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=2.248e^-3)
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_P	0.06709

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1387 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
3R	14774968	3R_14774968_SNP [dm3] 3R_18949246_SNP [dm6]	C	T	9.253e^-7	1	UPSTREAM CG42613 & 1 other INTRON CG42613
3L	15692813	3L_15692813_INS [dm3] 3L_15699713_INS [dm6]	T	TCTAT	2.690e^-6	1	UTR_5_PRIME comm2	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_sna BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_GATAe mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3R	18270922	3R_18270922_SNP [dm3] 3R_22445200_SNP [dm6]	C	T	5.098e^-6	1	SYNONYMOUS_CODING CG12499	TF binding site mE1_TFBS_sens
3L	12306706	3L_12306706_SNP [dm3] 3L_12313606_SNP [dm6]	G	A	5.380e^-6	1	INTERGENIC
3L	12306692	3L_12306692_SNP [dm3] 3L_12313592_SNP [dm6]	G	T	6.285e^-6	1	INTERGENIC
X	18763659	X_18763659_SNP [dm3] X_18869626_SNP [dm6]	T	C	6.662e^-6	1	INTRON CG34401	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	19846672	2L_19846672_SNP [dm3] 2L_19846672_SNP [dm6]	C	T	6.988e^-6	1	INTRON sick	TF binding site BDTNP1_TFBS_hb BDTNP1_TFBS_twi
3R	26447722	3R_26447722_SNP [dm3] 3R_30622000_SNP [dm6]	T	A	7.028e^-6	1	UPSTREAM CG44954 INTERGENIC	insulator Insulator_Class_II.mE01
2L	6826022	2L_6826022_DEL [dm3] 2L_6826022_DEL [dm6]	TGT	T	8.332e^-6	1	INTRON sens-2	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad
2L	6826035	2L_6826035_SNP [dm3] 2L_6826035_SNP [dm6]	T	A	8.332e^-6	1	INTRON sens-2	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad
X	14706551	X_14706551_SNP [dm3] X_14812518_SNP [dm6]	T	G	8.677e^-6	1	INTRON rut
2L	10454235	2L_10454235_SNP [dm3] 2L_10454235_SNP [dm6]	G	A	8.882e^-6	1	INTRON CG5322
X	14706544	X_14706544_SNP [dm3] X_14812511_SNP [dm6]	G	C	1.336e^-5	1	INTRON rut
2L	6826029	2L_6826029_DEL [dm3] 2L_6826029_DEL [dm6]	GGT	G	1.571e^-5	1	INTRON sens-2	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad
3R	23986624	3R_23986624_SNP [dm3] 3R_28160902_SNP [dm6]	G	C	1.756e^-5	1	INTRON CG34354
X	1190943	X_1190943_SNP [dm3] X_1296910_SNP [dm6]	T	C	1.803e^-5	1	INTRON DAAM	TF binding site mE1_TFBS_chinmo
3L	12521148	3L_12521148_SNP [dm3] 3L_12528048_SNP [dm6]	G	A	1.830e^-5	1	SYNONYMOUS_CODING nst	TF binding site mE1_TFBS_chinmo mE1_TFBS_sens
X	14460211	X_14460211_SNP [dm3] X_14566178_SNP [dm6]	A	G	2.096e^-5	1	INTERGENIC
3R	24284234	3R_24284234_SNP [dm3] 3R_28458512_SNP [dm6]	T	C	2.137e^-5	1	INTRON beat-VI
2L	4348619	2L_4348619_SNP [dm3] 2L_4348619_SNP [dm6]	C	G	2.139e^-5	1	UPSTREAM CR44699 DOWNSTREAM CR44697 EXON CR44698	TF binding site BDTNP1_TFBS_twi
2R	2869599	2R_2869599_SNP [dm3] 2R_6982094_SNP [dm6]	C	T	2.340e^-5	1	NON_SYNONYMOUS_CODING CG30156 UPSTREAM CR44171 INTRON vimar	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
X	1192858	X_1192858_SNP [dm3] X_1298825_SNP [dm6]	C	A	2.375e^-5	1	UPSTREAM CG32811 INTRON DAAM	TF binding site mE1_TFBS_chinmo
X	1190818	X_1190818_SNP [dm3] X_1296785_SNP [dm6]	T	G	2.508e^-5	1	INTRON DAAM	TF binding site mE1_TFBS_chinmo
3R	13040830	3R_13040830_SNP [dm3] 3R_17215108_SNP [dm6]	A	T	2.737e^-5	1	INTERGENIC
X	18763653	X_18763653_SNP [dm3] X_18869620_SNP [dm6]	A	G	2.778e^-5	1	INTRON CG34401	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	19469794	2L_19469794_SNP [dm3] 2L_19469794_SNP [dm6]	T	A	2.855e^-5	1	DOWNSTREAM CR45723 EXON CR45722
X	14460706	X_14460706_SNP [dm3] X_14566673_SNP [dm6]	A	C	3.063e^-5	1	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
X	14706552	X_14706552_SNP [dm3] X_14812519_SNP [dm6]	T	A	3.070e^-5	1	INTRON rut
3R	16815637	3R_16815637_SNP [dm3] 3R_20989915_SNP [dm6]	T	C	3.324e^-5	1	UPSTREAM Calx INTRON Calx
2L	3399120	2L_3399120_SNP [dm3] 2L_3399120_SNP [dm6]	T	A	3.612e^-5	1	DOWNSTREAM CG34175 INTERGENIC
2R	19640758	2R_19640758_SNP [dm3] 2R_23753235_SNP [dm6]	T	C	3.667e^-5	1	UTR_3_PRIME CG5532 DOWNSTREAM CG9850 & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv
2R	19640757	2R_19640757_SNP [dm3] 2R_23753234_SNP [dm6]	T	C	3.691e^-5	1	UTR_3_PRIME CG5532 DOWNSTREAM CG9850 & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv
2L	11376614	2L_11376614_INS [dm3] 2L_11376614_INS [dm6]	A	GC	3.992e^-5	1	INTERGENIC	regulatory region REDfly_CRMs
X	18775563	X_18775563_SNP [dm3] X_18881530_SNP [dm6]	A	G	4.004e^-5	1	UTR_3_PRIME CG34401 DOWNSTREAM CG34401
2R	14628468	2R_14628468_SNP [dm3] 2R_18740963_SNP [dm6]	C	T	4.178e^-5	1	INTRON Hs3st-A EXON CR30121
3R	18270603	3R_18270603_SNP [dm3] 3R_22444881_SNP [dm6]	G	A	4.380e^-5	1	SYNONYMOUS_CODING CG12499	TF binding site mE1_TFBS_sens
3R	18270679	3R_18270679_SNP [dm3] 3R_22444957_SNP [dm6]	T	A	4.380e^-5	1	SYNONYMOUS_CODING CG12499	TF binding site mE1_TFBS_sens
2R	5673274	2R_5673274_SNP [dm3] 2R_9785769_SNP [dm6]	A	G	4.525e^-5	1	INTRON CG1688
2R	5673285	2R_5673285_SNP [dm3] 2R_9785780_SNP [dm6]	T	G	4.525e^-5	1	INTRON CG1688
3L	2978526	3L_2978526_SNP [dm3] 3L_2978526_SNP [dm6]	C	A	4.635e^-5	1	INTERGENIC
2L	3763444	2L_3763444_SNP [dm3] 2L_3763444_SNP [dm6]	A	T	4.712e^-5	1	INTRON CG43707	TF binding site mE1_TFBS_chinmo
2R	5673276	2R_5673276_SNP [dm3] 2R_9785771_SNP [dm6]	C	A	4.719e^-5	1	INTRON CG1688
3R	4858555	3R_4858555_SNP [dm3] 3R_9032833_SNP [dm6]	A	T	4.924e^-5	1	INTRON neur	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3R	4858813	3R_4858813_SNP [dm3] 3R_9033091_SNP [dm6]	G	C	4.924e^-5	1	INTRON neur	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	1343349	3L_1343349_SNP [dm3] 3L_1343349_SNP [dm6]	A	T	4.939e^-5	1	UTR_3_PRIME Ptp61F UPSTREAM CG2199 DOWNSTREAM Ptp61F INTRON Ptp61F	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
X	1192856	X_1192856_SNP [dm3] X_1298823_SNP [dm6]	G	A	4.943e^-5	1	UPSTREAM CG32811 INTRON DAAM	TF binding site mE1_TFBS_chinmo
X	1194700	X_1194700_SNP [dm3] X_1300667_SNP [dm6]	C	T	5.149e^-5	1	INTRON DAAM
X	19743496	X_19743496_SNP [dm3] X_19849463_SNP [dm6]	C	A	5.229e^-5	1	UPSTREAM pico INTRON pico	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	9040820	3L_9040820_SNP [dm3] 3L_9047720_SNP [dm6]	C	T	5.356e^-5	1	SYNONYMOUS_CODING CG5144	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_sens
3L	10550946	3L_10550946_SNP [dm3] 3L_10557846_SNP [dm6]	G	T	5.395e^-5	1	DOWNSTREAM CG6527 INTRON A2bp1 & 1 other
2R	19640766	2R_19640766_SNP [dm3] 2R_23753243_SNP [dm6]	C	A	5.528e^-5	1	UTR_3_PRIME CG5532 DOWNSTREAM CG9850 & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv
X	16470198	X_16470198_SNP [dm3] X_16576165_SNP [dm6]	A	G	5.719e^-5	1	INTRON CanA-14F
X	13157211	X_13157211_SNP [dm3] X_13263178_SNP [dm6]	A	C	5.753e^-5	1	UTR_3_PRIME HDAC4 DOWNSTREAM comt & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	19640887	2R_19640887_SNP [dm3] 2R_23753364_SNP [dm6]	G	T	5.851e^-5	1	UTR_3_PRIME CG5532 DOWNSTREAM CG9850 & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA
2R	19640888	2R_19640888_SNP [dm3] 2R_23753365_SNP [dm6]	G	T	5.851e^-5	1	UTR_3_PRIME CG5532 DOWNSTREAM CG9850 & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA
X	1192821	X_1192821_SNP [dm3] X_1298788_SNP [dm6]	G	A	5.923e^-5	1	UPSTREAM CG32811 INTRON DAAM	TF binding site mE1_TFBS_chinmo
2L	4133333	2L_4133333_SNP [dm3] 2L_4133333_SNP [dm6]	T	G	6.002e^-5	1	INTERGENIC
X	1191919	X_1191919_SNP [dm3] X_1297886_SNP [dm6]	G	A	6.025e^-5	1	DOWNSTREAM CG32811 INTRON DAAM
3R	13041961	3R_13041961_SNP [dm3] 3R_17216239_SNP [dm6]	A	C	6.237e^-5	1	DOWNSTREAM CG31262 INTERGENIC
X	3148757	X_3148757_SNP [dm3] X_3254724_SNP [dm6]	G	C	6.284e^-5	1	INTRON dnc
X	3148758	X_3148758_SNP [dm3] X_3254725_SNP [dm6]	T	G	6.284e^-5	1	INTRON dnc
2L	719297	2L_719297_SNP [dm3] 2L_719297_SNP [dm6]	G	A	6.298e^-5	1	INTERGENIC
2R	6139669	2R_6139669_SNP [dm3] 2R_10252164_SNP [dm6]	A	T	6.324e^-5	1	UTR_5_PRIME Syb INTRON CG12913 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_sens
3R	8547099	3R_8547099_SNP [dm3] 3R_12721377_SNP [dm6]	C	G	6.405e^-5	1	UPSTREAM Men INTRON Men
X	14461578	X_14461578_SNP [dm3] X_14567545_SNP [dm6]	A	C	6.417e^-5	1	INTERGENIC
X	14461579	X_14461579_SNP [dm3] X_14567546_SNP [dm6]	T	A	6.417e^-5	1	INTERGENIC
X	14461582	X_14461582_SNP [dm3] X_14567549_SNP [dm6]	T	A	6.417e^-5	1	INTERGENIC
X	1192886	X_1192886_SNP [dm3] X_1298853_SNP [dm6]	A	G	6.464e^-5	1	UPSTREAM CG32811 INTRON DAAM	TF binding site mE1_TFBS_chinmo
3R	14812510	3R_14812510_SNP [dm3] 3R_18986788_SNP [dm6]	T	G	6.506e^-5	1	INTRON gukh	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
X	17121232	X_17121232_SNP [dm3] X_17227199_SNP [dm6]	G	T	7.018e^-5	1	UPSTREAM CG10598 INTERGENIC
X	14459739	X_14459739_SNP [dm3] X_14565706_SNP [dm6]	T	C	7.134e^-5	1	INTERGENIC
3R	18797339	3R_18797339_SNP [dm3] 3R_22971617_SNP [dm6]	C	G	7.290e^-5	1	INTERGENIC
2L	4133358	2L_4133358_SNP [dm3] 2L_4133358_SNP [dm6]	A	C	7.390e^-5	1	INTERGENIC
2R	12616052	2R_12616052_SNP [dm3] 2R_16728547_SNP [dm6]	C	T	7.422e^-5	1	INTRON CG30463
3R	13040856	3R_13040856_SNP [dm3] 3R_17215134_SNP [dm6]	C	T	7.540e^-5	1	INTERGENIC
X	14461348	X_14461348_SNP [dm3] X_14567315_SNP [dm6]	T	A	7.713e^-5	1	INTERGENIC
X	14461597	X_14461597_INS [dm3] X_14567564_INS [dm6]	T	TT	7.722e^-5	1	INTERGENIC
X	14461599	X_14461599_SNP [dm3] X_14567566_SNP [dm6]	T	G	7.722e^-5	1	INTERGENIC
X	8009406	X_8009406_SNP [dm3] X_8115373_SNP [dm6]	T	C	7.757e^-5	1	INTRON Gclc	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_GATAe mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3L	6574829	3L_6574829_SNP [dm3] 3L_6581729_SNP [dm6]	C	G	7.939e^-5	1	INTRON CG18769 & 1 other
3R	24401320	3R_24401320_SNP [dm3] 3R_28575598_SNP [dm6]	T	C	8.123e^-5	1	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_sens
X	14461351	X_14461351_SNP [dm3] X_14567318_SNP [dm6]	A	G	8.188e^-5	1	INTERGENIC
2L	9595431	2L_9595431_SNP [dm3] 2L_9595431_SNP [dm6]	C	T	8.250e^-5	1	INTERGENIC	regulatory region REDfly_CRMs
3L	7236924	3L_7236924_SNP [dm3] 3L_7243824_SNP [dm6]	G	T	8.265e^-5	1	UPSTREAM mei-P22 DOWNSTREAM Neos INTRON mRpL50	TF binding site mE1_TFBS_cad
2R	13259016	2R_13259016_SNP [dm3] 2R_17371511_SNP [dm6]	C	T	8.315e^-5	1	INTRON mbl
X	16470191	X_16470191_SNP [dm3] X_16576158_SNP [dm6]	T	A	8.356e^-5	1	INTRON CanA-14F
X	16470201	X_16470201_SNP [dm3] X_16576168_SNP [dm6]	A	T	8.356e^-5	1	INTRON CanA-14F
X	16470209	X_16470209_SNP [dm3] X_16576176_SNP [dm6]	C	G	8.356e^-5	1	INTRON CanA-14F
3L	14561076	3L_14561076_SNP [dm3] 3L_14567976_SNP [dm6]	T	C	8.389e^-5	1	SYNONYMOUS_CODING CG42758
2R	6138844	2R_6138844_DEL [dm3] 2R_10251339_DEL [dm6]	TCACCT	T	8.407e^-5	1	INTRON CG12913 & 1 other
X	5715275	X_5715275_SNP [dm3] X_5821242_SNP [dm6]	A	G	8.478e^-5	1	INTRON CG15765	TF binding site mE1_TFBS_eve mE1_TFBS_HSA
X	17149876	X_17149876_SNP [dm3] X_17255843_SNP [dm6]	C	T	8.576e^-5	1	INTRON f
X	16470002	X_16470002_SNP [dm3] X_16575969_SNP [dm6]	A	G	8.580e^-5	1	INTRON CanA-14F
X	14460441	X_14460441_SNP [dm3] X_14566408_SNP [dm6]	C	A	8.817e^-5	1	INTERGENIC
3L	16636037	3L_16636037_SNP [dm3] 3L_16642937_SNP [dm6]	A	C	8.941e^-5	1	INTRON Abl
2R	18747072	2R_18747072_INS [dm3] 2R_22859549_INS [dm6]	T	TAGCTAATT	9.284e^-5	1	UPSTREAM inaD INTERGENIC	TF binding site BDTNP1_TFBS_dl
3L	1828162	3L_1828162_SNP [dm3] 3L_1828162_SNP [dm6]	T	A	9.310e^-5	1	INTRON Cpr62Ba
3L	9845720	3L_9845720_SNP [dm3] 3L_9852620_SNP [dm6]	A	G	9.376e^-5	1	INTRON RasGAP1	TF binding site BDTNP1_TFBS_dl
3L	9845721	3L_9845721_SNP [dm3] 3L_9852621_SNP [dm6]	T	G	9.376e^-5	1	INTRON RasGAP1	TF binding site BDTNP1_TFBS_dl
3R	2953163	3R_2953163_SNP [dm3] 3R_7127441_SNP [dm6]	C	T	9.514e^-5	1	SYNONYMOUS_CODING CG10068 UPSTREAM CR42875 DOWNSTREAM CG10098	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens

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Missing results

By genomic position
Variant impact
Gene name

pc_FL_Hobo_HS phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results