_ttk mE1_TFBS_zfh1
2R	11519565	2R_11519565_SNP [dm3] 2R_15632060_SNP [dm6]	T	C	4.340e^-5	0.852	INTRON CG42524
2R	12125675	2R_12125675_SNP [dm3] 2R_16238170_SNP [dm6]	A	T	4.357e^-5	0.852	UTR_3_PRIME krimp DOWNSTREAM CG3687
2L	2325690	2L_2325690_SNP [dm3] 2L_2325690_SNP [dm6]	G	C	4.403e^-5	0.852	INTRON CG9967 & 1 other
3R	25953305	3R_25953305_SNP [dm3] 3R_30127583_SNP [dm6]	A	G	4.472e^-5	0.852	SYNONYMOUS_CODING Ppi1	TF binding site mE1_TFBS_chinmo
3R	13181560	3R_13181560_SNP [dm3] 3R_17355838_SNP [dm6]	A	T	4.473e^-5	0.852	INTRON beat-IIa	TF binding site mE1_TFBS_inv
2R	3012222	2R_3012222_SNP [dm3] 2R_7124717_SNP [dm6]	G	A	4.490e^-5	0.852	INTRON esn	TF binding site mE1_TFBS_chinmo
3L	1139879	3L_1139879_SNP [dm3] 3L_1139879_SNP [dm6]	C	G	4.543e^-5	0.852	DOWNSTREAM bab2 INTERGENIC	TF binding site mE1_TFBS_HSA
X	21892908	X_21892908_SNP [dm3] X_22491072_SNP [dm6]	C	G	4.586e^-5	0.852	UPSTREAM l_1_G0196 & 1 other INTRON l_1_G0196
2L	3326514	2L_3326514_SNP [dm3] 2L_3326514_SNP [dm6]	C	T	4.642e^-5	0.852	SYNONYMOUS_CODING CG33281
2R	5297312	2R_5297312_SNP [dm3] 2R_9409807_SNP [dm6]	T	C	4.646e^-5	0.852	UPSTREAM wun INTRON wun	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl

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By genomic position
Variant impact
Gene name

mn_Weight_PooledDiet phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results