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=3.483e^-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_2L_t	0.004008
In_2R_NS	0.077319

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
wolba	3.8041	0.0511
In_2L_t	8.2297	0.0163

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2198 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	5747125	2L_5747125_SNP [dm3] 2L_5747125_SNP [dm6]	G	A	1.972e^-6	0.718	SYNONYMOUS_CODING CG11029 INTRON CG11030	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
X	559628	X_559628_SNP [dm3] X_665595_SNP [dm6]	T	G	2.518e^-6	0.718	INTERGENIC	transposable element FlyBase
X	561877	X_561877_INS [dm3] X_667844_INS [dm6]	T	TTGT	3.198e^-6	0.718	INTERGENIC
3L	9166538	3L_9166538_SNP [dm3] 3L_9173438_SNP [dm6]	T	G	3.901e^-6	0.718	INTRON Rdl
3L	9170222	3L_9170222_SNP [dm3] 3L_9177122_SNP [dm6]	G	T	4.578e^-6	0.718	NON_SYNONYMOUS_CODING Rdl
3R	20444019	3R_20444019_SNP [dm3] 3R_24618297_SNP [dm6]	G	T	5.387e^-6	0.718	SYNONYMOUS_CODING mld	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3L	1699511	3L_1699511_SNP [dm3] 3L_1699511_SNP [dm6]	G	A	5.578e^-6	0.718	INTRON CG7991	TF binding site BDTNP1_TFBS_prd mE1_TFBS_HSA
X	561814	X_561814_SNP [dm3] X_667781_SNP [dm6]	G	C	5.870e^-6	0.718	INTERGENIC
2L	20535175	2L_20535175_SNP [dm3] 2L_20535175_SNP [dm6]	C	G	5.957e^-6	0.718	INTERGENIC
3R	5045868	3R_5045868_DEL [dm3] 3R_9220146_DEL [dm6]	AGAATAA	A	6.250e^-6	0.718	INTRON pum	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
3L	12699669	3L_12699669_SNP [dm3] 3L_12706569_SNP [dm6]	C	A	6.252e^-6	0.718	INTRON mirr	TF binding site BDTNP1_TFBS_da
3L	9355374	3L_9355374_SNP [dm3] 3L_9362274_SNP [dm6]	A	G	6.544e^-6	0.718	NON_SYNONYMOUS_CODING CG34456 DOWNSTREAM Klp67A & 1 other
3R	27111773	3R_27111773_SNP [dm3] 3R_31286051_SNP [dm6]	A	C	6.659e^-6	0.718	INTERGENIC
X	559663	X_559663_SNP [dm3] X_665630_SNP [dm6]	A	G	6.761e^-6	0.718	INTERGENIC	transposable element FlyBase
3L	9168818	3L_9168818_DEL [dm3] 3L_9175718_DEL [dm6]	ACAACTCAGCTA...	A	6.803e^-6	0.718	INTRON Rdl
2L	6019103	2L_6019103_SNP [dm3] 2L_6019103_SNP [dm6]	T	C	6.959e^-6	0.718	NON_SYNONYMOUS_CODING H2.0	TF binding site BDTNP1_TFBS_slp1 mE1_TFBS_cad mE1_TFBS_sens
3L	13203554	3L_13203554_SNP [dm3] 3L_13210454_SNP [dm6]	A	T	7.379e^-6	0.718	UPSTREAM tRNA:CR32129 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	12699724	3L_12699724_SNP [dm3] 3L_12706624_SNP [dm6]	T	A	7.481e^-6	0.718	INTRON mirr	TF binding site BDTNP1_TFBS_da
X	569303	X_569303_SNP [dm3] X_675270_SNP [dm6]	A	G	7.854e^-6	0.718	INTERGENIC	TF binding site BDTNP1_TFBS_twi
X	563131	X_563131_SNP [dm3] X_669098_SNP [dm6]	T	C	7.885e^-6	0.718	INTERGENIC
3R	14317672	3R_14317672_SNP [dm3] 3R_18491950_SNP [dm6]	G	A	9.066e^-6	0.745	INTRON fru	TF binding site BDTNP1_TFBS_twi
3R	23177373	3R_23177373_SNP [dm3] 3R_27351651_SNP [dm6]	T	A	9.503e^-6	0.745	INTRON CG42534
X	559604	X_559604_SNP [dm3] X_665571_SNP [dm6]	T	C	9.773e^-6	0.745	INTERGENIC	transposable element FlyBase
X	559630	X_559630_INS [dm3] X_665597_INS [dm6]	T	TGAATCTC	1.053e^-5	0.745	INTERGENIC	transposable element FlyBase
3L	11539460	3L_11539460_SNP [dm3] 3L_11546360_SNP [dm6]	C	T	1.057e^-5	0.745	INTRON Mob2
2R	16857695	2R_16857695_SNP [dm3] 2R_20970190_SNP [dm6]	A	C	1.089e^-5	0.745	INTERGENIC	TF binding site BDTNP1_TFBS_dl
X	569338	X_569338_SNP [dm3] X_675305_SNP [dm6]	G	A	1.109e^-5	0.745	INTERGENIC	TF binding site BDTNP1_TFBS_twi
2R	16199736	2R_16199736_SNP [dm3] 2R_20312231_SNP [dm6]	T	C	1.241e^-5	0.745	INTRON CG13868	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	12682419	3L_12682419_SNP [dm3] 3L_12689319_SNP [dm6]	G	C	1.248e^-5	0.745	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	560903	X_560903_SNP [dm3] X_666870_SNP [dm6]	A	G	1.279e^-5	0.745	INTERGENIC
X	561734	X_561734_DEL [dm3] X_667701_DEL [dm6]	GAATTACAAGCTAAACGTGA...	G	1.335e^-5	0.745	INTERGENIC
2R	9704862	2R_9704862_SNP [dm3] 2R_13817357_SNP [dm6]	A	G	1.337e^-5	0.745	SYNONYMOUS_CODING stj	TF binding site BDTNP1_TFBS_twi
X	561830	X_561830_SNP [dm3] X_667797_SNP [dm6]	C	G	1.405e^-5	0.745	INTERGENIC
2L	3481218	2L_3481218_SNP [dm3] 2L_3481218_SNP [dm6]	C	T	1.519e^-5	0.745	SYNONYMOUS_CODING CG15414	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
X	559535	X_559535_SNP [dm3] X_665502_SNP [dm6]	T	G	1.575e^-5	0.745	INTERGENIC	transposable element FlyBase
3L	1699505	3L_1699505_SNP [dm3] 3L_1699505_SNP [dm6]	G	T	1.580e^-5	0.745	INTRON CG7991	TF binding site BDTNP1_TFBS_prd mE1_TFBS_HSA
3R	16009334	3R_16009334_SNP [dm3] 3R_20183612_SNP [dm6]	T	C	1.620e^-5	0.745	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	14317712	3R_14317712_SNP [dm3] 3R_18491990_SNP [dm6]	G	C	1.625e^-5	0.745	INTRON fru
3R	27111842	3R_27111842_SNP [dm3] 3R_31286120_SNP [dm6]	A	C	1.691e^-5	0.745	INTERGENIC
X	559524	X_559524_SNP [dm3] X_665491_SNP [dm6]	A	G	1.695e^-5	0.745	INTERGENIC	transposable element FlyBase
2L	9765982	2L_9765982_SNP [dm3] 2L_9765982_SNP [dm6]	G	T	1.767e^-5	0.745	SYNONYMOUS_CODING ppk18 DOWNSTREAM und
3L	16145231	3L_16145231_SNP [dm3] 3L_16152131_SNP [dm6]	C	T	1.805e^-5	0.745	INTRON CG5151
X	573103	X_573103_SNP [dm3] X_679070_SNP [dm6]	C	G	1.811e^-5	0.745	INTERGENIC	TF binding site mE1_TFBS_chinmo
2L	2852345	2L_2852345_SNP [dm3] 2L_2852345_SNP [dm6]	G	A	1.897e^-5	0.745	INTRON CG3104
X	570408	X_570408_SNP [dm3] X_676375_SNP [dm6]	A	T	1.924e^-5	0.745	INTERGENIC	TF binding site BDTNP1_TFBS_prd mE1_TFBS_HSA
2R	9704679	2R_9704679_SNP [dm3] 2R_13817174_SNP [dm6]	T	C	1.965e^-5	0.745	SYNONYMOUS_CODING stj	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
X	565423	X_565423_SNP [dm3] X_671390_SNP [dm6]	G	A	1.966e^-5	0.745	INTERGENIC
3L	5206340	3L_5206340_SNP [dm3] 3L_5213240_SNP [dm6]	A	C	1.973e^-5	0.745	INTRON shep
3R	26403224	3R_26403224_SNP [dm3] 3R_30577502_SNP [dm6]	C	A	2.038e^-5	0.745	UTR_3_PRIME tmod INTRON tmod
X	561268	X_561268_SNP [dm3] X_667235_SNP [dm6]	T	A	2.115e^-5	0.745	INTERGENIC
3L	10858300	3L_10858300_SNP [dm3] 3L_10865200_SNP [dm6]	C	A	2.144e^-5	0.745	INTRON tna	TF binding site BDTNP1_TFBS_dl
X	564281	X_564281_DEL [dm3] X_670248_DEL [dm6]	TGCGCCCAGTTTT...	T	2.184e^-5	0.745	INTERGENIC
X	560352	X_560352_SNP [dm3] X_666319_SNP [dm6]	A	G	2.234e^-5	0.745	INTERGENIC
3L	9357894	3L_9357894_SNP [dm3] 3L_9364794_SNP [dm6]	C	A	2.236e^-5	0.745	SYNONYMOUS_CODING CG4447 INTRON Klp67A	TF binding site mE1_TFBS_cad mE1_TFBS_sens
3L	6179221	3L_6179221_SNP [dm3] 3L_6186121_SNP [dm6]	T	C	2.327e^-5	0.745	UTR_3_PRIME D19A DOWNSTREAM CG43293	TF binding site mE1_TFBS_cad
3L	1090646	3L_1090646_SNP [dm3] 3L_1090646_SNP [dm6]	C	T	2.363e^-5	0.745	INTRON bab1	regulatory region REDfly_CRMs
3L	12699672	3L_12699672_SNP [dm3] 3L_12706572_SNP [dm6]	T	G	2.438e^-5	0.745	INTRON mirr	TF binding site BDTNP1_TFBS_da
X	564852	X_564852_INS [dm3] X_670819_INS [dm6]	T	TT	2.531e^-5	0.745	INTERGENIC
3L	5206309	3L_5206309_SNP [dm3] 3L_5213209_SNP [dm6]	A	C	2.583e^-5	0.745	INTRON shep	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3L	5649135	3L_5649135_SNP [dm3] 3L_5656035_SNP [dm6]	C	A	2.584e^-5	0.745	INTRON lin-28	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3R	16009296	3R_16009296_INS [dm3] 3R_20183574_INS [dm6]	C	CA	2.634e^-5	0.745	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
X	574223	X_574223_SNP [dm3] X_680190_SNP [dm6]	G	T	2.662e^-5	0.745	INTERGENIC
X	13544884	X_13544884_INS [dm3] X_13650851_INS [dm6]	A	AT	2.696e^-5	0.745	INTRON NFAT	TF binding site mE1_TFBS_HSA
3R	26323796	3R_26323796_SNP [dm3] 3R_30498074_SNP [dm6]	C	A	2.745e^-5	0.745	INTRON PH4alphaNE1	TF binding site mE1_TFBS_chinmo
2R	9709385	2R_9709385_SNP [dm3] 2R_13821880_SNP [dm6]	T	G	2.857e^-5	0.745	UTR_5_PRIME fl_2_d INTRON fl_2_d
3L	8662324	3L_8662324_SNP [dm3] 3L_8669224_SNP [dm6]	C	A	2.904e^-5	0.745	INTERGENIC	regulatory region FlyBase TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb mE1_TFBS_cad
2L	5746522	2L_5746522_SNP [dm3] 2L_5746522_SNP [dm6]	T	C	2.961e^-5	0.745	SYNONYMOUS_CODING CG11029 INTRON CG11030	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
X	21138010	X_21138010_SNP [dm3] X_21266983_SNP [dm6]	T	C	3.029e^-5	0.745	INTRON CG32521
2R	13089762	2R_13089762_SNP [dm3] 2R_17202257_SNP [dm6]	G	A	3.043e^-5	0.745	INTERGENIC
2R	13089765	2R_13089765_SNP [dm3] 2R_17202260_SNP [dm6]	G	T	3.043e^-5	0.745	INTERGENIC
3L	805889	3L_805889_DEL [dm3] 3L_805889_DEL [dm6]	CA	C	3.068e^-5	0.745	INTERGENIC
2L	2827343	2L_2827343_SNP [dm3] 2L_2827343_SNP [dm6]	G	A	3.201e^-5	0.745	INTRON Duox
3R	21268751	3R_21268751_DEL [dm3] 3R_25443029_DEL [dm6]	TCCG	T	3.210e^-5	0.745	INTRON Fur1
2L	10746788	2L_10746788_SNP [dm3] 2L_10746788_SNP [dm6]	C	G	3.269e^-5	0.745	INTRON CG17124	TF binding site BDTNP1_TFBS_twi
X	563840	X_563840_SNP [dm3] X_669807_SNP [dm6]	T	G	3.280e^-5	0.745	INTERGENIC
X	566584	X_566584_SNP [dm3] X_672551_SNP [dm6]	G	C	3.308e^-5	0.745	INTERGENIC
3L	606777	3L_606777_SNP [dm3] 3L_606777_SNP [dm6]	C	G	3.330e^-5	0.745	UPSTREAM Reg-2 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_HSA
3R	25484621	3R_25484621_SNP [dm3] 3R_29658899_SNP [dm6]	T	C	3.373e^-5	0.745	UTR_5_PRIME Dop1R2
X	559552	X_559552_SNP [dm3] X_665519_SNP [dm6]	G	T	3.388e^-5	0.745	INTERGENIC	transposable element FlyBase
2R	18440073	2R_18440073_SNP [dm3] 2R_22552568_SNP [dm6]	A	T	3.460e^-5	0.745	DOWNSTREAM CG6018 INTRON px
3L	6578275	3L_6578275_SNP [dm3] 3L_6585175_SNP [dm6]	A	T	3.470e^-5	0.745	INTRON CG18769 & 1 other
2L	958456	2L_958456_SNP [dm3] 2L_958456_SNP [dm6]	A	G	3.474e^-5	0.745	DOWNSTREAM CG4341 INTERGENIC	TF binding site mE1_TFBS_chinmo
2L	15038076	2L_15038076_SNP [dm3] 2L_15038076_SNP [dm6]	T	C	3.512e^-5	0.745	NON_SYNONYMOUS_CODING CIAPIN1 DOWNSTREAM yellow-c	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cnc mE1_TFBS_sens
X	525143	X_525143_SNP [dm3] X_631110_SNP [dm6]	G	A	3.515e^-5	0.745	SYNONYMOUS_CODING l_1_1Bi	TF binding site mE1_TFBS_inv mE1_TFBS_sens
3L	10545793	3L_10545793_SNP [dm3] 3L_10552693_SNP [dm6]	T	G	3.612e^-5	0.745	INTRON A2bp1
2R	9704742	2R_9704742_SNP [dm3] 2R_13817237_SNP [dm6]	T	C	3.749e^-5	0.745	SYNONYMOUS_CODING stj	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	14317690	3R_14317690_SNP [dm3] 3R_18491968_SNP [dm6]	A	C	3.781e^-5	0.745	INTRON fru	TF binding site BDTNP1_TFBS_twi
3R	14170951	3R_14170951_DEL [dm3] 3R_18345229_DEL [dm6]	GA	G	3.781e^-5	0.745	INTRON CG15803
3L	12682391	3L_12682391_SNP [dm3] 3L_12689291_SNP [dm6]	A	C	3.796e^-5	0.745	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	12103714	3L_12103714_SNP [dm3] 3L_12110614_SNP [dm6]	A	T	3.818e^-5	0.745	INTERGENIC
3L	10001087	3L_10001087_SNP [dm3] 3L_10007987_SNP [dm6]	G	A	3.896e^-5	0.745	INTRON dpr6
2L	4717413	2L_4717413_SNP [dm3] 2L_4717413_SNP [dm6]	A	T	3.948e^-5	0.745	INTRON CG34351	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
X	18182577	X_18182577_SNP [dm3] X_18288544_SNP [dm6]	A	T	4.045e^-5	0.745	INTERGENIC	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad mE1_TFBS_inv
X	21138227	X_21138227_SNP [dm3] X_21267200_SNP [dm6]	A	T	4.052e^-5	0.745	INTRON CG32521
3L	5522754	3L_5522754_SNP [dm3] 3L_5529654_SNP [dm6]	C	T	4.074e^-5	0.745	UPSTREAM Lkr INTERGENIC
X	564349	X_564349_DEL [dm3] X_670316_DEL [dm6]	TCACCACAGGGGGCGGCGGG...	T	4.106e^-5	0.745	INTERGENIC
3R	10936838	3R_10936838_SNP [dm3] 3R_15111116_SNP [dm6]	T	C	4.145e^-5	0.745	INTRON CG42788
X	4042038	X_4042038_SNP [dm3] X_4148005_SNP [dm6]	T	C	4.152e^-5	0.745	INTRON Fas2	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
X	4042041	X_4042041_SNP [dm3] X_4148008_SNP [dm6]	T	G	4.152e^-5	0.745	INTRON Fas2	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
X	557374	X_557374_SNP [dm3] X_663341_SNP [dm6]	G	C	4.193e^-5	0.745	INTERGENIC	TF binding site mE1_TFBS_sens

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By genomic position
Variant impact
Gene name

mn_Aggressi_Isolated phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results