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=6.157e^-2)
Null hypothesis is not rejected (p>0.05).
Interpretation: 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_3R_K	5.7555	0.0563

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1117 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	16931983	2R_16931983_SNP [dm3] 2R_21044478_SNP [dm6]	C	A	3.913e^-6	0.924	INTERGENIC
2R	7255745	2R_7255745_SNP [dm3] 2R_11368240_SNP [dm6]	A	T	3.913e^-6	0.924	UPSTREAM CG13204 INTRON CG13204	TF binding site BDTNP1_TFBS_dl
2R	7255762	2R_7255762_DEL [dm3] 2R_11368257_DEL [dm6]	CC	C	3.913e^-6	0.924	UPSTREAM CG13204 INTRON CG13204	TF binding site BDTNP1_TFBS_dl
3R	25948639	3R_25948639_SNP [dm3] 3R_30122917_SNP [dm6]	G	A	5.926e^-6	0.924	SYNONYMOUS_CODING CG45072 DOWNSTREAM CG45073
3R	25948648	3R_25948648_SNP [dm3] 3R_30122926_SNP [dm6]	C	T	5.926e^-6	0.924	SYNONYMOUS_CODING CG45072 DOWNSTREAM CG45073
3R	25948650	3R_25948650_SNP [dm3] 3R_30122928_SNP [dm6]	A	G	5.926e^-6	0.924	SYNONYMOUS_CODING CG45072 DOWNSTREAM CG45073
3R	25948654	3R_25948654_SNP [dm3] 3R_30122932_SNP [dm6]	G	A	5.926e^-6	0.924	SYNONYMOUS_CODING CG45072 DOWNSTREAM CG45073
3R	25948657	3R_25948657_SNP [dm3] 3R_30122935_SNP [dm6]	T	G	5.926e^-6	0.924	SYNONYMOUS_CODING CG45072 DOWNSTREAM CG45073
2R	17076205	2R_17076205_SNP [dm3] 2R_21188700_SNP [dm6]	C	T	1.329e^-5	0.924	SYNONYMOUS_CODING tud
2R	18344690	2R_18344690_DEL [dm3] 2R_22457185_DEL [dm6]	CTT	C	1.584e^-5	0.924	INTRON CG10384
2L	1671772	2L_1671772_SNP [dm3] 2L_1671772_SNP [dm6]	G	A	1.635e^-5	0.924	INTRON chinmo
2L	4495897	2L_4495897_SNP [dm3] 2L_4495897_SNP [dm6]	T	C	1.635e^-5	0.924	SYNONYMOUS_CODING dp INTRON dp	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2L	4495933	2L_4495933_SNP [dm3] 2L_4495933_SNP [dm6]	A	G	1.635e^-5	0.924	SYNONYMOUS_CODING dp INTRON dp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2L	4495948	2L_4495948_SNP [dm3] 2L_4495948_SNP [dm6]	A	T	1.635e^-5	0.924	SYNONYMOUS_CODING dp INTRON dp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2R	3903088	2R_3903088_SNP [dm3] 2R_8015583_SNP [dm6]	G	C	1.635e^-5	0.924	DOWNSTREAM mir-4981 INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	21736718	2L_21736718_SNP [dm3] 2L_21736718_SNP [dm6]	C	G	2.040e^-5	0.924	INTERGENIC	transposable element FlyBase
3L	3785248	3L_3785248_SNP [dm3] 3L_3785248_SNP [dm6]	T	C	2.266e^-5	0.924	INTRON CG32264	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_hkb mE1_TFBS_sens mE1_TFBS_Ubx
3L	3785266	3L_3785266_SNP [dm3] 3L_3785266_SNP [dm6]	G	T	2.266e^-5	0.924	INTRON CG32264	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_hkb mE1_TFBS_sens mE1_TFBS_Ubx
2R	16931982	2R_16931982_SNP [dm3] 2R_21044477_SNP [dm6]	C	A	2.299e^-5	0.924	INTERGENIC
3R	25948696	3R_25948696_SNP [dm3] 3R_30122974_SNP [dm6]	C	T	2.368e^-5	0.924	SYNONYMOUS_CODING CG45072 DOWNSTREAM CG45073
3R	18894023	3R_18894023_SNP [dm3] 3R_23068301_SNP [dm6]	A	C	2.619e^-5	0.924	INTERGENIC	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3L	10616385	3L_10616385_SNP [dm3] 3L_10623285_SNP [dm6]	T	C	3.232e^-5	0.924	SYNONYMOUS_CODING CG42521
3R	18091786	3R_18091786_SNP [dm3] 3R_22266064_SNP [dm6]	C	T	3.306e^-5	0.924	INTRON SKIP
3L	3654797	3L_3654797_SNP [dm3] 3L_3654797_SNP [dm6]	C	T	4.003e^-5	0.924	UPSTREAM CG10862 INTERGENIC
3R	26802966	3R_26802966_SNP [dm3] 3R_30977244_SNP [dm6]	A	C	4.418e^-5	0.924	INTRON 5-HT7
3R	26803004	3R_26803004_SNP [dm3] 3R_30977282_SNP [dm6]	T	A	4.418e^-5	0.924	INTRON 5-HT7
X	2528819	X_2528819_SNP [dm3] X_2634786_SNP [dm6]	G	A	4.984e^-5	0.924	INTRON sgg	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl mE1_TFBS_zfh1
2L	10129860	2L_10129860_SNP [dm3] 2L_10129860_SNP [dm6]	A	G	5.393e^-5	0.924	INTRON CG44153
2L	10129868	2L_10129868_SNP [dm3] 2L_10129868_SNP [dm6]	T	A	5.393e^-5	0.924	INTRON CG44153
2L	10129873	2L_10129873_SNP [dm3] 2L_10129873_SNP [dm6]	T	C	5.393e^-5	0.924	INTRON CG44153
2L	10129876	2L_10129876_SNP [dm3] 2L_10129876_SNP [dm6]	C	T	5.393e^-5	0.924	INTRON CG44153
2R	10835459	2R_10835459_SNP [dm3] 2R_14947954_SNP [dm6]	A	G	5.393e^-5	0.924	SYNONYMOUS_CODING aPKC	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2R	14548532	2R_14548532_SNP [dm3] 2R_18661027_SNP [dm6]	T	G	5.393e^-5	0.924	UPSTREAM Gint3 & 1 other INTRON Gint3 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
2R	14589832	2R_14589832_SNP [dm3] 2R_18702327_SNP [dm6]	C	T	5.393e^-5	0.924	DOWNSTREAM Sik3 INTRON Sik3
2R	14589846	2R_14589846_SNP [dm3] 2R_18702341_SNP [dm6]	T	G	5.393e^-5	0.924	DOWNSTREAM Sik3 INTRON Sik3
2R	19274070	2R_19274070_SNP [dm3] 2R_23386547_SNP [dm6]	A	G	5.393e^-5	0.924	UTR_5_PRIME eIF2B-delta UPSTREAM eIF2B-delta & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_sens
2R	19274286	2R_19274286_SNP [dm3] 2R_23386763_SNP [dm6]	T	A	5.393e^-5	0.924	UPSTREAM eIF2B-delta & 1 other INTRON eIF2B-delta	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
2R	8839726	2R_8839726_SNP [dm3] 2R_12952221_SNP [dm6]	T	G	5.393e^-5	0.924	UTR_5_PRIME CG44251 & 1 other UPSTREAM CG13321
2R	17376406	2R_17376406_SNP [dm3] 2R_21488901_SNP [dm6]	A	C	5.535e^-5	0.924	INTRON Fkbp14
3L	9069091	3L_9069091_SNP [dm3] 3L_9075991_SNP [dm6]	C	A	5.827e^-5	0.924	INTRON Tequila	TF binding site mE1_TFBS_cad
2R	11916989	2R_11916989_SNP [dm3] 2R_16029484_SNP [dm6]	C	T	5.992e^-5	0.924	SPLICE_SITE_REGION CG8401 INTRON CG8401
3L	22412688	3L_22412688_DEL [dm3] 3L_22419588_DEL [dm6]	CCCCAAAGTCGAATCA...	C	5.992e^-5	0.924	INTERGENIC
3L	22412704	3L_22412704_INS [dm3] 3L_22419604_INS [dm6]	T	TTA	5.992e^-5	0.924	INTERGENIC
3L	6197240	3L_6197240_SNP [dm3] 3L_6204140_SNP [dm6]	A	G	5.992e^-5	0.924	UTR_3_PRIME LanA DOWNSTREAM CG8219	TF binding site mE1_TFBS_cad
3R	22469164	3R_22469164_INS [dm3] 3R_26643442_INS [dm6]	A	ACA	5.998e^-5	0.924	INTERGENIC	TF binding site mE1_TFBS_cnc
2R	12762616	2R_12762616_SNP [dm3] 2R_16875111_SNP [dm6]	G	A	6.498e^-5	0.924	UTR_3_PRIME CG8910 DOWNSTREAM CG6435
3R	17518267	3R_17518267_SNP [dm3] 3R_21692545_SNP [dm6]	A	C	6.709e^-5	0.924	INTRON CG31176
3R	17518723	3R_17518723_SNP [dm3] 3R_21693001_SNP [dm6]	T	C	6.709e^-5	0.924	INTRON CG31176
3R	17518770	3R_17518770_SNP [dm3] 3R_21693048_SNP [dm6]	T	C	6.709e^-5	0.924	INTRON CG31176
3R	26236311	3R_26236311_SNP [dm3] 3R_30410589_SNP [dm6]	C	T	6.737e^-5	0.924	INTERGENIC
3R	26236312	3R_26236312_SNP [dm3] 3R_30410590_SNP [dm6]	A	C	6.737e^-5	0.924	INTERGENIC
3R	26238649	3R_26238649_SNP [dm3] 3R_30412927_SNP [dm6]	T	C	6.737e^-5	0.924	INTERGENIC	TF binding site BDTNP1_TFBS_twi
X	792576	X_792576_SNP [dm3] X_898543_SNP [dm6]	A	G	6.782e^-5	0.924	INTRON CG43867
X	851090	X_851090_SNP [dm3] X_957057_SNP [dm6]	G	A	6.782e^-5	0.924	INTERGENIC	TF binding site mE1_TFBS_chinmo
2R	18201959	2R_18201959_SNP [dm3] 2R_22314454_SNP [dm6]	T	G	6.913e^-5	0.924	INTRON CR44758
2R	17685567	2R_17685567_SNP [dm3] 2R_21798062_SNP [dm6]	T	A	7.126e^-5	0.924	UTR_3_PRIME CG18735	TF binding site mE1_TFBS_chinmo
2R	17685580	2R_17685580_SNP [dm3] 2R_21798075_SNP [dm6]	A	T	7.126e^-5	0.924	SYNONYMOUS_CODING CG18735	TF binding site mE1_TFBS_chinmo
2R	19814078	2R_19814078_SNP [dm3] 2R_23926555_SNP [dm6]	C	T	7.126e^-5	0.924	UTR_3_PRIME Ca-P60A DOWNSTREAM Ca-P60A INTRON CG2812	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2L	4496151	2L_4496151_SNP [dm3] 2L_4496151_SNP [dm6]	C	T	7.138e^-5	0.924	NON_SYNONYMOUS_CODING dp INTRON dp	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	11119645	3L_11119645_INS [dm3] 3L_11126545_INS [dm6]	C	CCTGCC	7.138e^-5	0.924	INTRON CG42575	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA
3L	11119952	3L_11119952_SNP [dm3] 3L_11126852_SNP [dm6]	G	C	7.138e^-5	0.924	INTRON CG42575	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA
3R	20822964	3R_20822964_SNP [dm3] 3R_24997242_SNP [dm6]	A	G	7.138e^-5	0.924	INTRON tnc	TF binding site mE1_TFBS_chinmo
X	9201625	X_9201625_INS [dm3] X_9307592_INS [dm6]	A	ATGA	7.220e^-5	0.924	INTERGENIC
2R	7287157	2R_7287157_SNP [dm3] 2R_11399652_SNP [dm6]	G	C	7.314e^-5	0.924	DOWNSTREAM tRNA:CR30506 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	7287174	2R_7287174_INS [dm3] 2R_11399669_INS [dm6]	T	TG	7.314e^-5	0.924	DOWNSTREAM tRNA:CR30506 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	2357337	3R_2357337_INS [dm3] 3R_6531615_INS [dm6]	C	CGTC	7.518e^-5	0.924	UTR_3_PRIME dpr11
2R	17718701	2R_17718701_SNP [dm3] 2R_21831196_SNP [dm6]	T	A	8.023e^-5	0.924	INTRON CG13492
3R	23978622	3R_23978622_SNP [dm3] 3R_28152900_SNP [dm6]	T	C	8.023e^-5	0.924	INTRON CG34354
X	19361793	X_19361793_SNP [dm3] X_19467760_SNP [dm6]	G	T	8.023e^-5	0.924	INTRON kek5
X	19361818	X_19361818_SNP [dm3] X_19467785_SNP [dm6]	A	G	8.023e^-5	0.924	INTRON kek5
X	19361824	X_19361824_SNP [dm3] X_19467791_SNP [dm6]	C	T	8.023e^-5	0.924	INTRON kek5
3R	17518204	3R_17518204_SNP [dm3] 3R_21692482_SNP [dm6]	T	C	8.117e^-5	0.924	INTRON CG31176
3R	23820287	3R_23820287_SNP [dm3] 3R_27994565_SNP [dm6]	T	A	8.584e^-5	0.924	INTERGENIC
2L	8755034	2L_8755034_SNP [dm3] 2L_8755034_SNP [dm6]	C	G	8.585e^-5	0.924	INTERGENIC
X	12243357	X_12243357_SNP [dm3] X_12349324_SNP [dm6]	T	A	9.121e^-5	0.924	INTERGENIC	TF binding site BDTNP1_TFBS_dl
3L	3845078	3L_3845078_SNP [dm3] 3L_3845078_SNP [dm6]	C	A	9.283e^-5	0.924	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_HSA
2R	9348162	2R_9348162_SNP [dm3] 2R_13460657_SNP [dm6]	A	T	9.297e^-5	0.924	INTRON arr	TF binding site mE1_TFBS_chinmo
3L	9288639	3L_9288639_SNP [dm3] 3L_9295539_SNP [dm6]	T	C	9.536e^-5	0.924	INTERGENIC
2L	14044070	2L_14044070_SNP [dm3] 2L_14044070_SNP [dm6]	C	A	9.662e^-5	0.924	INTRON nAChRalpha5	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	20141297	2L_20141297_SNP [dm3] 2L_20141297_SNP [dm6]	C	G	1.008e^-4	0.924	INTERGENIC
2L	20141313	2L_20141313_SNP [dm3] 2L_20141313_SNP [dm6]	A	T	1.008e^-4	0.924	INTERGENIC
2L	20141508	2L_20141508_SNP [dm3] 2L_20141508_SNP [dm6]	C	A	1.008e^-4	0.924	INTERGENIC
2L	20142242	2L_20142242_SNP [dm3] 2L_20142242_SNP [dm6]	A	T	1.008e^-4	0.924	INTERGENIC
3R	26803104	3R_26803104_SNP [dm3] 3R_30977382_SNP [dm6]	A	T	1.037e^-4	0.924	INTRON 5-HT7
3L	2389151	3L_2389151_SNP [dm3] 3L_2389151_SNP [dm6]	G	T	1.045e^-4	0.924	UPSTREAM CG42787 DOWNSTREAM CG32299 & 1 other INTRON CG45186
2R	14344113	2R_14344113_SNP [dm3] 2R_18456608_SNP [dm6]	T	A	1.110e^-4	0.924	UTR_3_PRIME CG30116 DOWNSTREAM CG30116
2R	19414266	2R_19414266_SNP [dm3] 2R_23526743_SNP [dm6]	C	T	1.110e^-4	0.924	INTRON mi	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	12295018	3L_12295018_SNP [dm3] 3L_12301918_SNP [dm6]	G	C	1.110e^-4	0.924	DOWNSTREAM CR44551 EXON CR44550
3L	12295019	3L_12295019_SNP [dm3] 3L_12301919_SNP [dm6]	T	G	1.110e^-4	0.924	DOWNSTREAM CR44551 EXON CR44550
3L	12295085	3L_12295085_SNP [dm3] 3L_12301985_SNP [dm6]	A	G	1.110e^-4	0.924	DOWNSTREAM CR44551 & 1 other INTERGENIC
3L	12295091	3L_12295091_SNP [dm3] 3L_12301991_SNP [dm6]	A	G	1.110e^-4	0.924	DOWNSTREAM CR44551 & 1 other INTERGENIC
3L	12295123	3L_12295123_SNP [dm3] 3L_12302023_SNP [dm6]	G	A	1.110e^-4	0.924	DOWNSTREAM CR44551 & 1 other INTERGENIC
2L	1430755	2L_1430755_SNP [dm3] 2L_1430755_SNP [dm6]	C	T	1.154e^-4	0.924	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	1473790	2L_1473790_SNP [dm3] 2L_1473790_SNP [dm6]	C	A	1.154e^-4	0.924	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	19213603	2L_19213603_SNP [dm3] 2L_19213603_SNP [dm6]	A	G	1.154e^-4	0.924	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	22138597	2L_22138597_SNP [dm3] 2L_22138597_SNP [dm6]	A	G	1.154e^-4	0.924	INTRON CG42748	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
2L	3017690	2L_3017690_SNP [dm3] 2L_3017690_SNP [dm6]	C	A	1.154e^-4	0.924	SYNONYMOUS_CODING CG17224 UPSTREAM CG17264
2L	4726622	2L_4726622_SNP [dm3] 2L_4726622_SNP [dm6]	C	A	1.154e^-4	0.924	INTERGENIC	TF binding site mE1_TFBS_bab1
2R	2484053	2R_2484053_DEL [dm3] 2R_6596548_DEL [dm6]	GGAAGCG	G	1.154e^-4	0.924	INTRON jing	TF binding site BDTNP1_TFBS_dl
3R	21594364	3R_21594364_SNP [dm3] 3R_25768642_SNP [dm6]	G	T	1.218e^-4	0.924	INTERGENIC

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Missing results

By genomic position
Variant impact
Gene name

Ma549 LT50 (Wang et al 2017) phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results