DGRPool

GWAS results were computed on dm3 genome.

If you want to make an independent analysis with DGRP2 or PLINK2, you can find here prepared input files for this phenotype: DGRP2 results PLINK2 results

Full results

Phenotype distribution and association to known covariates

Shapiro-Wilk test of normality (p-value=4.609e^-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_2L_t	0.05179
In_3R_P	0.09293

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_3R_P	4.8028	0.0906

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2013 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	23494766	3R_23494766_SNP [dm3] 3R_27669044_SNP [dm6]	G	A	1.950e^-7	0.291	SYNONYMOUS_CODING unc80	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	26729549	3R_26729549_SNP [dm3] 3R_30903827_SNP [dm6]	G	A	4.407e^-7	0.291	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_chinmo mE1_TFBS_HSA
2L	6968839	2L_6968839_SNP [dm3] 2L_6968839_SNP [dm6]	G	A	5.681e^-7	0.291	UTR_3_PRIME snRNP-U1-70K DOWNSTREAM snRNP-U1-70K	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med
X	21902872	X_21902872_SNP [dm3] X_22501036_SNP [dm6]	T	A	7.131e^-7	0.291	NON_SYNONYMOUS_CODING l_1_G0196 INTRON l_1_G0196
3R	26723629	3R_26723629_SNP [dm3] 3R_30897907_SNP [dm6]	C	G	1.186e^-6	0.291	NON_SYNONYMOUS_CODING Cyp4c3
3L	19524744	3L_19524744_SNP [dm3] 3L_19531644_SNP [dm6]	A	T	1.208e^-6	0.291	INTERGENIC
2L	6965613	2L_6965613_SNP [dm3] 2L_6965613_SNP [dm6]	G	A	1.344e^-6	0.291	SYNONYMOUS_CODING Coprox	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
2L	6969567	2L_6969567_SNP [dm3] 2L_6969567_SNP [dm6]	C	A	1.380e^-6	0.291	UTR_3_PRIME snRNP-U1-70K DOWNSTREAM snRNP-U1-70K	TF binding site mE1_TFBS_sens
2L	6968350	2L_6968350_SNP [dm3] 2L_6968350_SNP [dm6]	G	A	1.395e^-6	0.291	UPSTREAM smt3 DOWNSTREAM snRNP-U1-70K INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_z mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_Ubx
3L	19524747	3L_19524747_SNP [dm3] 3L_19531647_SNP [dm6]	G	A	1.687e^-6	0.316	INTERGENIC
3R	26713324	3R_26713324_SNP [dm3] 3R_30887602_SNP [dm6]	T	A	1.872e^-6	0.319	INTRON Sap-r
3R	26713310	3R_26713310_SNP [dm3] 3R_30887588_SNP [dm6]	A	C	2.944e^-6	0.431	INTRON Sap-r
3R	23494660	3R_23494660_SNP [dm3] 3R_27668938_SNP [dm6]	C	T	2.984e^-6	0.431	INTRON unc80	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	22764850	3R_22764850_SNP [dm3] 3R_26939128_SNP [dm6]	T	G	3.358e^-6	0.45	SYNONYMOUS_CODING sda
2L	7453397	2L_7453397_SNP [dm3] 2L_7453397_SNP [dm6]	G	T	4.061e^-6	0.508	INTRON Gr28a
3R	25802116	3R_25802116_SNP [dm3] 3R_29976394_SNP [dm6]	A	C	5.421e^-6	0.621	INTERGENIC
X	9126675	X_9126675_SNP [dm3] X_9232642_SNP [dm6]	G	T	5.624e^-6	0.621	UPSTREAM CG12121 DOWNSTREAM Ir8a INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_h mE1_TFBS_HSA
3L	16550272	3L_16550272_SNP [dm3] 3L_16557172_SNP [dm6]	C	A	6.515e^-6	0.63	SYNONYMOUS_CODING CG4229	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
X	17658807	X_17658807_SNP [dm3] X_17764774_SNP [dm6]	C	G	6.635e^-6	0.63	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	21126037	3R_21126037_SNP [dm3] 3R_25300315_SNP [dm6]	G	T	6.717e^-6	0.63	UPSTREAM CG31288 & 1 other INTERGENIC
2L	7495110	2L_7495110_SNP [dm3] 2L_7495110_SNP [dm6]	A	C	8.084e^-6	0.71	INTRON Ziz	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
2L	6965902	2L_6965902_SNP [dm3] 2L_6965902_SNP [dm6]	A	T	8.329e^-6	0.71	DOWNSTREAM smt3 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi
2R	11113469	2R_11113469_SNP [dm3] 2R_15225964_SNP [dm6]	G	T	8.784e^-6	0.712	UPSTREAM CR44370 INTRON Fs	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	16606089	3L_16606089_SNP [dm3] 3L_16612989_SNP [dm6]	G	A	9.433e^-6	0.712	UPSTREAM Su_P_ DOWNSTREAM Mo25 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med mE1_TFBS_HSA
2R	16383975	2R_16383975_SNP [dm3] 2R_20496470_SNP [dm6]	A	G	9.494e^-6	0.712	INTERGENIC
3L	683252	3L_683252_SNP [dm3] 3L_683252_SNP [dm6]	G	T	1.075e^-5	0.759	SYNONYMOUS_CODING ebd1 UPSTREAM CG3386	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2L	6965897	2L_6965897_SNP [dm3] 2L_6965897_SNP [dm6]	G	A	1.114e^-5	0.759	DOWNSTREAM smt3 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi
2L	22137183	2L_22137183_SNP [dm3] 2L_22137183_SNP [dm6]	G	A	1.198e^-5	0.759	INTRON CG42748
X	3731271	X_3731271_SNP [dm3] X_3837238_SNP [dm6]	T	C	1.287e^-5	0.759	INTRON ec	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
2L	6959202	2L_6959202_SNP [dm3] 2L_6959202_SNP [dm6]	A	G	1.304e^-5	0.759	NON_SYNONYMOUS_CODING Atac1 DOWNSTREAM CG3430
2L	8989513	2L_8989513_SNP [dm3] 2L_8989513_SNP [dm6]	G	C	1.340e^-5	0.759	UTR_5_PRIME rost UPSTREAM rost
X	9126690	X_9126690_SNP [dm3] X_9232657_SNP [dm6]	A	G	1.392e^-5	0.759	UPSTREAM CG12121 DOWNSTREAM Ir8a INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_h mE1_TFBS_HSA
2R	17321947	2R_17321947_SNP [dm3] 2R_21434442_SNP [dm6]	T	G	1.402e^-5	0.759	INTRON Sdc
3L	16605774	3L_16605774_SNP [dm3] 3L_16612674_SNP [dm6]	G	T	1.402e^-5	0.759	SYNONYMOUS_CODING CG4101 UPSTREAM Su_P_ DOWNSTREAM Mo25	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med
3L	18781527	3L_18781527_SNP [dm3] 3L_18788427_SNP [dm6]	C	T	1.416e^-5	0.759	INTRON ftz-f1	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3L	13385094	3L_13385094_SNP [dm3] 3L_13391994_SNP [dm6]	C	G	1.474e^-5	0.763	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
X	9127299	X_9127299_SNP [dm3] X_9233266_SNP [dm6]	G	A	1.529e^-5	0.763	SYNONYMOUS_CODING Ir8a UPSTREAM CG12121	TF binding site BDTNP1_TFBS_sna mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3L	13360917	3L_13360917_DEL [dm3] 3L_13367817_DEL [dm6]	CC	C	1.593e^-5	0.763	INTERGENIC
3R	23799951	3R_23799951_SNP [dm3] 3R_27974229_SNP [dm6]	C	G	1.617e^-5	0.763	SYNONYMOUS_CODING betaTub97EF	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2L	7453394	2L_7453394_SNP [dm3] 2L_7453394_SNP [dm6]	C	A	1.628e^-5	0.763	INTRON Gr28a
3R	20979552	3R_20979552_SNP [dm3] 3R_25153830_SNP [dm6]	T	C	1.694e^-5	0.764	INTERGENIC
2L	7453392	2L_7453392_SNP [dm3] 2L_7453392_SNP [dm6]	T	C	1.747e^-5	0.764	INTRON Gr28a
3L	13359024	3L_13359024_SNP [dm3] 3L_13365924_SNP [dm6]	A	T	1.780e^-5	0.764	INTERGENIC
2L	5365754	2L_5365754_SNP [dm3] 2L_5365754_SNP [dm6]	A	C	1.791e^-5	0.764	UTR_3_PRIME nompC DOWNSTREAM nompC	TF binding site mE1_TFBS_bab1
2R	5663854	2R_5663854_DEL [dm3] 2R_9776349_DEL [dm6]	ATAATAATTTTCTA...	A	1.900e^-5	0.792	INTRON CG1688 EXON CR44207
2L	8702856	2L_8702856_SNP [dm3] 2L_8702856_SNP [dm6]	A	T	2.025e^-5	0.806	UPSTREAM CR44992 INTRON Hnf4
2L	22092301	2L_22092301_SNP [dm3] 2L_22092301_SNP [dm6]	G	C	2.033e^-5	0.806	INTERGENIC	transposable element FlyBase
3L	17274270	3L_17274270_SNP [dm3] 3L_17281170_SNP [dm6]	G	C	2.130e^-5	0.806	INTERGENIC
2R	6993126	2R_6993126_SNP [dm3] 2R_11105621_SNP [dm6]	G	C	2.180e^-5	0.806	INTRON luna	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
3L	13387357	3L_13387357_SNP [dm3] 3L_13394257_SNP [dm6]	C	T	2.186e^-5	0.806	INTERGENIC	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
3R	26713514	3R_26713514_SNP [dm3] 3R_30887792_SNP [dm6]	C	T	2.213e^-5	0.806	INTRON Sap-r
X	12166782	X_12166782_SNP [dm3] X_12272749_SNP [dm6]	G	A	2.235e^-5	0.806	INTRON Ten-a
X	9126966	X_9126966_SNP [dm3] X_9232933_SNP [dm6]	C	T	2.294e^-5	0.809	SYNONYMOUS_CODING Ir8a UPSTREAM CG12121	TF binding site BDTNP1_TFBS_twi mE1_TFBS_chinmo mE1_TFBS_sens
2L	6966102	2L_6966102_SNP [dm3] 2L_6966102_SNP [dm6]	A	T	2.367e^-5	0.809	DOWNSTREAM smt3 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi
2L	18224937	2L_18224937_SNP [dm3] 2L_18224937_SNP [dm6]	A	G	2.608e^-5	0.809	INTRON CG42750
2L	20865778	2L_20865778_SNP [dm3] 2L_20865778_SNP [dm6]	T	G	2.667e^-5	0.809	INTRON CG9338	TF binding site BDTNP1_TFBS_z mE1_TFBS_HSA
3R	11014100	3R_11014100_SNP [dm3] 3R_15188378_SNP [dm6]	A	T	2.758e^-5	0.809	NON_SYNONYMOUS_CODING Gyc88E	TF binding site mE1_TFBS_cad
3R	19964611	3R_19964611_SNP [dm3] 3R_24138889_SNP [dm6]	C	A	2.766e^-5	0.809	INTRON Npc2f	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	18149195	3L_18149195_SNP [dm3] 3L_18156095_SNP [dm6]	C	T	2.815e^-5	0.809	NON_SYNONYMOUS_CODING CG13699
3L	22540042	3L_22540042_SNP [dm3] 3L_22546942_SNP [dm6]	T	A	2.865e^-5	0.809	INTERGENIC
2L	7089169	2L_7089169_SNP [dm3] 2L_7089169_SNP [dm6]	T	C	2.868e^-5	0.809	INTERGENIC
3R	17941991	3R_17941991_SNP [dm3] 3R_22116269_SNP [dm6]	A	G	2.873e^-5	0.809	SYNONYMOUS_CODING Ir94b
2L	13430803	2L_13430803_SNP [dm3] 2L_13430803_SNP [dm6]	G	A	2.876e^-5	0.809	INTRON CG42784
3L	17405348	3L_17405348_SNP [dm3] 3L_17412248_SNP [dm6]	G	A	2.883e^-5	0.809	INTRON blot	TF binding site BDTNP1_TFBS_Med
3L	12157902	3L_12157902_SNP [dm3] 3L_12164802_SNP [dm6]	T	A	2.903e^-5	0.809	UTR_3_PRIME Rh7
3R	23154476	3R_23154476_SNP [dm3] 3R_27328754_SNP [dm6]	T	G	2.981e^-5	0.809	DOWNSTREAM CG3330 INTERGENIC
3R	10534838	3R_10534838_SNP [dm3] 3R_14709116_SNP [dm6]	G	T	2.997e^-5	0.809	INTRON kibra
3L	12817198	3L_12817198_SNP [dm3] 3L_12824098_SNP [dm6]	C	G	3.024e^-5	0.809	SYNONYMOUS_CODING CG42588 DOWNSTREAM CG10960
X	3011817	X_3011817_SNP [dm3] X_3117784_SNP [dm6]	G	T	3.060e^-5	0.809	INTRON kirre	TF binding site BDTNP1_TFBS_dl
2L	6956061	2L_6956061_SNP [dm3] 2L_6956061_SNP [dm6]	T	C	3.060e^-5	0.809	SYNONYMOUS_CODING CG13775 UPSTREAM CG3430	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	8533998	2R_8533998_SNP [dm3] 2R_12646493_SNP [dm6]	C	G	3.063e^-5	0.809	INTRON CG8785
2L	7089170	2L_7089170_SNP [dm3] 2L_7089170_SNP [dm6]	T	C	3.143e^-5	0.809	INTERGENIC
3L	9457888	3L_9457888_SNP [dm3] 3L_9464788_SNP [dm6]	T	C	3.150e^-5	0.809	INTRON CG44838	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	13365634	3L_13365634_SNP [dm3] 3L_13372534_SNP [dm6]	A	T	3.266e^-5	0.822	INTERGENIC
2L	6964591	2L_6964591_SNP [dm3] 2L_6964591_SNP [dm6]	C	G	3.287e^-5	0.822	NON_SYNONYMOUS_CODING Coprox UPSTREAM sip2	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3R	26726999	3R_26726999_SNP [dm3] 3R_30901277_SNP [dm6]	C	A	3.446e^-5	0.84	NON_SYNONYMOUS_CODING CG33483 DOWNSTREAM Cyp4c3
X	6219096	X_6219096_SNP [dm3] X_6325063_SNP [dm6]	T	G	3.490e^-5	0.84	NON_SYNONYMOUS_CODING CG15894	TF binding site BDTNP1_TFBS_sna mE1_TFBS_chinmo mE1_TFBS_HSA
3R	26720416	3R_26720416_SNP [dm3] 3R_30894694_SNP [dm6]	G	A	3.493e^-5	0.84	INTRON Cyp4c3	TF binding site mE1_TFBS_HSA
3R	21275170	3R_21275170_SNP [dm3] 3R_25449448_SNP [dm6]	A	G	3.688e^-5	0.862	INTRON Fur1	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	11113468	2R_11113468_SNP [dm3] 2R_15225963_SNP [dm6]	G	C	3.745e^-5	0.862	UPSTREAM CR44370 INTRON Fs	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	7088623	2L_7088623_SNP [dm3] 2L_7088623_SNP [dm6]	T	A	3.759e^-5	0.862	INTERGENIC
3L	14052556	3L_14052556_SNP [dm3] 3L_14059456_SNP [dm6]	A	G	3.896e^-5	0.862	INTRON CG32138
3R	5768800	3R_5768800_SNP [dm3] 3R_9943078_SNP [dm6]	T	G	3.936e^-5	0.862	INTRON Glut4EF
3L	17405321	3L_17405321_SNP [dm3] 3L_17412221_SNP [dm6]	A	T	3.974e^-5	0.862	INTRON blot	TF binding site BDTNP1_TFBS_Med
X	12088603	X_12088603_SNP [dm3] X_12194570_SNP [dm6]	G	A	3.975e^-5	0.862	INTRON Ten-a
2L	7498096	2L_7498096_SNP [dm3] 2L_7498096_SNP [dm6]	A	T	3.993e^-5	0.862	UTR_3_PRIME RapGAP1 UPSTREAM Obp28a
3R	5120235	3R_5120235_SNP [dm3] 3R_9294513_SNP [dm6]	G	T	3.998e^-5	0.862	UTR_3_PRIME CG8861 DOWNSTREAM CG8861
2L	18222855	2L_18222855_SNP [dm3] 2L_18222855_SNP [dm6]	G	C	4.117e^-5	0.877	INTRON CG42750
2L	14278150	2L_14278150_SNP [dm3] 2L_14278150_SNP [dm6]	A	T	4.196e^-5	0.884	DOWNSTREAM CG32971 INTRON wb
2L	7454579	2L_7454579_SNP [dm3] 2L_7454579_SNP [dm6]	G	A	4.253e^-5	0.886	UPSTREAM Gr28a DOWNSTREAM Gr28b INTERGENIC
2L	3261061	2L_3261061_SNP [dm3] 2L_3261061_SNP [dm6]	A	T	4.497e^-5	0.906	DOWNSTREAM CR45338 EXON CR45337
3L	16617880	3L_16617880_SNP [dm3] 3L_16624780_SNP [dm6]	C	T	4.530e^-5	0.906	NON_SYNONYMOUS_CODING Abl	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	6958617	2L_6958617_SNP [dm3] 2L_6958617_SNP [dm6]	C	A	4.671e^-5	0.906	DOWNSTREAM Atac1 INTRON CG3430
2L	6964815	2L_6964815_SNP [dm3] 2L_6964815_SNP [dm6]	G	A	4.849e^-5	0.906	SYNONYMOUS_CODING Coprox UPSTREAM sip2	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2L	18220472	2L_18220472_SNP [dm3] 2L_18220472_SNP [dm6]	C	T	5.175e^-5	0.906	INTRON CG42750
X	11238477	X_11238477_SNP [dm3] X_11344444_SNP [dm6]	A	C	5.212e^-5	0.906	UTR_3_PRIME CG34348 DOWNSTREAM CG1597
3R	23003416	3R_23003416_DEL [dm3] 3R_27177694_DEL [dm6]	ATA	A	5.214e^-5	0.906	INTRON Ser	TF binding site mE1_TFBS_cad
3R	23003431	3R_23003431_SNP [dm3] 3R_27177709_SNP [dm6]	T	G	5.214e^-5	0.906	INTRON Ser	TF binding site mE1_TFBS_cad
3R	23003428	3R_23003428_SNP [dm3] 3R_27177706_SNP [dm6]	A	C	5.231e^-5	0.906	INTRON Ser	TF binding site mE1_TFBS_cad
2R	17243079	2R_17243079_SNP [dm3] 2R_21355574_SNP [dm6]	T	C	5.323e^-5	0.906	UTR_3_PRIME cv-2

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posteriorLength phenotype

Phenotype distribution and association to known covariates

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GWAS results