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=7.708e^-11)
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
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

18131 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	15698796	3R_15698796_SNP [dm3] 3R_19873074_SNP [dm6]	C	A	2.238e^-220	4.065e^-215	INTRON CG4562
3R	15825399	3R_15825399_SNP [dm3] 3R_19999677_SNP [dm6]	C	A	2.238e^-220	4.065e^-215	INTRON Hs6st
3R	16211333	3R_16211333_SNP [dm3] 3R_20385611_SNP [dm6]	C	A	2.238e^-220	4.065e^-215	INTRON Gfrl
3R	16233940	3R_16233940_SNP [dm3] 3R_20408218_SNP [dm6]	T	A	2.238e^-220	4.065e^-215	UPSTREAM CG10881 & 1 other INTRON Gfrl
3R	16294030	3R_16294030_SNP [dm3] 3R_20468308_SNP [dm6]	G	T	2.238e^-220	4.065e^-215	INTRON Gfrl
3R	16433016	3R_16433016_SNP [dm3] 3R_20607294_SNP [dm6]	G	A	2.238e^-220	4.065e^-215	SYNONYMOUS_CODING bon	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	18545492	3R_18545492_SNP [dm3] 3R_22719770_SNP [dm6]	G	T	2.238e^-220	4.065e^-215	INTRON wge	TF binding site mE1_TFBS_sens
3R	18548485	3R_18548485_SNP [dm3] 3R_22722763_SNP [dm6]	G	T	2.238e^-220	4.065e^-215	SYNONYMOUS_CODING Irp-1A	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3R	18675621	3R_18675621_SNP [dm3] 3R_22849899_SNP [dm6]	A	G	2.238e^-220	4.065e^-215	INTERGENIC
3R	18810854	3R_18810854_SNP [dm3] 3R_22985132_SNP [dm6]	C	A	2.238e^-220	4.065e^-215	INTRON Nha2
3R	15820211	3R_15820211_SNP [dm3] 3R_19994489_SNP [dm6]	G	T	1.820e^-216	2.543e^-211	INTRON Hs6st	TF binding site BDTNP1_TFBS_twi mE1_TFBS_sens
3R	16010376	3R_16010376_SNP [dm3] 3R_20184654_SNP [dm6]	A	G	1.820e^-216	2.543e^-211	INTERGENIC
3R	16010475	3R_16010475_SNP [dm3] 3R_20184753_SNP [dm6]	G	A	1.820e^-216	2.543e^-211	INTERGENIC
3R	24135922	3R_24135922_SNP [dm3] 3R_28310200_SNP [dm6]	T	G	5.303e^-211	6.468e^-206	INTERGENIC	TF binding site mE1_TFBS_bab1
3R	18486674	3R_18486674_SNP [dm3] 3R_22660952_SNP [dm6]	C	A	5.341e^-211	6.468e^-206	INTRON CG45058
3R	18576715	3R_18576715_SNP [dm3] 3R_22750993_SNP [dm6]	G	A	9.325e^-211	1.059e^-205	UTR_5_PRIME Usp12-46 & 1 other UPSTREAM rumi	TF binding site BDTNP1_TFBS_Med mE1_TFBS_bab1 mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl mE1_TFBS_Ubx
3R	15994645	3R_15994645_DEL [dm3] 3R_20168923_DEL [dm6]	AA	A	5.792e^-209	6.189e^-204	UPSTREAM CG5023 INTERGENIC
X	2855966	X_2855966_DEL [dm3] X_2961933_DEL [dm6]	AA	A	2.075e^-197	2.094e^-192	INTRON kirre & 1 other
2R	14770128	2R_14770128_SNP [dm3] 2R_18882623_SNP [dm6]	A	C	2.407e^-189	2.301e^-184	INTRON sano
2R	11296197	2R_11296197_SNP [dm3] 2R_15408692_SNP [dm6]	G	A	7.155e^-22	6.498e^-17	UPSTREAM Mtk INTRON CG43729	regulatory region REDfly_CRMs
X	10784119	X_10784119_INS [dm3] X_10890086_INS [dm6]	A	AA	1.743e^-21	1.508e^-16	INTRON Ork1
3R	16005089	3R_16005089_SNP [dm3] 3R_20179367_SNP [dm6]	C	G	1.183e^-20	9.342e^-16	INTERGENIC
3R	16431313	3R_16431313_SNP [dm3] 3R_20605591_SNP [dm6]	G	T	1.183e^-20	9.342e^-16	UPSTREAM tRNA:CR31506 INTRON bon	TF binding site mE1_TFBS_cad
X	16987709	X_16987709_SNP [dm3] X_17093676_SNP [dm6]	G	A	2.781e^-20	2.104e^-15	INTRON CG16700 & 1 other
3R	13880058	3R_13880058_INS [dm3] 3R_18054336_INS [dm6]	A	ACCTGGCTCCAA...	3.836e^-20	2.787e^-15	INTERGENIC	TF binding site BDTNP1_TFBS_z
3R	15768682	3R_15768682_SNP [dm3] 3R_19942960_SNP [dm6]	C	T	4.797e^-20	3.005e^-15	INTRON Hs6st
3R	16010034	3R_16010034_SNP [dm3] 3R_20184312_SNP [dm6]	T	G	4.797e^-20	3.005e^-15	INTERGENIC	TF binding site BDTNP1_TFBS_twi
3R	16387550	3R_16387550_SNP [dm3] 3R_20561828_SNP [dm6]	T	A	4.797e^-20	3.005e^-15	DOWNSTREAM CG10877 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
3R	18545173	3R_18545173_SNP [dm3] 3R_22719451_SNP [dm6]	T	C	4.797e^-20	3.005e^-15	INTRON wge
3R	16010497	3R_16010497_SNP [dm3] 3R_20184775_SNP [dm6]	G	A	4.967e^-20	3.007e^-15	INTERGENIC
3R	16989964	3R_16989964_SNP [dm3] 3R_21164242_SNP [dm6]	C	T	1.851e^-19	1.085e^-14	SYNONYMOUS_CODING CG5810 DOWNSTREAM Snmp1 INTRON SNF4Agamma	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	18721665	3R_18721665_SNP [dm3] 3R_22895943_SNP [dm6]	G	A	6.387e^-19	3.626e^-14	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	15759886	3R_15759886_SNP [dm3] 3R_19934164_SNP [dm6]	G	A	7.441e^-19	4.096e^-14	SYNONYMOUS_CODING mira INTRON Hs6st	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3R	15768692	3R_15768692_SNP [dm3] 3R_19942970_SNP [dm6]	A	G	8.493e^-19	4.537e^-14	INTRON Hs6st
3R	16387531	3R_16387531_SNP [dm3] 3R_20561809_SNP [dm6]	T	C	3.302e^-18	1.714e^-13	DOWNSTREAM CG10877 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
2L	10654046	2L_10654046_SNP [dm3] 2L_10654046_SNP [dm6]	A	T	9.221e^-11	3.895e^-6	SYNONYMOUS_CODING CG17098	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	10694686	2L_10694686_SNP [dm3] 2L_10694686_SNP [dm6]	A	G	9.221e^-11	3.895e^-6	UPSTREAM CR44181 & 1 other DOWNSTREAM CG7300 INTERGENIC
2L	10700449	2L_10700449_SNP [dm3] 2L_10700449_SNP [dm6]	G	A	9.221e^-11	3.895e^-6	SYNONYMOUS_CODING Lip1	TF binding site mE1_TFBS_cad
2L	11241912	2L_11241912_SNP [dm3] 2L_11241912_SNP [dm6]	T	C	9.221e^-11	3.895e^-6	INTRON ab	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_inv
2L	11642752	2L_11642752_SNP [dm3] 2L_11642752_SNP [dm6]	A	G	9.221e^-11	3.895e^-6	INTERGENIC
2L	4199102	2L_4199102_SNP [dm3] 2L_4199102_SNP [dm6]	A	G	9.221e^-11	3.895e^-6	UTR_3_PRIME ft	TF binding site mE1_TFBS_cad
2L	4866612	2L_4866612_SNP [dm3] 2L_4866612_SNP [dm6]	G	A	9.221e^-11	3.895e^-6	INTRON pog
2L	7153675	2L_7153675_SNP [dm3] 2L_7153675_SNP [dm6]	G	A	9.221e^-11	3.895e^-6	INTRON Pvf3
2L	1129261	2L_1129261_SNP [dm3] 2L_1129261_SNP [dm6]	G	A	1.382e^-10	4.150e^-6	UPSTREAM CG4552 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA
2L	11792160	2L_11792160_SNP [dm3] 2L_11792160_SNP [dm6]	C	G	1.382e^-10	4.150e^-6	SYNONYMOUS_CODING Tsp33B DOWNSTREAM CG14937	TF binding site mE1_TFBS_cad
2L	13742352	2L_13742352_SNP [dm3] 2L_13742352_SNP [dm6]	A	G	1.382e^-10	4.150e^-6	INTERGENIC
2L	2223837	2L_2223837_SNP [dm3] 2L_2223837_SNP [dm6]	G	A	1.382e^-10	4.150e^-6	SYNONYMOUS_CODING papi	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	4198688	2L_4198688_SNP [dm3] 2L_4198688_SNP [dm6]	A	T	1.382e^-10	4.150e^-6	UTR_3_PRIME ft UPSTREAM CG3714
2L	4253942	2L_4253942_SNP [dm3] 2L_4253942_SNP [dm6]	A	C	1.382e^-10	4.150e^-6	INTERGENIC
2L	4698035	2L_4698035_SNP [dm3] 2L_4698035_SNP [dm6]	C	G	1.382e^-10	4.150e^-6	INTRON CG34351
2R	768725	2R_768725_SNP [dm3] 2R_4881220_SNP [dm6]	T	C	1.685e^-10	4.150e^-6	INTERGENIC
2L	4689867	2L_4689867_SNP [dm3] 2L_4689867_SNP [dm6]	A	G	1.974e^-10	4.150e^-6	SYNONYMOUS_CODING CG3251 DOWNSTREAM Elba3	TF binding site BDTNP1_TFBS_sna mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2L	6894577	2L_6894577_SNP [dm3] 2L_6894577_SNP [dm6]	A	G	1.974e^-10	4.150e^-6	INTRON Nlg2
2L	9131097	2L_9131097_DEL [dm3] 2L_9131097_DEL [dm6]	AA	A	1.974e^-10	4.150e^-6	INTRON CG32982
2L	10654044	2L_10654044_SNP [dm3] 2L_10654044_SNP [dm6]	T	A	2.152e^-10	4.150e^-6	NON_SYNONYMOUS_CODING CG17098	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	10132860	2L_10132860_SNP [dm3] 2L_10132860_SNP [dm6]	G	T	2.787e^-10	4.150e^-6	INTRON CG44153
2L	10132900	2L_10132900_SNP [dm3] 2L_10132900_SNP [dm6]	A	T	2.787e^-10	4.150e^-6	INTRON CG44153
2L	10362930	2L_10362930_SNP [dm3] 2L_10362930_SNP [dm6]	T	A	2.787e^-10	4.150e^-6	UPSTREAM pim & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
2L	10632917	2L_10632917_SNP [dm3] 2L_10632917_SNP [dm6]	G	T	2.787e^-10	4.150e^-6	INTRON CG7329	TF binding site mE1_TFBS_inv
2L	10694685	2L_10694685_SNP [dm3] 2L_10694685_SNP [dm6]	G	A	2.787e^-10	4.150e^-6	UPSTREAM CR44181 & 1 other DOWNSTREAM CG7300 INTERGENIC
2L	1102849	2L_1102849_SNP [dm3] 2L_1102849_SNP [dm6]	G	A	2.787e^-10	4.150e^-6	UPSTREAM CG4629 DOWNSTREAM mtRNApol INTERGENIC
2L	1103586	2L_1103586_SNP [dm3] 2L_1103586_SNP [dm6]	C	T	2.787e^-10	4.150e^-6	UTR_3_PRIME mtRNApol	TF binding site mE1_TFBS_cad
2L	1115092	2L_1115092_SNP [dm3] 2L_1115092_SNP [dm6]	G	A	2.787e^-10	4.150e^-6	UTR_3_PRIME Pino DOWNSTREAM CG14340
2L	11240934	2L_11240934_SNP [dm3] 2L_11240934_SNP [dm6]	A	G	2.787e^-10	4.150e^-6	INTRON ab
2L	11442714	2L_11442714_SNP [dm3] 2L_11442714_SNP [dm6]	T	A	2.787e^-10	4.150e^-6	INTRON salm
2L	11492299	2L_11492299_SNP [dm3] 2L_11492299_SNP [dm6]	C	T	2.787e^-10	4.150e^-6	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
2L	11509846	2L_11509846_SNP [dm3] 2L_11509846_SNP [dm6]	C	G	2.787e^-10	4.150e^-6	SYNONYMOUS_CODING CG6509 UTR_3_PRIME CG6509
2L	11583300	2L_11583300_SNP [dm3] 2L_11583300_SNP [dm6]	C	T	2.787e^-10	4.150e^-6	INTRON kek2
2L	11583302	2L_11583302_SNP [dm3] 2L_11583302_SNP [dm6]	G	C	2.787e^-10	4.150e^-6	INTRON kek2
2L	11640067	2L_11640067_SNP [dm3] 2L_11640067_SNP [dm6]	C	T	2.787e^-10	4.150e^-6	INTERGENIC
2L	11642408	2L_11642408_SNP [dm3] 2L_11642408_SNP [dm6]	G	A	2.787e^-10	4.150e^-6	INTERGENIC
2L	11642986	2L_11642986_SNP [dm3] 2L_11642986_SNP [dm6]	G	A	2.787e^-10	4.150e^-6	INTERGENIC
2L	11649035	2L_11649035_SNP [dm3] 2L_11649035_SNP [dm6]	G	A	2.787e^-10	4.150e^-6	UPSTREAM CG6614 INTERGENIC	TF binding site BDTNP1_TFBS_da
2L	11652415	2L_11652415_SNP [dm3] 2L_11652415_SNP [dm6]	A	C	2.787e^-10	4.150e^-6	UPSTREAM CG4983 & 1 other INTERGENIC
2L	11691970	2L_11691970_INS [dm3] 2L_11691970_INS [dm6]	C	CTTT	2.787e^-10	4.150e^-6	INTERGENIC
2L	11798433	2L_11798433_SNP [dm3] 2L_11798433_SNP [dm6]	T	A	2.787e^-10	4.150e^-6	UPSTREAM snoRNA:Me18S-A934 INTRON crol	TF binding site mE1_TFBS_cad
2L	12186215	2L_12186215_SNP [dm3] 2L_12186215_SNP [dm6]	G	C	2.787e^-10	4.150e^-6	INTRON aret	TF binding site BDTNP1_TFBS_dl mE1_TFBS_eve mE1_TFBS_HSA
2L	12186217	2L_12186217_INS [dm3] 2L_12186217_INS [dm6]	G	GCATTTTTAGGCA...	2.787e^-10	4.150e^-6	INTRON aret	TF binding site BDTNP1_TFBS_dl mE1_TFBS_eve mE1_TFBS_HSA
2L	12186220	2L_12186220_INS [dm3] 2L_12186220_INS [dm6]	T	TCAACCT	2.787e^-10	4.150e^-6	INTRON aret	TF binding site BDTNP1_TFBS_dl mE1_TFBS_eve mE1_TFBS_HSA
2L	12186242	2L_12186242_SNP [dm3] 2L_12186242_SNP [dm6]	T	G	2.787e^-10	4.150e^-6	INTRON aret	TF binding site BDTNP1_TFBS_dl mE1_TFBS_eve mE1_TFBS_HSA
2L	12186245	2L_12186245_SNP [dm3] 2L_12186245_SNP [dm6]	C	G	2.787e^-10	4.150e^-6	INTRON aret	TF binding site BDTNP1_TFBS_dl mE1_TFBS_eve mE1_TFBS_HSA
2L	12186247	2L_12186247_SNP [dm3] 2L_12186247_SNP [dm6]	T	A	2.787e^-10	4.150e^-6	INTRON aret	TF binding site BDTNP1_TFBS_dl mE1_TFBS_eve mE1_TFBS_HSA
2L	13231077	2L_13231077_SNP [dm3] 2L_13231077_SNP [dm6]	C	T	2.787e^-10	4.150e^-6	UPSTREAM Prosalpha6T DOWNSTREAM CG16815 INTERGENIC	TF binding site BDTNP1_TFBS_hb
2L	2222893	2L_2222893_SNP [dm3] 2L_2222893_SNP [dm6]	G	T	2.787e^-10	4.150e^-6	UPSTREAM papi INTRON papi
2L	2223820	2L_2223820_SNP [dm3] 2L_2223820_SNP [dm6]	C	T	2.787e^-10	4.150e^-6	SYNONYMOUS_CODING papi	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	2224293	2L_2224293_SNP [dm3] 2L_2224293_SNP [dm6]	T	A	2.787e^-10	4.150e^-6	NON_SYNONYMOUS_CODING papi	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	2224550	2L_2224550_SNP [dm3] 2L_2224550_SNP [dm6]	A	G	2.787e^-10	4.150e^-6	DOWNSTREAM CG15387 INTRON papi	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	2224600	2L_2224600_SNP [dm3] 2L_2224600_SNP [dm6]	C	T	2.787e^-10	4.150e^-6	SYNONYMOUS_CODING papi DOWNSTREAM CG15387	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	2225903	2L_2225903_SNP [dm3] 2L_2225903_SNP [dm6]	T	C	2.787e^-10	4.150e^-6	SYNONYMOUS_CODING CG15387 UPSTREAM rti DOWNSTREAM papi & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_Ubx
2L	2226793	2L_2226793_SNP [dm3] 2L_2226793_SNP [dm6]	A	G	2.787e^-10	4.150e^-6	UTR_5_PRIME rti UPSTREAM CG15387 EXON CR44114	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_z mE1_TFBS_hkb mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_Ubx
2L	2232767	2L_2232767_SNP [dm3] 2L_2232767_SNP [dm6]	T	C	2.787e^-10	4.150e^-6	SYNONYMOUS_CODING Sec24CD
2L	2232812	2L_2232812_SNP [dm3] 2L_2232812_SNP [dm6]	A	G	2.787e^-10	4.150e^-6	SYNONYMOUS_CODING Sec24CD
2L	2238790	2L_2238790_SNP [dm3] 2L_2238790_SNP [dm6]	A	G	2.787e^-10	4.150e^-6	SYNONYMOUS_CODING Tengl2 UPSTREAM Tengl3 DOWNSTREAM Tengl1
2L	3429092	2L_3429092_SNP [dm3] 2L_3429092_SNP [dm6]	A	C	2.787e^-10	4.150e^-6	INTERGENIC
2L	4199077	2L_4199077_DEL [dm3] 2L_4199077_DEL [dm6]	GGG	G	2.787e^-10	4.150e^-6	UTR_3_PRIME ft	TF binding site mE1_TFBS_cad
2L	4199088	2L_4199088_SNP [dm3] 2L_4199088_SNP [dm6]	T	C	2.787e^-10	4.150e^-6	UTR_3_PRIME ft	TF binding site mE1_TFBS_cad
2L	4199112	2L_4199112_DEL [dm3] 2L_4199112_DEL [dm6]	AAGAGCAT	A	2.787e^-10	4.150e^-6	UTR_3_PRIME ft	TF binding site mE1_TFBS_cad
2L	4204993	2L_4204993_SNP [dm3] 2L_4204993_SNP [dm6]	C	T	2.787e^-10	4.150e^-6	SYNONYMOUS_CODING ft	TF binding site mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens
2L	4496665	2L_4496665_SNP [dm3] 2L_4496665_SNP [dm6]	A	G	2.787e^-10	4.150e^-6	SYNONYMOUS_CODING dp INTRON dp	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_sens
2L	4496666	2L_4496666_SNP [dm3] 2L_4496666_SNP [dm6]	A	G	2.787e^-10	4.150e^-6	NON_SYNONYMOUS_CODING dp INTRON dp	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_sens

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By genomic position
Variant impact
Gene name

pc_MB_Alpha_Abnormal phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results