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=3.446e^-2)
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_K	0.05822

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_3R_K	4.3506	0.037

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1662 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	16381834	2L_16381834_SNP [dm3] 2L_16381834_SNP [dm6]	A	T	9.694e^-7	0.903	INTERGENIC
X	5993793	X_5993793_SNP [dm3] X_6099760_SNP [dm6]	G	A	9.799e^-7	0.903	INTRON Nep1
3L	4844676	3L_4844676_SNP [dm3] 3L_4844676_SNP [dm6]	G	C	2.153e^-6	0.964	INTERGENIC
X	18994455	X_18994455_SNP [dm3] X_19100422_SNP [dm6]	C	T	2.613e^-6	0.964	INTERGENIC
X	18994500	X_18994500_SNP [dm3] X_19100467_SNP [dm6]	G	C	2.613e^-6	0.964	INTERGENIC
3R	3142113	3R_3142113_SNP [dm3] 3R_7316391_SNP [dm6]	C	T	3.348e^-6	1	SYNONYMOUS_CODING CG10029
3L	5263945	3L_5263945_INS [dm3] 3L_5270845_INS [dm6]	T	TT	4.183e^-6	1	INTRON shep
3L	4078009	3L_4078009_SNP [dm3] 3L_4078009_SNP [dm6]	A	G	4.450e^-6	1	INTRON Gad1
X	5993764	X_5993764_SNP [dm3] X_6099731_SNP [dm6]	A	G	6.013e^-6	1	INTRON Nep1
X	5993699	X_5993699_SNP [dm3] X_6099666_SNP [dm6]	G	A	6.166e^-6	1	SYNONYMOUS_CODING Nep1
X	8877647	X_8877647_SNP [dm3] X_8983614_SNP [dm6]	T	A	6.364e^-6	1	DOWNSTREAM CG12662 INTRON rdgA & 1 other
X	8877493	X_8877493_SNP [dm3] X_8983460_SNP [dm6]	A	G	8.467e^-6	1	DOWNSTREAM CG12662 INTRON rdgA & 1 other
X	8877507	X_8877507_SNP [dm3] X_8983474_SNP [dm6]	C	T	8.467e^-6	1	DOWNSTREAM CG12662 INTRON rdgA & 1 other
3L	5263939	3L_5263939_SNP [dm3] 3L_5270839_SNP [dm6]	C	T	9.147e^-6	1	INTRON shep
3R	3204159	3R_3204159_SNP [dm3] 3R_7378437_SNP [dm6]	T	G	1.004e^-5	1	INTERGENIC
3L	5721636	3L_5721636_SNP [dm3] 3L_5728536_SNP [dm6]	T	A	1.021e^-5	1	SYNONYMOUS_CODING sif
2L	16381822	2L_16381822_SNP [dm3] 2L_16381822_SNP [dm6]	T	A	1.023e^-5	1	INTERGENIC
3R	3337597	3R_3337597_SNP [dm3] 3R_7511875_SNP [dm6]	T	A	1.154e^-5	1	INTRON alpha-Est8
2R	17645313	2R_17645313_SNP [dm3] 2R_21757808_SNP [dm6]	C	T	1.325e^-5	1	SYNONYMOUS_CODING Grx-1
X	8877508	X_8877508_SNP [dm3] X_8983475_SNP [dm6]	G	T	1.536e^-5	1	DOWNSTREAM CG12662 INTRON rdgA & 1 other
3L	8685456	3L_8685456_SNP [dm3] 3L_8692356_SNP [dm6]	G	T	1.543e^-5	1	UPSTREAM CR44526 INTERGENIC	TF binding site mE1_TFBS_cad
3L	9367749	3L_9367749_SNP [dm3] 3L_9374649_SNP [dm6]	C	T	1.570e^-5	1	SYNONYMOUS_CODING Hsp22 UTR_3_PRIME Hsp67Bb UPSTREAM CG4461 DOWNSTREAM Hsp67Bb	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
2L	20318067	2L_20318067_SNP [dm3] 2L_20318067_SNP [dm6]	C	A	1.633e^-5	1	UPSTREAM CR43606 INTRON spir
3R	15049450	3R_15049450_SNP [dm3] 3R_19223728_SNP [dm6]	C	G	1.644e^-5	1	INTRON vib
2L	11884121	2L_11884121_SNP [dm3] 2L_11884121_SNP [dm6]	C	T	1.748e^-5	1	INTRON Pde1c
2L	11884146	2L_11884146_SNP [dm3] 2L_11884146_SNP [dm6]	T	A	1.748e^-5	1	INTRON Pde1c
2L	11884214	2L_11884214_SNP [dm3] 2L_11884214_SNP [dm6]	T	C	1.748e^-5	1	INTRON Pde1c
2L	11884217	2L_11884217_SNP [dm3] 2L_11884217_SNP [dm6]	T	A	1.748e^-5	1	INTRON Pde1c
2L	11884242	2L_11884242_SNP [dm3] 2L_11884242_SNP [dm6]	T	C	1.748e^-5	1	INTRON Pde1c
3R	9640515	3R_9640515_SNP [dm3] 3R_13814793_SNP [dm6]	A	G	1.789e^-5	1	UPSTREAM CR43641 DOWNSTREAM tal-AA & 3 others INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
3R	3003127	3R_3003127_SNP [dm3] 3R_7177405_SNP [dm6]	C	A	1.862e^-5	1	INTRON sas
2L	19404134	2L_19404134_SNP [dm3] 2L_19404134_SNP [dm6]	A	G	1.865e^-5	1	SYNONYMOUS_CODING Pax UPSTREAM snmRNA:359	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
X	8877483	X_8877483_SNP [dm3] X_8983450_SNP [dm6]	A	T	2.020e^-5	1	DOWNSTREAM CG12662 INTRON rdgA & 1 other
3R	20132993	3R_20132993_SNP [dm3] 3R_24307271_SNP [dm6]	C	A	2.110e^-5	1	INTRON crb	TF binding site mE1_TFBS_cad
3L	1015925	3L_1015925_SNP [dm3] 3L_1015925_SNP [dm6]	A	T	2.232e^-5	1	INTRON trio
3L	9366687	3L_9366687_SNP [dm3] 3L_9373587_SNP [dm6]	A	G	2.239e^-5	1	UTR_5_PRIME Hsp22 UTR_3_PRIME Hsp67Bb UPSTREAM Hsp22 DOWNSTREAM Hsp67Bb	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_D mE1_TFBS_Dll mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_Trl
3R	3203595	3R_3203595_SNP [dm3] 3R_7377873_SNP [dm6]	A	G	2.416e^-5	1	INTERGENIC	TF binding site mE1_TFBS_HSA
2L	15437176	2L_15437176_SNP [dm3] 2L_15437176_SNP [dm6]	A	C	2.568e^-5	1	DOWNSTREAM CR44861 INTERGENIC
X	8877678	X_8877678_SNP [dm3] X_8983645_SNP [dm6]	G	A	2.583e^-5	1	UTR_3_PRIME CG12662 INTRON rdgA & 1 other
3R	15049435	3R_15049435_SNP [dm3] 3R_19223713_SNP [dm6]	G	T	2.693e^-5	1	INTRON vib
2R	13497643	2R_13497643_SNP [dm3] 2R_17610138_SNP [dm6]	C	T	2.718e^-5	1	INTRON CG10936
3R	3141367	3R_3141367_SNP [dm3] 3R_7315645_SNP [dm6]	A	T	2.894e^-5	1	UTR_3_PRIME CG10029 DOWNSTREAM CG10029
3R	3327248	3R_3327248_SNP [dm3] 3R_7501526_SNP [dm6]	A	G	2.966e^-5	1	SYNONYMOUS_CODING CG1287 INTRON alpha-Est9	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2L	9181840	2L_9181840_SNP [dm3] 2L_9181840_SNP [dm6]	G	A	2.983e^-5	1	INTRON tai
3R	15794908	3R_15794908_INS [dm3] 3R_19969186_INS [dm6]	G	TGATGGTTA	3.002e^-5	1	INTRON Hs6st
3L	8005744	3L_8005744_SNP [dm3] 3L_8012644_SNP [dm6]	C	T	3.012e^-5	1	INTRON nmo
2L	20359518	2L_20359518_SNP [dm3] 2L_20359518_SNP [dm6]	C	T	3.029e^-5	1	DOWNSTREAM RtGEF INTRON RtGEF
3R	3139444	3R_3139444_SNP [dm3] 3R_7313722_SNP [dm6]	A	T	3.176e^-5	1	UPSTREAM CR44334 INTERGENIC	TF binding site mE1_TFBS_HSA
2L	9184705	2L_9184705_SNP [dm3] 2L_9184705_SNP [dm6]	T	G	3.339e^-5	1	INTRON tai
2L	5817714	2L_5817714_SNP [dm3] 2L_5817714_SNP [dm6]	G	C	3.362e^-5	1	DOWNSTREAM CG31644 INTERGENIC
X	13131843	X_13131843_SNP [dm3] X_13237810_SNP [dm6]	C	G	3.383e^-5	1	INTRON mew	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3R	16233311	3R_16233311_SNP [dm3] 3R_20407589_SNP [dm6]	C	G	3.486e^-5	1	UPSTREAM CG10881 INTRON Gfrl & 1 other
X	5993947	X_5993947_SNP [dm3] X_6099914_SNP [dm6]	G	A	3.659e^-5	1	INTRON Nep1
3L	8151198	3L_8151198_SNP [dm3] 3L_8158098_SNP [dm6]	G	A	3.878e^-5	1	INTRON CG42445
X	18017736	X_18017736_SNP [dm3] X_18123703_SNP [dm6]	A	C	3.897e^-5	1	UPSTREAM mir-969 DOWNSTREAM CR45606 & 1 other INTERGENIC
2L	8738928	2L_8738928_SNP [dm3] 2L_8738928_SNP [dm6]	A	T	3.984e^-5	1	INTRON raw
3L	9367569	3L_9367569_SNP [dm3] 3L_9374469_SNP [dm6]	C	T	4.039e^-5	1	SYNONYMOUS_CODING Hsp22 UTR_3_PRIME Hsp67Bb UPSTREAM CG4461 DOWNSTREAM Hsp67Bb	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
3L	9367609	3L_9367609_SNP [dm3] 3L_9374509_SNP [dm6]	C	T	4.039e^-5	1	SYNONYMOUS_CODING Hsp22 UTR_3_PRIME Hsp67Bb UPSTREAM CG4461 DOWNSTREAM Hsp67Bb	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
2R	20250121	2R_20250121_SNP [dm3] 2R_24362598_SNP [dm6]	T	C	4.086e^-5	1	INTRON bs & 1 other	TF binding site mE1_TFBS_chinmo
2L	1089803	2L_1089803_SNP [dm3] 2L_1089803_SNP [dm6]	C	G	4.135e^-5	1	INTRON CG4629	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi
3L	3473428	3L_3473428_SNP [dm3] 3L_3473428_SNP [dm6]	T	A	4.175e^-5	1	INTRON CG42324
X	18233208	X_18233208_SNP [dm3] X_18339175_SNP [dm6]	G	A	4.190e^-5	1	INTRON CG6123
2L	9154790	2L_9154790_SNP [dm3] 2L_9154790_SNP [dm6]	A	T	4.293e^-5	1	INTRON CG32982
2L	9154797	2L_9154797_SNP [dm3] 2L_9154797_SNP [dm6]	T	A	4.293e^-5	1	INTRON CG32982
3R	3337663	3R_3337663_SNP [dm3] 3R_7511941_SNP [dm6]	G	A	4.429e^-5	1	SYNONYMOUS_CODING alpha-Est8
3R	2915609	3R_2915609_SNP [dm3] 3R_7089887_SNP [dm6]	G	C	4.484e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_sens mE1_TFBS_zfh1
2L	1313293	2L_1313293_SNP [dm3] 2L_1313293_SNP [dm6]	G	A	4.764e^-5	1	INTERGENIC
2L	10028813	2L_10028813_SNP [dm3] 2L_10028813_SNP [dm6]	A	T	4.903e^-5	1	SYNONYMOUS_CODING CG13127
2R	16665531	2R_16665531_INS [dm3] 2R_20778026_INS [dm6]	G	GTTTAG	4.957e^-5	1	UPSTREAM CG43710 DOWNSTREAM CG43711 INTERGENIC
2R	19431294	2R_19431294_SNP [dm3] 2R_23543771_SNP [dm6]	T	C	5.250e^-5	1	UPSTREAM CG30185 INTRON Gr59f	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	16233328	3R_16233328_SNP [dm3] 3R_20407606_SNP [dm6]	G	A	5.356e^-5	1	UPSTREAM CG10881 INTRON Gfrl & 1 other
X	8081592	X_8081592_SNP [dm3] X_8187559_SNP [dm6]	A	C	5.483e^-5	1	INTRON sdt	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	11319829	3L_11319829_SNP [dm3] 3L_11326729_SNP [dm6]	T	A	5.561e^-5	1	INTERGENIC
2R	16469876	2R_16469876_SNP [dm3] 2R_20582371_SNP [dm6]	T	A	5.601e^-5	1	UPSTREAM qsm INTRON qsm	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
2L	9154780	2L_9154780_DEL [dm3] 2L_9154780_DEL [dm6]	AG	A	5.601e^-5	1	INTRON CG32982
2L	14478806	2L_14478806_SNP [dm3] 2L_14478806_SNP [dm6]	T	A	5.693e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	14478836	2L_14478836_SNP [dm3] 2L_14478836_SNP [dm6]	A	C	5.693e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	9154802	2L_9154802_SNP [dm3] 2L_9154802_SNP [dm6]	A	G	5.787e^-5	1	INTRON CG32982
2L	16910436	2L_16910436_SNP [dm3] 2L_16910436_SNP [dm6]	C	T	5.863e^-5	1	UPSTREAM ApepP INTRON tweek
2R	19097551	2R_19097551_SNP [dm3] 2R_23210028_SNP [dm6]	T	C	5.906e^-5	1	DOWNSTREAM LS2 INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_hkb mE1_TFBS_HSA mE1_TFBS_sens
X	18017761	X_18017761_INS [dm3] X_18123728_INS [dm6]	A	ACAA	5.985e^-5	1	UPSTREAM mir-969 DOWNSTREAM CR45606 & 1 other INTERGENIC
2R	16665509	2R_16665509_SNP [dm3] 2R_20778004_SNP [dm6]	A	C	6.005e^-5	1	UPSTREAM CG43710 DOWNSTREAM CG43711 INTERGENIC
X	11816530	X_11816530_DEL [dm3] X_11922497_DEL [dm6]	AATC	A	6.188e^-5	1	INTRON Sclp
2L	17037950	2L_17037950_SNP [dm3] 2L_17037950_SNP [dm6]	T	A	6.193e^-5	1	INTERGENIC
3R	3149052	3R_3149052_SNP [dm3] 3R_7323330_SNP [dm6]	G	A	6.197e^-5	1	INTERGENIC
2R	6276504	2R_6276504_SNP [dm3] 2R_10388999_SNP [dm6]	G	T	6.310e^-5	1	INTRON CG42732
3R	3337549	3R_3337549_SNP [dm3] 3R_7511827_SNP [dm6]	T	A	6.396e^-5	1	INTRON alpha-Est8
3L	11319854	3L_11319854_SNP [dm3] 3L_11326754_SNP [dm6]	A	G	6.744e^-5	1	INTERGENIC
X	10428361	X_10428361_SNP [dm3] X_10534328_SNP [dm6]	G	A	6.758e^-5	1	INTRON spri
3L	10075631	3L_10075631_SNP [dm3] 3L_10082531_SNP [dm6]	G	C	6.852e^-5	1	INTRON dpr6
3L	10075632	3L_10075632_SNP [dm3] 3L_10082532_SNP [dm6]	T	A	6.852e^-5	1	INTRON dpr6
2R	12595530	2R_12595530_SNP [dm3] 2R_16708025_SNP [dm6]	G	A	6.959e^-5	1	INTRON CG30463
2R	16966248	2R_16966248_SNP [dm3] 2R_21078743_SNP [dm6]	T	C	6.992e^-5	1	INTRON Treh
2L	14478337	2L_14478337_SNP [dm3] 2L_14478337_SNP [dm6]	C	T	6.994e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Kr
3L	8685912	3L_8685912_SNP [dm3] 3L_8692812_SNP [dm6]	A	G	7.044e^-5	1	EXON CR44526	TF binding site mE1_TFBS_cad
2R	15368957	2R_15368957_SNP [dm3] 2R_19481452_SNP [dm6]	G	A	7.196e^-5	1	UTR_3_PRIME par-1 INTRON par-1
2L	20359515	2L_20359515_SNP [dm3] 2L_20359515_SNP [dm6]	T	G	7.209e^-5	1	DOWNSTREAM RtGEF INTRON RtGEF
3R	3141366	3R_3141366_SNP [dm3] 3R_7315644_SNP [dm6]	G	C	7.228e^-5	1	UTR_3_PRIME CG10029 DOWNSTREAM CG10029
2L	20363184	2L_20363184_SNP [dm3] 2L_20363184_SNP [dm6]	T	C	7.420e^-5	1	UTR_3_PRIME RtGEF INTRON RtGEF	TF binding site mE1_TFBS_cad
2L	11884873	2L_11884873_SNP [dm3] 2L_11884873_SNP [dm6]	A	T	7.424e^-5	1	INTRON Pde1c

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By genomic position
Variant impact
Gene name

se_TAG_Glycerol phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results