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=3.062e^-12)
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
No significant result.

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	5.6771	0.0585

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2201 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
2L	12455303	2L_12455303_SNP [dm3] 2L_12455303_SNP [dm6]	A	T	1.887e^-7	0.306	DOWNSTREAM bun & 1 other INTERGENIC
2L	12454739	2L_12454739_SNP [dm3] 2L_12454739_SNP [dm6]	A	C	5.008e^-7	0.306	DOWNSTREAM bun EXON CR17024	TF binding site mE1_TFBS_sens
2L	12455321	2L_12455321_SNP [dm3] 2L_12455321_SNP [dm6]	A	C	7.486e^-7	0.306	DOWNSTREAM bun & 1 other INTERGENIC
2L	12454543	2L_12454543_SNP [dm3] 2L_12454543_SNP [dm6]	A	C	8.812e^-7	0.306	DOWNSTREAM bun EXON CR17024	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	12454619	2L_12454619_SNP [dm3] 2L_12454619_SNP [dm6]	C	G	1.082e^-6	0.306	DOWNSTREAM bun EXON CR17024	TF binding site mE1_TFBS_sens
2L	12454666	2L_12454666_SNP [dm3] 2L_12454666_SNP [dm6]	C	T	1.118e^-6	0.306	DOWNSTREAM bun EXON CR17024	TF binding site mE1_TFBS_sens
2L	12454835	2L_12454835_SNP [dm3] 2L_12454835_SNP [dm6]	T	C	1.143e^-6	0.306	DOWNSTREAM bun EXON CR17024	TF binding site mE1_TFBS_sens
2L	12454840	2L_12454840_SNP [dm3] 2L_12454840_SNP [dm6]	A	C	1.434e^-6	0.336	DOWNSTREAM bun EXON CR17024	TF binding site mE1_TFBS_sens
2L	8032221	2L_8032221_SNP [dm3] 2L_8032221_SNP [dm6]	T	C	1.614e^-6	0.336	UTR_5_PRIME Cka INTRON CG7367	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd mE1_TFBS_Trl
X	21946828	X_21946828_SNP [dm3] X_22544992_SNP [dm6]	A	G	2.677e^-6	0.502	UPSTREAM CG17599 INTERGENIC
2L	12455323	2L_12455323_SNP [dm3] 2L_12455323_SNP [dm6]	C	G	3.351e^-6	0.571	DOWNSTREAM bun & 1 other INTERGENIC
2R	9469833	2R_9469833_SNP [dm3] 2R_13582328_SNP [dm6]	C	T	4.034e^-6	0.631	INTRON CG6191 & 1 other
2L	12458406	2L_12458406_SNP [dm3] 2L_12458406_SNP [dm6]	C	T	4.506e^-6	0.65	INTRON bun	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
2R	6638139	2R_6638139_SNP [dm3] 2R_10750634_SNP [dm6]	C	T	5.136e^-6	0.665	INTRON CG33144
2L	12454527	2L_12454527_SNP [dm3] 2L_12454527_SNP [dm6]	A	G	5.436e^-6	0.665	EXON CR17024	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	13839935	2R_13839935_INS [dm3] 2R_17952430_INS [dm6]	G	GG	5.972e^-6	0.665	INTERGENIC
X	18400989	X_18400989_SNP [dm3] X_18506956_SNP [dm6]	G	C	6.025e^-6	0.665	INTRON Ggt-1	TF binding site BDTNP1_TFBS_dl mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl mE1_TFBS_ttk
2R	11690786	2R_11690786_SNP [dm3] 2R_15803281_SNP [dm6]	C	T	7.666e^-6	0.756	INTRON Zasp52 & 1 other
2L	12455312	2L_12455312_SNP [dm3] 2L_12455312_SNP [dm6]	C	G	7.752e^-6	0.756	DOWNSTREAM bun & 1 other INTERGENIC
2L	12455846	2L_12455846_SNP [dm3] 2L_12455846_SNP [dm6]	G	T	8.246e^-6	0.756	UTR_3_PRIME bun DOWNSTREAM CR17024 & 1 other
X	21948257	X_21948257_SNP [dm3] X_22546421_SNP [dm6]	T	C	8.675e^-6	0.756	UPSTREAM CG17601 INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_kn
3R	9382844	3R_9382844_SNP [dm3] 3R_13557122_SNP [dm6]	C	T	9.000e^-6	0.756	INTERGENIC
2R	8913557	2R_8913557_SNP [dm3] 2R_13026052_SNP [dm6]	T	C	1.009e^-5	0.756	INTERGENIC
2L	3880311	2L_3880311_SNP [dm3] 2L_3880311_SNP [dm6]	G	A	1.022e^-5	0.756	UPSTREAM capu INTRON capu
2L	12320003	2L_12320003_INS [dm3] 2L_12320003_INS [dm6]	T	TT	1.091e^-5	0.756	INTERGENIC
3L	7852205	3L_7852205_SNP [dm3] 3L_7859105_SNP [dm6]	T	A	1.123e^-5	0.756	INTRON Pdp1
2L	12455318	2L_12455318_SNP [dm3] 2L_12455318_SNP [dm6]	G	A	1.127e^-5	0.756	DOWNSTREAM bun & 1 other INTERGENIC
2R	6896965	2R_6896965_SNP [dm3] 2R_11009460_SNP [dm6]	G	A	1.136e^-5	0.756	INTRON luna	TF binding site mE1_TFBS_inv
3L	953429	3L_953429_SNP [dm3] 3L_953429_SNP [dm6]	A	G	1.195e^-5	0.756	INTRON Glut1
3L	7852135	3L_7852135_SNP [dm3] 3L_7859035_SNP [dm6]	G	C	1.210e^-5	0.756	INTRON Pdp1
2R	6966549	2R_6966549_SNP [dm3] 2R_11079044_SNP [dm6]	G	T	1.369e^-5	0.77	INTRON luna	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
X	21948258	X_21948258_SNP [dm3] X_22546422_SNP [dm6]	G	A	1.373e^-5	0.77	UPSTREAM CG17601 INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_kn
2L	12454867	2L_12454867_SNP [dm3] 2L_12454867_SNP [dm6]	A	C	1.400e^-5	0.77	DOWNSTREAM bun EXON CR17024
3L	3349836	3L_3349836_SNP [dm3] 3L_3349836_SNP [dm6]	C	A	1.483e^-5	0.77	UPSTREAM kst INTRON kst	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	12320029	2L_12320029_SNP [dm3] 2L_12320029_SNP [dm6]	A	G	1.498e^-5	0.77	INTERGENIC
2L	10493336	2L_10493336_SNP [dm3] 2L_10493336_SNP [dm6]	G	T	1.515e^-5	0.77	NON_SYNONYMOUS_CODING Myo31DF	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3L	7852125	3L_7852125_SNP [dm3] 3L_7859025_SNP [dm6]	T	C	1.577e^-5	0.77	INTRON Pdp1
2R	6896964	2R_6896964_SNP [dm3] 2R_11009459_SNP [dm6]	G	T	1.590e^-5	0.77	INTRON luna	TF binding site mE1_TFBS_inv
2R	18027433	2R_18027433_SNP [dm3] 2R_22139928_SNP [dm6]	A	G	1.601e^-5	0.77	UPSTREAM gom DOWNSTREAM CG11269 INTRON a
3R	9499968	3R_9499968_SNP [dm3] 3R_13674246_SNP [dm6]	C	T	1.676e^-5	0.773	UTR_5_PRIME Task6 DOWNSTREAM CG9588	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Trl
3L	10487644	3L_10487644_SNP [dm3] 3L_10494544_SNP [dm6]	G	A	1.711e^-5	0.773	INTRON A2bp1
X	14742959	X_14742959_SNP [dm3] X_14848926_SNP [dm6]	G	C	1.730e^-5	0.773	UPSTREAM CG9522 INTRON Flo2
2L	10726045	2L_10726045_SNP [dm3] 2L_10726045_SNP [dm6]	G	A	1.926e^-5	0.84	UTR_5_PRIME CG6431 INTRON CG6431
X	3546696	X_3546696_SNP [dm3] X_3652663_SNP [dm6]	A	C	2.020e^-5	0.84	INTRON AstA-R1
X	8275218	X_8275218_SNP [dm3] X_8381185_SNP [dm6]	G	A	2.032e^-5	0.84	INTERGENIC
X	8275181	X_8275181_SNP [dm3] X_8381148_SNP [dm6]	G	C	2.123e^-5	0.84	INTERGENIC
2L	10824324	2L_10824324_SNP [dm3] 2L_10824324_SNP [dm6]	G	A	2.129e^-5	0.84	INTRON Nos
2L	9829979	2L_9829979_SNP [dm3] 2L_9829979_SNP [dm6]	T	C	2.165e^-5	0.84	INTRON nAChRalpha6	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2L	12454517	2L_12454517_SNP [dm3] 2L_12454517_SNP [dm6]	A	C	2.199e^-5	0.84	EXON CR17024	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	5385071	2R_5385071_SNP [dm3] 2R_9497566_SNP [dm6]	G	A	2.411e^-5	0.84	INTRON Wnt2	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2L	9598676	2L_9598676_SNP [dm3] 2L_9598676_SNP [dm6]	G	T	2.535e^-5	0.84	DOWNSTREAM CG4382 INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi
2R	11690808	2R_11690808_SNP [dm3] 2R_15803303_SNP [dm6]	G	T	2.576e^-5	0.84	INTRON Zasp52 & 1 other
2R	5385103	2R_5385103_SNP [dm3] 2R_9497598_SNP [dm6]	G	A	2.688e^-5	0.84	INTRON Wnt2	TF binding site mE1_TFBS_chinmo
3L	19601788	3L_19601788_DEL [dm3] 3L_19608688_DEL [dm6]	TTATA	GG	2.715e^-5	0.84	DOWNSTREAM CG9372 INTRON Lon
3R	23415814	3R_23415814_SNP [dm3] 3R_27590092_SNP [dm6]	C	G	2.737e^-5	0.84	SYNONYMOUS_CODING CG5639	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
X	4750618	X_4750618_SNP [dm3] X_4856585_SNP [dm6]	A	T	2.777e^-5	0.84	INTRON CG42594
3L	7280098	3L_7280098_DEL [dm3] 3L_7286998_DEL [dm6]	TTT	T	2.819e^-5	0.84	INTRON unc-13-4A
X	21948261	X_21948261_SNP [dm3] X_22546425_SNP [dm6]	A	C	2.849e^-5	0.84	UPSTREAM CG17601 INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_kn
2R	18027440	2R_18027440_SNP [dm3] 2R_22139935_SNP [dm6]	A	G	2.948e^-5	0.84	UTR_5_PRIME gom DOWNSTREAM CG11269 INTRON a
3R	6046672	3R_6046672_SNP [dm3] 3R_10220950_SNP [dm6]	T	C	2.978e^-5	0.84	UTR_3_PRIME Syn
X	21946848	X_21946848_SNP [dm3] X_22545012_SNP [dm6]	G	A	2.988e^-5	0.84	UPSTREAM CG17599 INTERGENIC
3L	7280104	3L_7280104_SNP [dm3] 3L_7287004_SNP [dm6]	T	A	2.994e^-5	0.84	INTRON unc-13-4A
X	14080134	X_14080134_SNP [dm3] X_14186101_SNP [dm6]	T	A	3.151e^-5	0.84	DOWNSTREAM CG32603 INTERGENIC
3L	1514278	3L_1514278_SNP [dm3] 3L_1514278_SNP [dm6]	C	T	3.164e^-5	0.84	INTRON Psa & 1 other	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
X	16159557	X_16159557_SNP [dm3] X_16265524_SNP [dm6]	G	A	3.175e^-5	0.84	SYNONYMOUS_CODING CG12507
X	6726368	X_6726368_SNP [dm3] X_6832335_SNP [dm6]	T	G	3.191e^-5	0.84	SYNONYMOUS_CODING CG12796 INTRON nonC	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
X	21948260	X_21948260_SNP [dm3] X_22546424_SNP [dm6]	A	T	3.279e^-5	0.84	UPSTREAM CG17601 INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_kn
2R	13693381	2R_13693381_SNP [dm3] 2R_17805876_SNP [dm6]	A	C	3.309e^-5	0.84	INTRON grh	TF binding site BDTNP1_TFBS_dl mE1_TFBS_sbb
3R	5696291	3R_5696291_SNP [dm3] 3R_9870569_SNP [dm6]	T	A	3.340e^-5	0.84	INTERGENIC
2L	8767254	2L_8767254_SNP [dm3] 2L_8767254_SNP [dm6]	G	A	3.349e^-5	0.84	SYNONYMOUS_CODING CG9463
2R	11101445	2R_11101445_SNP [dm3] 2R_15213940_SNP [dm6]	A	G	3.404e^-5	0.84	UPSTREAM row DOWNSTREAM CG8093 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_Ubx
2R	11101448	2R_11101448_SNP [dm3] 2R_15213943_SNP [dm6]	C	G	3.404e^-5	0.84	UPSTREAM row DOWNSTREAM CG8093 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_Ubx
X	3547095	X_3547095_DEL [dm3] X_3653062_DEL [dm6]	TT	T	3.448e^-5	0.84	INTRON AstA-R1
2L	4546212	2L_4546212_SNP [dm3] 2L_4546212_SNP [dm6]	G	C	3.530e^-5	0.84	SYNONYMOUS_CODING dp INTRON dp	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	12456233	2L_12456233_SNP [dm3] 2L_12456233_SNP [dm6]	A	T	3.535e^-5	0.84	UTR_3_PRIME bun DOWNSTREAM bun
2L	7352016	2L_7352016_SNP [dm3] 2L_7352016_SNP [dm6]	A	G	3.552e^-5	0.84	SYNONYMOUS_CODING Wnt6	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_HSA
X	15489962	X_15489962_SNP [dm3] X_15595929_SNP [dm6]	A	C	3.628e^-5	0.84	INTERGENIC
3L	5588040	3L_5588040_SNP [dm3] 3L_5594940_SNP [dm6]	T	G	3.711e^-5	0.84	UPSTREAM CG5150 INTRON CG10592	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
2L	18751046	2L_18751046_SNP [dm3] 2L_18751046_SNP [dm6]	T	A	3.729e^-5	0.84	INTERGENIC
2R	13250795	2R_13250795_SNP [dm3] 2R_17363290_SNP [dm6]	T	G	3.832e^-5	0.84	NON_SYNONYMOUS_CODING mbl INTRON mbl	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2R	10704004	2R_10704004_SNP [dm3] 2R_14816499_SNP [dm6]	T	A	3.851e^-5	0.84	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA
2L	6102446	2L_6102446_SNP [dm3] 2L_6102446_SNP [dm6]	T	A	3.858e^-5	0.84	INTRON stai
2L	4811238	2L_4811238_SNP [dm3] 2L_4811238_SNP [dm6]	T	C	3.859e^-5	0.84	DOWNSTREAM CR45297 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_en mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_Trl mE1_TFBS_Ubx mE1_TFBS_zfh1
3L	499820	3L_499820_SNP [dm3] 3L_499820_SNP [dm6]	G	T	3.872e^-5	0.84	DOWNSTREAM CG34267 INTRON klar
3L	490692	3L_490692_SNP [dm3] 3L_490692_SNP [dm6]	G	A	3.873e^-5	0.84	UTR_5_PRIME klar INTRON klar	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_jumu mE1_TFBS_Trl
2L	6230080	2L_6230080_SNP [dm3] 2L_6230080_SNP [dm6]	T	A	3.902e^-5	0.84	INTERGENIC	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
2L	16333418	2L_16333418_SNP [dm3] 2L_16333418_SNP [dm6]	T	C	3.969e^-5	0.84	NON_SYNONYMOUS_CODING CG31817	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	7635058	3R_7635058_SNP [dm3] 3R_11809336_SNP [dm6]	T	A	4.018e^-5	0.84	INTRON ClC-a	TF binding site mE1_TFBS_cad
X	16543776	X_16543776_INS [dm3] X_16649743_INS [dm6]	A	ACACCCATA	4.129e^-5	0.84	UTR_3_PRIME mthl1 DOWNSTREAM mthl1
3L	2052667	3L_2052667_SNP [dm3] 3L_2052667_SNP [dm6]	T	A	4.164e^-5	0.84	NON_SYNONYMOUS_CODING sls INTRON sls	TF binding site mE1_TFBS_sens
2R	8925229	2R_8925229_SNP [dm3] 2R_13037724_SNP [dm6]	T	C	4.174e^-5	0.84	INTERGENIC
2L	5974817	2L_5974817_SNP [dm3] 2L_5974817_SNP [dm6]	G	C	4.216e^-5	0.84	INTRON chic
2R	9787599	2R_9787599_SNP [dm3] 2R_13900094_SNP [dm6]	T	C	4.266e^-5	0.84	INTRON shot
2L	9413990	2L_9413990_SNP [dm3] 2L_9413990_SNP [dm6]	G	T	4.418e^-5	0.84	INTRON Shawl
3L	3314946	3L_3314946_SNP [dm3] 3L_3314946_SNP [dm6]	T	C	4.438e^-5	0.84	UPSTREAM Drsl3 & 1 other DOWNSTREAM ZnT63C & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	3604252	2L_3604252_SNP [dm3] 2L_3604252_SNP [dm6]	C	A	4.481e^-5	0.84	UTR_3_PRIME odd	TF binding site BDTNP1_TFBS_da
2L	6005978	2L_6005978_SNP [dm3] 2L_6005978_SNP [dm6]	A	G	4.575e^-5	0.84	SYNONYMOUS_CODING Gal EXON CR43866
3L	12316365	3L_12316365_DEL [dm3] 3L_12323265_DEL [dm6]	TG	T	4.610e^-5	0.84	INTERGENIC
2L	10847969	2L_10847969_SNP [dm3] 2L_10847969_SNP [dm6]	A	G	4.613e^-5	0.84	SYNONYMOUS_CODING porin UPSTREAM Porin2
X	16543809	X_16543809_SNP [dm3] X_16649776_SNP [dm6]	T	C	4.825e^-5	0.84	UTR_3_PRIME mthl1 DOWNSTREAM mthl1

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By genomic position
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Nuclear_Breadth_Cov phenotype

Phenotype distribution and association to known covariates

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GWAS results