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=2.166e^-4)
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_P	0.05521

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1499 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	15742241	2R_15742241_SNP [dm3] 2R_19854736_SNP [dm6]	G	A	5.688e^-7	0.809	INTERGENIC	TF binding site BDTNP1_TFBS_da
2L	14190966	2L_14190966_SNP [dm3] 2L_14190966_SNP [dm6]	A	G	2.276e^-6	0.809	INTRON Dyrk2
2R	12011490	2R_12011490_SNP [dm3] 2R_16123985_SNP [dm6]	C	T	3.229e^-6	0.809	UPSTREAM spin INTRON CG30095	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_disco mE1_TFBS_Ubx
2R	15742229	2R_15742229_SNP [dm3] 2R_19854724_SNP [dm6]	G	A	3.648e^-6	0.809	INTERGENIC	TF binding site BDTNP1_TFBS_da
3L	3755412	3L_3755412_SNP [dm3] 3L_3755412_SNP [dm6]	T	A	3.920e^-6	0.809	UPSTREAM ppk27 INTRON CG32264
3L	2559825	3L_2559825_SNP [dm3] 3L_2559825_SNP [dm6]	T	A	5.467e^-6	0.809	INTRON msn
3R	17680946	3R_17680946_SNP [dm3] 3R_21855224_SNP [dm6]	A	G	5.828e^-6	0.809	INTRON glec	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3R	17680952	3R_17680952_SNP [dm3] 3R_21855230_SNP [dm6]	C	T	5.828e^-6	0.809	INTRON glec	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2L	15154495	2L_15154495_SNP [dm3] 2L_15154495_SNP [dm6]	C	T	5.979e^-6	0.809	INTERGENIC
2R	11428439	2R_11428439_SNP [dm3] 2R_15540934_SNP [dm6]	G	A	6.237e^-6	0.809	SYNONYMOUS_CODING CG8187 UPSTREAM Vha36-1 DOWNSTREAM CG30467	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Ubx
2R	13336270	2R_13336270_SNP [dm3] 2R_17448765_SNP [dm6]	C	T	7.333e^-6	0.809	UTR_3_PRIME mthl3
X	18274472	X_18274472_SNP [dm3] X_18380439_SNP [dm6]	A	G	8.550e^-6	0.809	SYNONYMOUS_CODING CG6179 UPSTREAM por	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	409947	3L_409947_SNP [dm3] 3L_409947_SNP [dm6]	C	T	1.036e^-5	0.809	INTERGENIC	TF binding site BDTNP1_TFBS_dl
X	18276023	X_18276023_SNP [dm3] X_18381990_SNP [dm6]	T	A	1.132e^-5	0.809	DOWNSTREAM CG6179 INTRON betaCOP	TF binding site mE1_TFBS_cad mE1_TFBS_sens
X	18276050	X_18276050_SNP [dm3] X_18382017_SNP [dm6]	A	C	1.132e^-5	0.809	DOWNSTREAM CG6179 INTRON betaCOP	TF binding site mE1_TFBS_cad mE1_TFBS_sens
3L	17929647	3L_17929647_SNP [dm3] 3L_17936547_SNP [dm6]	A	C	1.157e^-5	0.809	DOWNSTREAM CG43173 INTRON CG43174
2L	3871494	2L_3871494_SNP [dm3] 2L_3871494_SNP [dm6]	T	G	1.190e^-5	0.809	UTR_3_PRIME CG31957 DOWNSTREAM Cep97	TF binding site mE1_TFBS_sens
2L	3871502	2L_3871502_SNP [dm3] 2L_3871502_SNP [dm6]	A	C	1.190e^-5	0.809	UTR_3_PRIME CG31957 DOWNSTREAM Cep97	TF binding site mE1_TFBS_sens
2L	9735452	2L_9735452_SNP [dm3] 2L_9735452_SNP [dm6]	T	A	1.312e^-5	0.809	INTRON Nckx30C
3L	18489485	3L_18489485_SNP [dm3] 3L_18496385_SNP [dm6]	T	A	1.379e^-5	0.809	INTRON AstC-R2
3R	13789150	3R_13789150_SNP [dm3] 3R_17963428_SNP [dm6]	G	T	1.379e^-5	0.809	INTRON cpo
2R	13022706	2R_13022706_SNP [dm3] 2R_17135201_SNP [dm6]	T	A	1.568e^-5	0.809	UTR_3_PRIME CG11400 UPSTREAM CR44391 DOWNSTREAM CG11400	transposable element FlyBase
3L	13198565	3L_13198565_SNP [dm3] 3L_13205465_SNP [dm6]	C	T	1.585e^-5	0.809	INTERGENIC
3L	13198585	3L_13198585_DEL [dm3] 3L_13205485_DEL [dm6]	CAATAATAC	C	1.585e^-5	0.809	INTERGENIC
3L	13198599	3L_13198599_SNP [dm3] 3L_13205499_SNP [dm6]	A	T	1.585e^-5	0.809	INTERGENIC
3L	13198606	3L_13198606_SNP [dm3] 3L_13205506_SNP [dm6]	A	G	1.585e^-5	0.809	INTERGENIC
3L	13198624	3L_13198624_SNP [dm3] 3L_13205524_SNP [dm6]	A	C	1.585e^-5	0.809	INTERGENIC
3L	13198645	3L_13198645_SNP [dm3] 3L_13205545_SNP [dm6]	T	C	1.585e^-5	0.809	INTERGENIC
3L	13198725	3L_13198725_INS [dm3] 3L_13205625_INS [dm6]	A	ATATTA	1.585e^-5	0.809	INTERGENIC
3L	13198727	3L_13198727_DEL [dm3] 3L_13205627_DEL [dm6]	TTGCGTC	T	1.585e^-5	0.809	INTERGENIC
X	19647173	X_19647173_SNP [dm3] X_19753140_SNP [dm6]	T	G	1.611e^-5	0.809	INTRON Pmp70	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt mE1_TFBS_HSA
3L	7440778	3L_7440778_SNP [dm3] 3L_7447678_SNP [dm6]	G	T	1.613e^-5	0.809	INTRON CG42458	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3R	17785987	3R_17785987_SNP [dm3] 3R_21960265_SNP [dm6]	T	C	1.661e^-5	0.809	INTRON Eip93F
3L	9753723	3L_9753723_SNP [dm3] 3L_9760623_SNP [dm6]	C	A	1.774e^-5	0.809	UPSTREAM CR45407 & 1 other INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2L	3088883	2L_3088883_SNP [dm3] 2L_3088883_SNP [dm6]	C	G	1.797e^-5	0.809	INTRON toc	TF binding site BDTNP1_TFBS_slp1 mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA
2L	3088901	2L_3088901_SNP [dm3] 2L_3088901_SNP [dm6]	C	G	1.797e^-5	0.809	INTRON toc	TF binding site BDTNP1_TFBS_slp1 mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA
2L	3088903	2L_3088903_SNP [dm3] 2L_3088903_SNP [dm6]	T	C	1.797e^-5	0.809	INTRON toc	TF binding site BDTNP1_TFBS_slp1 mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA
2L	3088933	2L_3088933_SNP [dm3] 2L_3088933_SNP [dm6]	C	A	1.797e^-5	0.809	INTRON toc	TF binding site BDTNP1_TFBS_slp1 mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA
3R	13413265	3R_13413265_SNP [dm3] 3R_17587543_SNP [dm6]	T	G	1.802e^-5	0.809	INTERGENIC
3R	27277773	3R_27277773_SNP [dm3] 3R_31452051_SNP [dm6]	T	C	1.810e^-5	0.809	INTRON Gprk2	TF binding site mE1_TFBS_cad
2R	15742067	2R_15742067_SNP [dm3] 2R_19854562_SNP [dm6]	C	A	1.889e^-5	0.809	INTERGENIC
3L	3582380	3L_3582380_SNP [dm3] 3L_3582380_SNP [dm6]	G	A	2.094e^-5	0.809	INTRON Eip63E
3L	3582551	3L_3582551_SNP [dm3] 3L_3582551_SNP [dm6]	A	T	2.094e^-5	0.809	INTRON Eip63E	TF binding site mE1_TFBS_inv
3L	3582607	3L_3582607_SNP [dm3] 3L_3582607_SNP [dm6]	T	A	2.094e^-5	0.809	INTRON Eip63E	TF binding site mE1_TFBS_inv
3L	3582616	3L_3582616_SNP [dm3] 3L_3582616_SNP [dm6]	C	T	2.094e^-5	0.809	INTRON Eip63E	TF binding site mE1_TFBS_inv
3L	3693654	3L_3693654_SNP [dm3] 3L_3693654_SNP [dm6]	G	T	2.094e^-5	0.809	DOWNSTREAM CR43485 INTERGENIC
3L	3803698	3L_3803698_SNP [dm3] 3L_3803698_SNP [dm6]	C	T	2.094e^-5	0.809	DOWNSTREAM ntc INTRON CG32264
2R	12011772	2R_12011772_SNP [dm3] 2R_16124267_SNP [dm6]	T	A	2.253e^-5	0.853	UPSTREAM spin INTRON CG30095	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_h mE1_TFBS_Ubx
3R	6252747	3R_6252747_SNP [dm3] 3R_10427025_SNP [dm6]	C	T	2.304e^-5	0.854	INTERGENIC
3L	13198710	3L_13198710_SNP [dm3] 3L_13205610_SNP [dm6]	T	A	2.510e^-5	0.912	INTERGENIC
2R	12011764	2R_12011764_SNP [dm3] 2R_16124259_SNP [dm6]	G	T	2.567e^-5	0.914	SPLICE_SITE_REGION CG30095 UPSTREAM spin INTRON CG30095	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_h mE1_TFBS_Ubx
3R	8111740	3R_8111740_SNP [dm3] 3R_12286018_SNP [dm6]	T	A	2.695e^-5	0.915	INTRON svp
3L	5000122	3L_5000122_SNP [dm3] 3L_5000122_SNP [dm6]	A	T	2.837e^-5	0.915	INTRON Con	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Ubx
2R	6746350	2R_6746350_SNP [dm3] 2R_10858845_SNP [dm6]	T	G	2.851e^-5	0.915	UPSTREAM CR44302 INTRON CG30015
2R	12011783	2R_12011783_SNP [dm3] 2R_16124278_SNP [dm6]	C	T	2.873e^-5	0.915	UPSTREAM spin INTRON CG30095	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_h mE1_TFBS_Ubx
2R	12011813	2R_12011813_SNP [dm3] 2R_16124308_SNP [dm6]	T	A	2.873e^-5	0.915	UPSTREAM spin INTRON CG30095	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_h mE1_TFBS_Ubx
2L	3088896	2L_3088896_SNP [dm3] 2L_3088896_SNP [dm6]	G	T	2.952e^-5	0.915	INTRON toc	TF binding site BDTNP1_TFBS_slp1 mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA
2L	3576944	2L_3576944_SNP [dm3] 2L_3576944_SNP [dm6]	G	A	2.967e^-5	0.915	DOWNSTREAM CG43815 INTERGENIC
2R	13022757	2R_13022757_DEL [dm3] 2R_17135252_DEL [dm6]	AA	A	2.998e^-5	0.915	UTR_3_PRIME CG11400 UPSTREAM CR44391 DOWNSTREAM CG11400	transposable element FlyBase
3L	13198724	3L_13198724_SNP [dm3] 3L_13205624_SNP [dm6]	A	T	3.021e^-5	0.915	INTERGENIC
3R	25166558	3R_25166558_SNP [dm3] 3R_29340836_SNP [dm6]	A	T	3.152e^-5	0.939	INTERGENIC
2R	11394515	2R_11394515_SNP [dm3] 2R_15507010_SNP [dm6]	C	A	3.235e^-5	0.948	NON_SYNONYMOUS_CODING Ir52d	TF binding site mE1_TFBS_HSA
2R	13336250	2R_13336250_DEL [dm3] 2R_17448745_DEL [dm6]	ATA	A	3.300e^-5	0.952	UTR_3_PRIME mthl3
2L	10039575	2L_10039575_SNP [dm3] 2L_10039575_SNP [dm6]	A	T	3.551e^-5	0.998	DOWNSTREAM obst-B INTERGENIC
2R	19244613	2R_19244613_SNP [dm3] 2R_23357090_SNP [dm6]	T	G	3.571e^-5	0.998	SYNONYMOUS_CODING CG3500 UPSTREAM CG9875 DOWNSTREAM Rpi	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
X	18274265	X_18274265_SNP [dm3] X_18380232_SNP [dm6]	C	G	3.736e^-5	0.998	SYNONYMOUS_CODING CG6179 UPSTREAM por	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_HSA
2L	14190955	2L_14190955_SNP [dm3] 2L_14190955_SNP [dm6]	A	G	3.816e^-5	0.998	INTRON Dyrk2
2L	14920525	2L_14920525_SNP [dm3] 2L_14920525_SNP [dm6]	C	T	3.817e^-5	0.998	INTRON CG42313
2L	10358018	2L_10358018_SNP [dm3] 2L_10358018_SNP [dm6]	G	A	3.904e^-5	0.998	UTR_3_PRIME CG5045 DOWNSTREAM Cand1 & 1 other
2R	13230658	2R_13230658_SNP [dm3] 2R_17343153_SNP [dm6]	T	C	3.906e^-5	0.998	INTRON mbl
2R	5309887	2R_5309887_SNP [dm3] 2R_9422382_SNP [dm6]	A	G	3.943e^-5	0.998	UTR_3_PRIME CG13955	TF binding site BDTNP1_TFBS_twi mE1_TFBS_chinmo mE1_TFBS_HSA
2R	12011568	2R_12011568_SNP [dm3] 2R_16124063_SNP [dm6]	C	T	4.047e^-5	0.998	UPSTREAM spin INTRON CG30095	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_disco mE1_TFBS_Ubx
2R	12011582	2R_12011582_SNP [dm3] 2R_16124077_SNP [dm6]	C	T	4.047e^-5	0.998	SPLICE_SITE_REGION CG30095 UPSTREAM spin INTRON CG30095	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_disco mE1_TFBS_Ubx
2R	12011805	2R_12011805_SNP [dm3] 2R_16124300_SNP [dm6]	G	A	4.185e^-5	0.998	UPSTREAM spin INTRON CG30095	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_h mE1_TFBS_Ubx
2R	12011816	2R_12011816_SNP [dm3] 2R_16124311_SNP [dm6]	C	T	4.185e^-5	0.998	UPSTREAM spin INTRON CG30095	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_h mE1_TFBS_Ubx
X	18274373	X_18274373_SNP [dm3] X_18380340_SNP [dm6]	A	G	4.219e^-5	0.998	SYNONYMOUS_CODING CG6179 UPSTREAM por	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
X	10736639	X_10736639_SNP [dm3] X_10842606_SNP [dm6]	C	A	4.243e^-5	0.998	NON_SYNONYMOUS_CODING CG15209 DOWNSTREAM CG32669 INTRON sbr
X	18273658	X_18273658_SNP [dm3] X_18379625_SNP [dm6]	A	G	4.324e^-5	0.998	SYNONYMOUS_CODING por UPSTREAM CG6179	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	19299675	2R_19299675_SNP [dm3] 2R_23412152_SNP [dm6]	A	G	4.374e^-5	0.998	DOWNSTREAM CG9812 INTERGENIC
2R	9107939	2R_9107939_SNP [dm3] 2R_13220434_SNP [dm6]	C	T	4.490e^-5	0.998	SYNONYMOUS_CODING CG17059 UPSTREAM CG4646 DOWNSTREAM Fsn	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_Ubx
3R	17680882	3R_17680882_SNP [dm3] 3R_21855160_SNP [dm6]	A	G	4.506e^-5	0.998	INTRON glec	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3R	17680897	3R_17680897_SNP [dm3] 3R_21855175_SNP [dm6]	C	T	4.506e^-5	0.998	INTRON glec	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3R	21943996	3R_21943996_SNP [dm3] 3R_26118274_SNP [dm6]	T	G	4.562e^-5	0.998	INTRON CG31324
2R	15153312	2R_15153312_SNP [dm3] 2R_19265807_SNP [dm6]	C	T	4.697e^-5	1	INTERGENIC	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3L	7410630	3L_7410630_SNP [dm3] 3L_7417530_SNP [dm6]	A	G	4.764e^-5	1	INTERGENIC
3R	17680664	3R_17680664_SNP [dm3] 3R_21854942_SNP [dm6]	G	A	4.816e^-5	1	INTRON glec	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna mE1_TFBS_HSA mE1_TFBS_Trl
3R	6267495	3R_6267495_SNP [dm3] 3R_10441773_SNP [dm6]	T	C	4.879e^-5	1	INTERGENIC
3R	17544331	3R_17544331_SNP [dm3] 3R_21718609_SNP [dm6]	A	T	4.948e^-5	1	SYNONYMOUS_CODING CG31176	TF binding site BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3R	10749642	3R_10749642_SNP [dm3] 3R_14923920_SNP [dm6]	G	A	4.968e^-5	1	UPSTREAM CR45598 DOWNSTREAM Sdr INTERGENIC
3L	1723350	3L_1723350_SNP [dm3] 3L_1723350_SNP [dm6]	T	C	4.984e^-5	1	UPSTREAM CG18171 INTRON drpr
2R	13022780	2R_13022780_SNP [dm3] 2R_17135275_SNP [dm6]	A	T	5.025e^-5	1	UTR_3_PRIME CG11400 UPSTREAM CR44391 DOWNSTREAM CG11400
2R	15742383	2R_15742383_SNP [dm3] 2R_19854878_SNP [dm6]	C	T	5.167e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi
2R	10634110	2R_10634110_SNP [dm3] 2R_14746605_SNP [dm6]	T	A	5.202e^-5	1	UTR_3_PRIME Dro UPSTREAM AttA DOWNSTREAM Dro
3R	20924771	3R_20924771_SNP [dm3] 3R_25099049_SNP [dm6]	C	T	5.226e^-5	1	INTRON CG33095 & 1 other
3R	5475976	3R_5475976_SNP [dm3] 3R_9650254_SNP [dm6]	A	T	5.244e^-5	1	UTR_3_PRIME Dh44 DOWNSTREAM Dh44 & 1 other
2R	17956194	2R_17956194_SNP [dm3] 2R_22068689_SNP [dm6]	C	A	5.490e^-5	1	DOWNSTREAM CG44249 INTRON Snp
3R	6264469	3R_6264469_SNP [dm3] 3R_10438747_SNP [dm6]	G	C	5.701e^-5	1	INTERGENIC	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	6276969	3R_6276969_SNP [dm3] 3R_10451247_SNP [dm6]	C	T	5.701e^-5	1	INTERGENIC
3L	18070745	3L_18070745_SNP [dm3] 3L_18077645_SNP [dm6]	T	C	5.782e^-5	1	EXON CR45392	TF binding site mE1_TFBS_Trl
3R	10878027	3R_10878027_SNP [dm3] 3R_15052305_SNP [dm6]	T	G	5.785e^-5	1	INTERGENIC

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Missing results

By genomic position
Variant impact
Gene name

pc_Deletion_PElem_SC phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results