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=2.898e^-16)
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

3145 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
3L	12377573	3L_12377573_INS [dm3] 3L_12384473_INS [dm6]	T	TGGTGCATGTAAGTACGTGA...	7.859e^-8	0.07	INTRON Ncc69
2L	9469433	2L_9469433_SNP [dm3] 2L_9469433_SNP [dm6]	C	T	1.457e^-7	0.07	UPSTREAM CR43769 INTERGENIC
X	9868764	X_9868764_SNP [dm3] X_9974731_SNP [dm6]	G	A	2.021e^-7	0.07	INTRON CG43386
3L	18213459	3L_18213459_DEL [dm3] 3L_18220359_DEL [dm6]	GAACCA	G	2.247e^-7	0.07	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Kr mE1_TFBS_zfh1
3L	18213468	3L_18213468_SNP [dm3] 3L_18220368_SNP [dm6]	A	G	2.247e^-7	0.07	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Kr mE1_TFBS_zfh1
3L	18213472	3L_18213472_SNP [dm3] 3L_18220372_SNP [dm6]	T	A	2.247e^-7	0.07	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Kr mE1_TFBS_zfh1
2L	9280130	2L_9280130_SNP [dm3] 2L_9280130_SNP [dm6]	A	T	5.337e^-7	0.119	INTRON Ggamma30A
3L	12377557	3L_12377557_SNP [dm3] 3L_12384457_SNP [dm6]	A	T	5.403e^-7	0.119	INTRON Ncc69
2L	9280176	2L_9280176_SNP [dm3] 2L_9280176_SNP [dm6]	T	G	5.703e^-7	0.119	INTRON Ggamma30A
3L	8606750	3L_8606750_SNP [dm3] 3L_8613650_SNP [dm6]	C	T	7.060e^-7	0.132	SPLICE_SITE_REGION CG6282 INTRON CG6282
3L	5238270	3L_5238270_SNP [dm3] 3L_5245170_SNP [dm6]	A	G	8.827e^-7	0.151	INTRON shep
3R	14626457	3R_14626457_SNP [dm3] 3R_18800735_SNP [dm6]	T	G	9.764e^-7	0.153	UTR_3_PRIME CG18208
X	7489772	X_7489772_SNP [dm3] X_7595739_SNP [dm6]	T	A	1.153e^-6	0.166	INTERGENIC	regulatory region REDfly_CRMs
2L	8893211	2L_8893211_SNP [dm3] 2L_8893211_SNP [dm6]	G	A	1.314e^-6	0.176	INTERGENIC
2L	8892181	2L_8892181_SNP [dm3] 2L_8892181_SNP [dm6]	C	T	1.655e^-6	0.207	DOWNSTREAM CG42713 INTERGENIC
X	10280202	X_10280202_DEL [dm3] X_10386169_DEL [dm6]	TT	T	1.959e^-6	0.23	UTR_5_PRIME flw UPSTREAM Psf3	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	1264742	3R_1264742_SNP [dm3] 3R_5439020_SNP [dm6]	T	C	2.516e^-6	0.254	INTRON CG14669	TF binding site BDTNP1_TFBS_ftz mE1_TFBS_HSA
3L	12377542	3L_12377542_SNP [dm3] 3L_12384442_SNP [dm6]	G	A	2.529e^-6	0.254	INTRON Ncc69
2L	10461455	2L_10461455_SNP [dm3] 2L_10461455_SNP [dm6]	T	C	2.581e^-6	0.254	SYNONYMOUS_CODING LM408	TF binding site mE1_TFBS_cad
2R	18436654	2R_18436654_SNP [dm3] 2R_22549149_SNP [dm6]	C	A	2.705e^-6	0.254	UPSTREAM CG6018 INTRON px
2L	9280115	2L_9280115_SNP [dm3] 2L_9280115_SNP [dm6]	A	T	3.242e^-6	0.282	INTRON Ggamma30A
X	15579895	X_15579895_SNP [dm3] X_15685862_SNP [dm6]	A	T	3.438e^-6	0.282	NON_SYNONYMOUS_CODING CG15599	TF binding site BDTNP1_TFBS_prd mE1_TFBS_sens
2R	18439022	2R_18439022_SNP [dm3] 2R_22551517_SNP [dm6]	T	C	3.463e^-6	0.282	SYNONYMOUS_CODING CG6018 INTRON px	TF binding site mE1_TFBS_cad mE1_TFBS_sens
3L	18213474	3L_18213474_SNP [dm3] 3L_18220374_SNP [dm6]	C	G	3.981e^-6	0.286	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Kr mE1_TFBS_zfh1
3L	12377544	3L_12377544_SNP [dm3] 3L_12384444_SNP [dm6]	T	A	4.154e^-6	0.286	INTRON Ncc69
2L	7063426	2L_7063426_SNP [dm3] 2L_7063426_SNP [dm6]	A	T	4.155e^-6	0.286	UTR_3_PRIME Mnn1 UPSTREAM Sem1 DOWNSTREAM Mnn1	TF binding site mE1_TFBS_cnc
3R	14626385	3R_14626385_SNP [dm3] 3R_18800663_SNP [dm6]	T	C	4.170e^-6	0.286	UTR_3_PRIME CG18208
3R	7174174	3R_7174174_SNP [dm3] 3R_11348452_SNP [dm6]	A	G	4.316e^-6	0.286	UTR_5_PRIME KP78b UTR_3_PRIME KP78a UPSTREAM KP78b INTRON pros	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_sens
X	5364874	X_5364874_SNP [dm3] X_5470841_SNP [dm6]	C	T	4.428e^-6	0.286	INTRON SPR
2L	8891353	2L_8891353_SNP [dm3] 2L_8891353_SNP [dm6]	T	G	4.811e^-6	0.297	UPSTREAM CG42713 INTERGENIC
3R	14626440	3R_14626440_SNP [dm3] 3R_18800718_SNP [dm6]	G	C	4.907e^-6	0.297	UTR_3_PRIME CG18208
2L	15800951	2L_15800951_SNP [dm3] 2L_15800951_SNP [dm6]	G	A	5.155e^-6	0.298	INTERGENIC
X	19158571	X_19158571_SNP [dm3] X_19264538_SNP [dm6]	T	A	5.403e^-6	0.298	INTRON Vav	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
3L	1679278	3L_1679278_SNP [dm3] 3L_1679278_SNP [dm6]	A	C	5.510e^-6	0.298	INTRON CG7991
X	5364846	X_5364846_SNP [dm3] X_5470813_SNP [dm6]	T	C	5.626e^-6	0.298	INTRON SPR
3L	19439891	3L_19439891_SNP [dm3] 3L_19446791_SNP [dm6]	G	A	5.746e^-6	0.298	UPSTREAM Chd3 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
X	11237150	X_11237150_INS [dm3] X_11343117_INS [dm6]	T	TT	5.885e^-6	0.298	INTRON CG34348
X	19158603	X_19158603_DEL [dm3] X_19264570_DEL [dm6]	TCCTATCTCTGTCT...	T	7.025e^-6	0.313	INTRON Vav	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
3R	1266966	3R_1266966_SNP [dm3] 3R_5441244_SNP [dm6]	C	T	7.027e^-6	0.313	INTRON CG14669
3L	8606061	3L_8606061_SNP [dm3] 3L_8612961_SNP [dm6]	C	T	7.115e^-6	0.313	INTRON CG6282
X	15452358	X_15452358_SNP [dm3] X_15558325_SNP [dm6]	T	G	7.153e^-6	0.313	INTERGENIC
X	17746469	X_17746469_SNP [dm3] X_17852436_SNP [dm6]	C	T	7.270e^-6	0.313	NON_SYNONYMOUS_CODING CG32554 DOWNSTREAM CG6506 & 1 other	TF binding site BDTNP1_TFBS_dl
2L	9280177	2L_9280177_SNP [dm3] 2L_9280177_SNP [dm6]	A	G	7.451e^-6	0.313	INTRON Ggamma30A
3L	18213458	3L_18213458_SNP [dm3] 3L_18220358_SNP [dm6]	G	T	7.481e^-6	0.313	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Kr mE1_TFBS_zfh1
X	7480202	X_7480202_SNP [dm3] X_7586169_SNP [dm6]	A	G	7.745e^-6	0.313	UPSTREAM CG12689 INTERGENIC	regulatory region REDfly_CRMs
2L	9281645	2L_9281645_INS [dm3] 2L_9281645_INS [dm6]	T	TAAATA	7.787e^-6	0.313	INTRON Ggamma30A
X	2365996	X_2365996_SNP [dm3] X_2471963_SNP [dm6]	A	C	7.846e^-6	0.313	INTRON trol
X	20023391	X_20023391_SNP [dm3] X_20129358_SNP [dm6]	T	A	8.242e^-6	0.322	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
3L	2834652	3L_2834652_SNP [dm3] 3L_2834652_SNP [dm6]	G	A	8.684e^-6	0.331	INTRON CG43444
2L	5806748	2L_5806748_SNP [dm3] 2L_5806748_SNP [dm6]	A	G	8.908e^-6	0.331	SYNONYMOUS_CODING CG11034 UTR_3_PRIME CG11034	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2L	11485213	2L_11485213_SNP [dm3] 2L_11485213_SNP [dm6]	A	G	9.007e^-6	0.331	UTR_5_PRIME CG43355 & 1 other UPSTREAM sala	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad
2L	9280160	2L_9280160_SNP [dm3] 2L_9280160_SNP [dm6]	T	A	9.179e^-6	0.331	INTRON Ggamma30A
2L	11485212	2L_11485212_SNP [dm3] 2L_11485212_SNP [dm6]	C	T	9.617e^-6	0.336	UTR_5_PRIME CG43355 & 1 other UPSTREAM sala	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad
3R	5140182	3R_5140182_SNP [dm3] 3R_9314460_SNP [dm6]	G	T	9.670e^-6	0.336	INTRON CG8861
X	16129102	X_16129102_SNP [dm3] X_16235069_SNP [dm6]	G	A	1.003e^-5	0.34	INTERGENIC
X	18154327	X_18154327_SNP [dm3] X_18260294_SNP [dm6]	A	G	1.017e^-5	0.34	UPSTREAM CG15059 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3R	7224260	3R_7224260_SNP [dm3] 3R_11398538_SNP [dm6]	C	A	1.079e^-5	0.349	UTR_3_PRIME pros
2R	14072994	2R_14072994_SNP [dm3] 2R_18185489_SNP [dm6]	G	C	1.102e^-5	0.349	INTRON CG33958	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	7098803	3R_7098803_SNP [dm3] 3R_11273081_SNP [dm6]	C	A	1.111e^-5	0.349	INTRON CR31386
X	10381386	X_10381386_SNP [dm3] X_10487353_SNP [dm6]	C	A	1.118e^-5	0.349	UPSTREAM CG32687 INTERGENIC
2L	8096361	2L_8096361_INS [dm3] 2L_8096361_INS [dm6]	C	CGGTTTTCTTTAAAT...	1.145e^-5	0.349	INTRON Bsg
X	11737371	X_11737371_SNP [dm3] X_11843338_SNP [dm6]	T	C	1.154e^-5	0.349	SYNONYMOUS_CODING CG15740	TF binding site BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	19439872	3L_19439872_SNP [dm3] 3L_19446772_SNP [dm6]	G	A	1.217e^-5	0.362	UPSTREAM Chd3 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
3L	3800402	3L_3800402_SNP [dm3] 3L_3800402_SNP [dm6]	T	G	1.236e^-5	0.362	NON_SYNONYMOUS_CODING CG32264 INTRON CG32264	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
X	16095942	X_16095942_SNP [dm3] X_16201909_SNP [dm6]	A	T	1.257e^-5	0.363	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
X	3008258	X_3008258_SNP [dm3] X_3114225_SNP [dm6]	T	A	1.315e^-5	0.369	INTRON kirre
3R	27458721	3R_27458721_SNP [dm3] 3R_31632999_SNP [dm6]	A	G	1.319e^-5	0.369	INTRON kek6
3L	2580216	3L_2580216_SNP [dm3] 3L_2580216_SNP [dm6]	C	T	1.426e^-5	0.388	INTRON msn	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA
X	17750806	X_17750806_SNP [dm3] X_17856773_SNP [dm6]	G	C	1.429e^-5	0.388	UPSTREAM CG6762 & 1 other DOWNSTREAM CR43981 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cnc mE1_TFBS_HSA
X	17693891	X_17693891_SNP [dm3] X_17799858_SNP [dm6]	A	T	1.448e^-5	0.388	INTRON OdsH	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
3L	17683823	3L_17683823_SNP [dm3] 3L_17690723_SNP [dm6]	T	C	1.485e^-5	0.388	INTRON Ccn
X	10185991	X_10185991_SNP [dm3] X_10291958_SNP [dm6]	T	G	1.508e^-5	0.388	INTRON alpha-Man-I
3R	5410565	3R_5410565_SNP [dm3] 3R_9584843_SNP [dm6]	G	T	1.516e^-5	0.388	INTRON CG8301	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	18197816	2R_18197816_SNP [dm3] 2R_22310311_SNP [dm6]	G	T	1.530e^-5	0.388	UPSTREAM wdp INTRON wdp
X	17741219	X_17741219_SNP [dm3] X_17847186_SNP [dm6]	C	T	1.583e^-5	0.396	SYNONYMOUS_CODING Ucp4A UTR_3_PRIME Ucp4A DOWNSTREAM CG15814	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2L	12188129	2L_12188129_SNP [dm3] 2L_12188129_SNP [dm6]	C	A	1.619e^-5	0.396	INTRON aret
3L	5238268	3L_5238268_SNP [dm3] 3L_5245168_SNP [dm6]	G	T	1.624e^-5	0.396	INTRON shep
2L	8887520	2L_8887520_SNP [dm3] 2L_8887520_SNP [dm6]	T	C	1.666e^-5	0.401	EXON CR44415	TF binding site mE1_TFBS_cad mE1_TFBS_cnc
2L	14326965	2L_14326965_SNP [dm3] 2L_14326965_SNP [dm6]	C	T	1.747e^-5	0.407	SYNONYMOUS_CODING wb DOWNSTREAM wb
2R	11965490	2R_11965490_SNP [dm3] 2R_16077985_SNP [dm6]	C	T	1.776e^-5	0.407	DOWNSTREAM CR43415 INTERGENIC
2L	15337740	2L_15337740_SNP [dm3] 2L_15337740_SNP [dm6]	C	T	1.781e^-5	0.407	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
X	14441430	X_14441430_SNP [dm3] X_14547397_SNP [dm6]	A	T	1.816e^-5	0.407	INTERGENIC
3L	1773058	3L_1773058_SNP [dm3] 3L_1773058_SNP [dm6]	C	T	1.819e^-5	0.407	SYNONYMOUS_CODING CG13933 UPSTREAM CR44351	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
2L	5804599	2L_5804599_SNP [dm3] 2L_5804599_SNP [dm6]	G	C	1.822e^-5	0.407	UPSTREAM CG11034 DOWNSTREAM CG7239 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3R	23852615	3R_23852615_SNP [dm3] 3R_28026893_SNP [dm6]	C	T	1.903e^-5	0.414	INTRON CG34362
3R	23682129	3R_23682129_SNP [dm3] 3R_27856407_SNP [dm6]	T	G	1.910e^-5	0.414	INTRON CG34353	TF binding site mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_inv
3R	25002934	3R_25002934_SNP [dm3] 3R_29177212_SNP [dm6]	C	A	1.919e^-5	0.414	INTRON CG14509
X	12332193	X_12332193_SNP [dm3] X_12438160_SNP [dm6]	C	A	2.054e^-5	0.435	INTRON Pkcdelta
2R	16086048	2R_16086048_SNP [dm3] 2R_20198543_SNP [dm6]	G	T	2.089e^-5	0.435	INTERGENIC
3R	16175110	3R_16175110_SNP [dm3] 3R_20349388_SNP [dm6]	C	T	2.095e^-5	0.435	INTERGENIC
3R	4793654	3R_4793654_SNP [dm3] 3R_8967932_SNP [dm6]	C	A	2.111e^-5	0.435	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_cad
3L	18444670	3L_18444670_SNP [dm3] 3L_18451570_SNP [dm6]	G	A	2.153e^-5	0.439	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Kr
3R	7100702	3R_7100702_SNP [dm3] 3R_11274980_SNP [dm6]	C	T	2.181e^-5	0.44	INTRON CR31386
3R	27232351	3R_27232351_SNP [dm3] 3R_31406629_SNP [dm6]	G	A	2.248e^-5	0.443	INTRON Gprk2	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi
3R	27081378	3R_27081378_SNP [dm3] 3R_31255656_SNP [dm6]	C	A	2.263e^-5	0.443	SYNONYMOUS_CODING spn-F UPSTREAM CG1750	TF binding site BDTNP1_TFBS_prd mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	12697709	3R_12697709_SNP [dm3] 3R_16871987_SNP [dm6]	A	C	2.279e^-5	0.443	INTRON iab-8	TF binding site mE1_TFBS_cad
3R	16410331	3R_16410331_SNP [dm3] 3R_20584609_SNP [dm6]	G	A	2.291e^-5	0.443	INTRON CG16953
3R	5749736	3R_5749736_SNP [dm3] 3R_9924014_SNP [dm6]	G	T	2.354e^-5	0.451	INTRON Glut4EF
2R	14073082	2R_14073082_SNP [dm3] 2R_18185577_SNP [dm6]	G	A	2.385e^-5	0.452	INTRON CG33958	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
X	13977559	X_13977559_SNP [dm3] X_14083526_SNP [dm6]	T	A	2.506e^-5	0.463	INTERGENIC	TF binding site BDTNP1_TFBS_z mE1_TFBS_HSA

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Missing results

By genomic position
Variant impact
Gene name

pc_SegregVariants_X phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results