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=9.999e^-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

Covariate	p-value	Significance
In_2R_NS	0.05705
In_3R_K	0.03913

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2R_NS	5.2145	0.0737

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2328 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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Search:

Chromosome	Position	ID	Reference	Variant	p-value	FDR_BH	Transcript annotation	Binding site annotation
3R	2266130	3R_2266130_SNP [dm3] 3R_6440408_SNP [dm6]	T	C	8.330e^-8	0.156	SYNONYMOUS_CODING gpp	TF binding site mE1_TFBS_cad
3R	2266228	3R_2266228_SNP [dm3] 3R_6440506_SNP [dm6]	C	T	3.799e^-7	0.356	SYNONYMOUS_CODING gpp	TF binding site mE1_TFBS_cad mE1_TFBS_sens
3L	7585469	3L_7585469_SNP [dm3] 3L_7592369_SNP [dm6]	A	C	1.059e^-6	0.578	UPSTREAM CG33275 INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	15388601	2L_15388601_SNP [dm3] 2L_15388601_SNP [dm6]	A	T	1.761e^-6	0.578	INTERGENIC
2L	8351480	2L_8351480_SNP [dm3] 2L_8351480_SNP [dm6]	T	C	1.949e^-6	0.578	UPSTREAM Mur29B DOWNSTREAM CG7778 INTERGENIC
3L	1898203	3L_1898203_SNP [dm3] 3L_1898203_SNP [dm6]	G	A	1.961e^-6	0.578	UPSTREAM CG1887 INTRON CG1887
3R	26574481	3R_26574481_SNP [dm3] 3R_30748759_SNP [dm6]	T	C	2.194e^-6	0.578	INTERGENIC
2L	15388600	2L_15388600_SNP [dm3] 2L_15388600_SNP [dm6]	T	C	2.467e^-6	0.578	INTERGENIC
2L	4567296	2L_4567296_SNP [dm3] 2L_4567296_SNP [dm6]	C	T	3.088e^-6	0.591	INTRON dp
3L	11233537	3L_11233537_SNP [dm3] 3L_11240437_SNP [dm6]	T	C	3.154e^-6	0.591	INTERGENIC
X	14263189	X_14263189_SNP [dm3] X_14369156_SNP [dm6]	A	T	4.484e^-6	0.764	INTRON dpr8
3L	11233539	3L_11233539_SNP [dm3] 3L_11240439_SNP [dm6]	A	G	4.918e^-6	0.768	INTERGENIC
3L	17588927	3L_17588927_SNP [dm3] 3L_17595827_SNP [dm6]	A	G	8.528e^-6	0.794	INTRON Eip74EF
2L	7901123	2L_7901123_SNP [dm3] 2L_7901123_SNP [dm6]	C	G	8.915e^-6	0.794	INTRON Snoo
2L	9251474	2L_9251474_SNP [dm3] 2L_9251474_SNP [dm6]	A	T	9.006e^-6	0.794	UTR_3_PRIME borr UPSTREAM aust & 1 other
3L	21152323	3L_21152323_SNP [dm3] 3L_21159223_SNP [dm6]	C	A	1.045e^-5	0.794	INTRON Ac78C	TF binding site mE1_TFBS_inv
3L	2904513	3L_2904513_SNP [dm3] 3L_2904513_SNP [dm6]	T	A	1.101e^-5	0.794	INTRON Shab
2R	9498110	2R_9498110_SNP [dm3] 2R_13610605_SNP [dm6]	C	A	1.157e^-5	0.794	INTERGENIC
2R	9498117	2R_9498117_SNP [dm3] 2R_13610612_SNP [dm6]	C	T	1.157e^-5	0.794	INTERGENIC
2R	11418863	2R_11418863_SNP [dm3] 2R_15531358_SNP [dm6]	G	C	1.208e^-5	0.794	UTR_5_PRIME Khc-73 INTRON Khc-73	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad
3R	27010374	3R_27010374_SNP [dm3] 3R_31184652_SNP [dm6]	T	C	1.217e^-5	0.794	SYNONYMOUS_CODING mesh
3R	2495969	3R_2495969_SNP [dm3] 3R_6670247_SNP [dm6]	T	G	1.239e^-5	0.794	INTRON lab	regulatory region FlyBase REDfly_CRMs
2R	9498107	2R_9498107_SNP [dm3] 2R_13610602_SNP [dm6]	T	G	1.243e^-5	0.794	INTERGENIC
2L	15281222	2L_15281222_SNP [dm3] 2L_15281222_SNP [dm6]	A	G	1.251e^-5	0.794	DOWNSTREAM CR45349 INTERGENIC
3R	24267354	3R_24267354_SNP [dm3] 3R_28441632_SNP [dm6]	C	G	1.280e^-5	0.794	INTRON beat-VI
3L	5044337	3L_5044337_DEL [dm3] 3L_5044337_DEL [dm6]	TT	T	1.310e^-5	0.794	INTRON Con
2R	11385484	2R_11385484_SNP [dm3] 2R_15497979_SNP [dm6]	C	G	1.338e^-5	0.794	UPSTREAM CG12964 INTERGENIC
3R	22713569	3R_22713569_SNP [dm3] 3R_26887847_SNP [dm6]	T	C	1.346e^-5	0.794	INTRON T48	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad
2R	14967723	2R_14967723_SNP [dm3] 2R_19080218_SNP [dm6]	G	A	1.486e^-5	0.794	INTRON 5-HT1A
3R	21086869	3R_21086869_SNP [dm3] 3R_25261147_SNP [dm6]	A	T	1.541e^-5	0.794	UTR_3_PRIME CG10425 DOWNSTREAM CG11857
2L	10497668	2L_10497668_SNP [dm3] 2L_10497668_SNP [dm6]	T	C	1.544e^-5	0.794	INTRON Myo31DF
2L	15281202	2L_15281202_DEL [dm3] 2L_15281202_DEL [dm6]	CC	T	1.581e^-5	0.794	DOWNSTREAM CR45349 INTERGENIC
2L	15281172	2L_15281172_SNP [dm3] 2L_15281172_SNP [dm6]	G	A	1.596e^-5	0.794	DOWNSTREAM CR45349 INTERGENIC
3R	21197275	3R_21197275_SNP [dm3] 3R_25371553_SNP [dm6]	G	T	1.634e^-5	0.794	INTRON Fur1
2R	19198653	2R_19198653_SNP [dm3] 2R_23311130_SNP [dm6]	A	T	1.727e^-5	0.794	INTERGENIC
3L	17593846	3L_17593846_SNP [dm3] 3L_17600746_SNP [dm6]	C	T	1.835e^-5	0.794	INTRON Eip74EF
2R	17419139	2R_17419139_SNP [dm3] 2R_21531634_SNP [dm6]	T	A	1.885e^-5	0.794	INTRON Egfr EXON CR44725
3R	23625839	3R_23625839_SNP [dm3] 3R_27800117_SNP [dm6]	G	T	1.941e^-5	0.794	INTRON CG34353
3L	2513633	3L_2513633_SNP [dm3] 3L_2513633_SNP [dm6]	G	T	1.955e^-5	0.794	SYNONYMOUS_CODING Spn	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2R	15796372	2R_15796372_SNP [dm3] 2R_19908867_SNP [dm6]	C	T	2.017e^-5	0.794	DOWNSTREAM CR44573 INTERGENIC
3L	17582187	3L_17582187_SNP [dm3] 3L_17589087_SNP [dm6]	T	A	2.040e^-5	0.794	INTRON Eip74EF
2R	17419153	2R_17419153_DEL [dm3] 2R_21531648_DEL [dm6]	ATA	A	2.127e^-5	0.794	INTRON Egfr EXON CR44725
2R	9451104	2R_9451104_SNP [dm3] 2R_13563599_SNP [dm6]	C	G	2.131e^-5	0.794	INTERGENIC	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_kni BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_D mE1_TFBS_eve mE1_TFBS_inv mE1_TFBS_Kr mE1_TFBS_sens mE1_TFBS_Trl mE1_TFBS_zfh1
3R	25744754	3R_25744754_SNP [dm3] 3R_29919032_SNP [dm6]	A	G	2.267e^-5	0.794	SPLICE_SITE_REGION trp INTRON trp	TF binding site mE1_TFBS_chinmo
2L	5128873	2L_5128873_SNP [dm3] 2L_5128873_SNP [dm6]	T	C	2.282e^-5	0.794	SYNONYMOUS_CODING Msp300 INTRON Msp300	TF binding site mE1_TFBS_cad mE1_TFBS_sens
3R	21875957	3R_21875957_SNP [dm3] 3R_26050235_SNP [dm6]	A	T	2.294e^-5	0.794	NON_SYNONYMOUS_CODING Exo84 DOWNSTREAM gro
2R	17539826	2R_17539826_SNP [dm3] 2R_21652321_SNP [dm6]	T	C	2.315e^-5	0.794	UPSTREAM CG30284 INTRON CG10082
2L	6240312	2L_6240312_SNP [dm3] 2L_6240312_SNP [dm6]	A	T	2.317e^-5	0.794	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_Kr
3R	17740201	3R_17740201_SNP [dm3] 3R_21914479_SNP [dm6]	G	A	2.351e^-5	0.794	NON_SYNONYMOUS_CODING CG17843 DOWNSTREAM CG6690
2L	6240325	2L_6240325_DEL [dm3] 2L_6240325_DEL [dm6]	ACAATA	A	2.424e^-5	0.794	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_Kr
2L	11410638	2L_11410638_INS [dm3] 2L_11410638_INS [dm6]	A	AA	2.436e^-5	0.794	INTERGENIC	regulatory region REDfly_CRMs
2R	12281986	2R_12281986_SNP [dm3] 2R_16394481_SNP [dm6]	A	T	2.479e^-5	0.794	INTRON Sema-2b
3R	14515675	3R_14515675_SNP [dm3] 3R_18689953_SNP [dm6]	T	C	2.482e^-5	0.794	SYNONYMOUS_CODING Muc91C	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2R	15327699	2R_15327699_SNP [dm3] 2R_19440194_SNP [dm6]	T	C	2.658e^-5	0.794	SPLICE_SITE_REGION Spt5 SYNONYMOUS_CODING Spt5	TF binding site mE1_TFBS_sens
3R	23234906	3R_23234906_SNP [dm3] 3R_27409184_SNP [dm6]	A	G	2.745e^-5	0.794	INTRON side
X	20431701	X_20431701_SNP [dm3] X_20560674_SNP [dm6]	A	C	2.884e^-5	0.794	INTRON RunxB
3L	2904506	3L_2904506_SNP [dm3] 3L_2904506_SNP [dm6]	A	T	2.951e^-5	0.794	INTRON Shab
3R	24925502	3R_24925502_SNP [dm3] 3R_29099780_SNP [dm6]	C	A	2.981e^-5	0.794	NON_SYNONYMOUS_CODING CG11873	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
X	20431774	X_20431774_SNP [dm3] X_20560747_SNP [dm6]	T	C	3.014e^-5	0.794	INTRON RunxB
2L	6240301	2L_6240301_INS [dm3] 2L_6240301_INS [dm6]	G	GGAGCCATTTTGAGGCATGA...	3.047e^-5	0.794	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_Kr
3R	17143883	3R_17143883_SNP [dm3] 3R_21318161_SNP [dm6]	T	A	3.061e^-5	0.794	DOWNSTREAM CG16791 & 1 other INTERGENIC
3L	12946044	3L_12946044_SNP [dm3] 3L_12952944_SNP [dm6]	G	A	3.079e^-5	0.794	NON_SYNONYMOUS_CODING CG10752
2R	19199228	2R_19199228_SNP [dm3] 2R_23311705_SNP [dm6]	C	G	3.080e^-5	0.794	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2R	19199608	2R_19199608_SNP [dm3] 2R_23312085_SNP [dm6]	G	A	3.081e^-5	0.794	DOWNSTREAM HP1Lcsd INTERGENIC	TF binding site mE1_TFBS_inv
2R	14966137	2R_14966137_SNP [dm3] 2R_19078632_SNP [dm6]	G	A	3.161e^-5	0.794	INTRON 5-HT1A
2R	18880362	2R_18880362_SNP [dm3] 2R_22992839_SNP [dm6]	G	A	3.233e^-5	0.794	DOWNSTREAM CG9896 INTRON twi
X	3207004	X_3207004_SNP [dm3] X_3312971_SNP [dm6]	G	A	3.363e^-5	0.794	DOWNSTREAM CR44886 INTRON dnc
2L	621199	2L_621199_SNP [dm3] 2L_621199_SNP [dm6]	C	A	3.770e^-5	0.794	START_GAINED lectin-21Cb UTR_5_PRIME lectin-21Cb	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	14658920	2R_14658920_SNP [dm3] 2R_18771415_SNP [dm6]	A	T	3.892e^-5	0.794	UPSTREAM Mctp INTRON Mctp
X	5872225	X_5872225_SNP [dm3] X_5978192_SNP [dm6]	T	A	3.932e^-5	0.794	INTRON Grip
2L	15281177	2L_15281177_SNP [dm3] 2L_15281177_SNP [dm6]	T	G	4.038e^-5	0.794	DOWNSTREAM CR45349 INTERGENIC
2R	12804971	2R_12804971_SNP [dm3] 2R_16917466_SNP [dm6]	A	T	4.130e^-5	0.794	INTERGENIC	TF binding site mE1_TFBS_ftz_f1
2R	5590898	2R_5590898_SNP [dm3] 2R_9703393_SNP [dm6]	C	G	4.143e^-5	0.794	UPSTREAM CG30002 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi
X	18636517	X_18636517_INS [dm3] X_18742484_INS [dm6]	A	ATTGCGA	4.160e^-5	0.794	INTERGENIC
2L	14696348	2L_14696348_SNP [dm3] 2L_14696348_SNP [dm6]	A	C	4.208e^-5	0.794	INTERGENIC
2R	16541975	2R_16541975_SNP [dm3] 2R_20654470_SNP [dm6]	C	T	4.235e^-5	0.794	INTRON Lrt & 1 other
2R	14836624	2R_14836624_INS [dm3] 2R_18949119_INS [dm6]	T	TT	4.246e^-5	0.794	INTRON sano
2R	6435388	2R_6435388_SNP [dm3] 2R_10547883_SNP [dm6]	T	A	4.283e^-5	0.794	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
X	12371580	X_12371580_SNP [dm3] X_12477547_SNP [dm6]	C	G	4.298e^-5	0.794	UTR_3_PRIME CG42258 DOWNSTREAM CG42258
3L	13611747	3L_13611747_SNP [dm3] 3L_13618647_SNP [dm6]	G	C	4.338e^-5	0.794	INTRON bru-3
3L	1585439	3L_1585439_SNP [dm3] 3L_1585439_SNP [dm6]	T	A	4.421e^-5	0.794	INTRON CG13917
2L	15195340	2L_15195340_SNP [dm3] 2L_15195340_SNP [dm6]	T	C	4.508e^-5	0.794	INTRON CG4168
2R	17875679	2R_17875679_SNP [dm3] 2R_21988174_SNP [dm6]	G	T	4.558e^-5	0.794	UTR_3_PRIME CG34370	TF binding site mE1_TFBS_cad
3R	26574483	3R_26574483_SNP [dm3] 3R_30748761_SNP [dm6]	G	A	4.639e^-5	0.794	INTERGENIC
3L	21244565	3L_21244565_SNP [dm3] 3L_21251465_SNP [dm6]	A	T	4.648e^-5	0.794	INTRON Eip78C
X	1201258	X_1201258_SNP [dm3] X_1307225_SNP [dm6]	T	G	4.651e^-5	0.794	INTRON DAAM
2L	19323097	2L_19323097_SNP [dm3] 2L_19323097_SNP [dm6]	T	A	4.759e^-5	0.794	EXON CR45700	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_sens
3R	21253217	3R_21253217_SNP [dm3] 3R_25427495_SNP [dm6]	A	G	4.898e^-5	0.794	INTRON Fur1
X	13055757	X_13055757_SNP [dm3] X_13161724_SNP [dm6]	G	T	4.958e^-5	0.794	UTR_3_PRIME CG12096 & 1 other DOWNSTREAM CG12096
X	20759542	X_20759542_SNP [dm3] X_20888515_SNP [dm6]	C	A	4.965e^-5	0.794	INTRON shakB
3L	11233518	3L_11233518_INS [dm3] 3L_11240418_INS [dm6]	T	TC	4.984e^-5	0.794	INTERGENIC
2R	19198885	2R_19198885_SNP [dm3] 2R_23311362_SNP [dm6]	G	A	5.012e^-5	0.794	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2L	11745583	2L_11745583_SNP [dm3] 2L_11745583_SNP [dm6]	A	G	5.090e^-5	0.794	INTERGENIC
3L	21338121	3L_21338121_SNP [dm3] 3L_21345021_SNP [dm6]	T	G	5.112e^-5	0.794	UTR_3_PRIME ebd2 INTRON CG32436	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	21738772	3R_21738772_SNP [dm3] 3R_25913050_SNP [dm6]	G	T	5.199e^-5	0.794	DOWNSTREAM CG42235 INTRON CG42235
3L	12474390	3L_12474390_SNP [dm3] 3L_12481290_SNP [dm6]	C	A	5.222e^-5	0.794	INTRON CG10663
2R	16541977	2R_16541977_SNP [dm3] 2R_20654472_SNP [dm6]	G	T	5.230e^-5	0.794	INTRON Lrt & 1 other
3L	8010476	3L_8010476_SNP [dm3] 3L_8017376_SNP [dm6]	T	A	5.237e^-5	0.794	INTRON nmo
2R	12804957	2R_12804957_DEL [dm3] 2R_16917452_DEL [dm6]	TG	T	5.338e^-5	0.794	INTERGENIC	TF binding site mE1_TFBS_ftz_f1
3R	21086792	3R_21086792_SNP [dm3] 3R_25261070_SNP [dm6]	A	C	5.426e^-5	0.794	UTR_3_PRIME CG10425 DOWNSTREAM CG11857

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By genomic position
Variant impact
Gene name

W2 Vial 1 ascension (cm) phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results