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=1.435e^-5)
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
wolba	0.0788

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_3R_P	6.123	0.0468

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2508 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	13354218	3L_13354218_SNP [dm3] 3L_13361118_SNP [dm6]	G	T	1.123e^-6	0.604	INTERGENIC
3L	8418022	3L_8418022_SNP [dm3] 3L_8424922_SNP [dm6]	A	T	1.146e^-6	0.604	UPSTREAM Cbl INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med
2R	17283346	2R_17283346_SNP [dm3] 2R_21395841_SNP [dm6]	C	A	1.196e^-6	0.604	INTRON Sdc
3L	12971864	3L_12971864_SNP [dm3] 3L_12978764_SNP [dm6]	C	G	1.287e^-6	0.604	INTERGENIC
3L	8418035	3L_8418035_SNP [dm3] 3L_8424935_SNP [dm6]	G	C	1.625e^-6	0.61	UPSTREAM Cbl INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med
2L	9338578	2L_9338578_SNP [dm3] 2L_9338578_SNP [dm6]	T	A	2.630e^-6	0.632	INTRON Eaat1
2L	9338573	2L_9338573_SNP [dm3] 2L_9338573_SNP [dm6]	C	T	2.693e^-6	0.632	INTRON Eaat1
2L	5509171	2L_5509171_SNP [dm3] 2L_5509171_SNP [dm6]	A	T	4.083e^-6	0.632	INTERGENIC
2L	8139667	2L_8139667_SNP [dm3] 2L_8139667_SNP [dm6]	T	A	4.293e^-6	0.632	SYNONYMOUS_CODING CG8552 START_GAINED CG8552 UTR_5_PRIME CG8552	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
X	17176035	X_17176035_SNP [dm3] X_17282002_SNP [dm6]	A	C	4.659e^-6	0.632	NON_SYNONYMOUS_CODING CG8664 UPSTREAM CG5445	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
2L	2023777	2L_2023777_SNP [dm3] 2L_2023777_SNP [dm6]	T	C	6.982e^-6	0.632	UPSTREAM CG4238 INTRON CG4238
X	11183788	X_11183788_SNP [dm3] X_11289755_SNP [dm6]	C	T	7.592e^-6	0.632	INTRON CG44422
3R	17064834	3R_17064834_INS [dm3] 3R_21239112_INS [dm6]	C	GATCA	8.468e^-6	0.632	INTERGENIC	regulatory region REDfly_CRMs
2L	7046292	2L_7046292_SNP [dm3] 2L_7046292_SNP [dm6]	C	T	8.566e^-6	0.632	UTR_5_PRIME milt INTRON milt	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	13376837	3L_13376837_SNP [dm3] 3L_13383737_SNP [dm6]	A	G	8.617e^-6	0.632	SYNONYMOUS_CODING ImpL1	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	10107924	2L_10107924_SNP [dm3] 2L_10107924_SNP [dm6]	A	C	8.684e^-6	0.632	INTRON CG44153 & 1 other
3L	15440146	3L_15440146_SNP [dm3] 3L_15447046_SNP [dm6]	T	A	9.638e^-6	0.632	INTERGENIC
X	16436846	X_16436846_SNP [dm3] X_16542813_SNP [dm6]	A	G	1.011e^-5	0.632	UTR_3_PRIME CG9902 DOWNSTREAM CG9902	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
X	16436853	X_16436853_SNP [dm3] X_16542820_SNP [dm6]	G	C	1.011e^-5	0.632	UTR_3_PRIME CG9902 DOWNSTREAM CG9902	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
X	17177038	X_17177038_INS [dm3] X_17283005_INS [dm6]	T	TGGAAGATCATCCAGATAGG...	1.036e^-5	0.632	UPSTREAM CG8664 DOWNSTREAM CG8661 INTRON CG5445	TF binding site mE1_TFBS_inv
2R	3588178	2R_3588178_SNP [dm3] 2R_7700673_SNP [dm6]	T	A	1.046e^-5	0.632	SYNONYMOUS_CODING CG30496 INTRON CG30493	TF binding site mE1_TFBS_sens
3L	15440151	3L_15440151_DEL [dm3] 3L_15447051_DEL [dm6]	ATAAT	A	1.064e^-5	0.632	INTERGENIC
3L	15440148	3L_15440148_SNP [dm3] 3L_15447048_SNP [dm6]	A	C	1.080e^-5	0.632	INTERGENIC
2L	8529492	2L_8529492_SNP [dm3] 2L_8529492_SNP [dm6]	T	A	1.083e^-5	0.632	UTR_5_PRIME CG17834 UPSTREAM lmgA & 1 other INTRON CG17834	TF binding site BDTNP1_TFBS_prd
3L	12622164	3L_12622164_DEL [dm3] 3L_12629064_DEL [dm6]	TTGTAAC	T	1.132e^-5	0.632	INTRON CR32111
3L	15440158	3L_15440158_SNP [dm3] 3L_15447058_SNP [dm6]	T	A	1.133e^-5	0.632	INTERGENIC
X	6686683	X_6686683_SNP [dm3] X_6792650_SNP [dm6]	A	C	1.141e^-5	0.632	INTRON C3G
3R	7531144	3R_7531144_SNP [dm3] 3R_11705422_SNP [dm6]	A	C	1.142e^-5	0.632	DOWNSTREAM I-t INTERGENIC
X	13406514	X_13406514_SNP [dm3] X_13512481_SNP [dm6]	A	T	1.205e^-5	0.632	INTRON Neto
2R	19942587	2R_19942587_SNP [dm3] 2R_24055064_SNP [dm6]	T	C	1.252e^-5	0.632	UPSTREAM CG13563 INTRON ppk29
3L	4957043	3L_4957043_SNP [dm3] 3L_4957043_SNP [dm6]	A	G	1.272e^-5	0.632	INTRON Con
3R	24660135	3R_24660135_SNP [dm3] 3R_28834413_SNP [dm6]	C	A	1.286e^-5	0.632	NON_SYNONYMOUS_CODING Apc	TF binding site mE1_TFBS_chinmo
X	3776115	X_3776115_SNP [dm3] X_3882082_SNP [dm6]	T	A	1.315e^-5	0.632	SYNONYMOUS_CODING VhaAC39-1	TF binding site mE1_TFBS_cad
3L	13350340	3L_13350340_SNP [dm3] 3L_13357240_SNP [dm6]	C	T	1.340e^-5	0.632	DOWNSTREAM Nplp2 INTERGENIC
3R	26712880	3R_26712880_SNP [dm3] 3R_30887158_SNP [dm6]	G	A	1.343e^-5	0.632	INTRON Sap-r	TF binding site mE1_TFBS_cad
3L	12882349	3L_12882349_SNP [dm3] 3L_12889249_SNP [dm6]	A	C	1.429e^-5	0.632	UPSTREAM CG43894 DOWNSTREAM CR45748 & 1 other INTERGENIC
3R	24660139	3R_24660139_SNP [dm3] 3R_28834417_SNP [dm6]	T	C	1.508e^-5	0.632	SYNONYMOUS_CODING Apc	TF binding site mE1_TFBS_chinmo
3R	22951521	3R_22951521_SNP [dm3] 3R_27125799_SNP [dm6]	A	G	1.527e^-5	0.632	SYNONYMOUS_CODING CG6051	TF binding site BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo
X	10589020	X_10589020_SNP [dm3] X_10694987_SNP [dm6]	A	G	1.584e^-5	0.632	INTRON X11Lbeta
2R	16980850	2R_16980850_SNP [dm3] 2R_21093345_SNP [dm6]	G	A	1.590e^-5	0.632	INTRON CG34396
2L	11372121	2L_11372121_SNP [dm3] 2L_11372121_SNP [dm6]	A	C	1.648e^-5	0.632	SYNONYMOUS_CODING salr	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3L	2158308	3L_2158308_SNP [dm3] 3L_2158308_SNP [dm6]	C	T	1.663e^-5	0.632	SYNONYMOUS_CODING CG15822	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
X	18228818	X_18228818_SNP [dm3] X_18334785_SNP [dm6]	G	A	1.759e^-5	0.632	INTRON CG6123
2L	6091666	2L_6091666_SNP [dm3] 2L_6091666_SNP [dm6]	A	C	1.809e^-5	0.632	NON_SYNONYMOUS_CODING CG45075 UTR_5_PRIME Kr-h1 INTRON Kr-h1	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
X	15876969	X_15876969_SNP [dm3] X_15982936_SNP [dm6]	A	C	1.846e^-5	0.632	UTR_5_PRIME CG9170 UPSTREAM CG8931	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_Ubx
2R	3572008	2R_3572008_SNP [dm3] 2R_7684503_SNP [dm6]	C	A	1.946e^-5	0.632	INTRON CG1399
3R	26712730	3R_26712730_SNP [dm3] 3R_30887008_SNP [dm6]	C	A	1.958e^-5	0.632	INTRON Sap-r	TF binding site mE1_TFBS_cad
X	17176796	X_17176796_SNP [dm3] X_17282763_SNP [dm6]	T	C	1.962e^-5	0.632	UTR_5_PRIME CG5445 UPSTREAM CG8664 DOWNSTREAM CG8661	TF binding site BDTNP1_TFBS_da mE1_TFBS_inv
3L	5982519	3L_5982519_SNP [dm3] 3L_5989419_SNP [dm6]	T	C	1.981e^-5	0.632	INTERGENIC
X	6899942	X_6899942_SNP [dm3] X_7005909_SNP [dm6]	T	C	1.991e^-5	0.632	INTRON Inx7
2L	19504320	2L_19504320_SNP [dm3] 2L_19504320_SNP [dm6]	A	T	1.999e^-5	0.632	SYNONYMOUS_CODING CG10188	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	19504326	2L_19504326_SNP [dm3] 2L_19504326_SNP [dm6]	C	T	1.999e^-5	0.632	SYNONYMOUS_CODING CG10188	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	18535988	3L_18535988_SNP [dm3] 3L_18542888_SNP [dm6]	C	T	2.003e^-5	0.632	INTERGENIC
2L	17096658	2L_17096658_SNP [dm3] 2L_17096658_SNP [dm6]	A	T	2.019e^-5	0.632	INTERGENIC
2L	19504932	2L_19504932_SNP [dm3] 2L_19504932_SNP [dm6]	C	T	2.108e^-5	0.632	SYNONYMOUS_CODING CG10188	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	9563201	3L_9563201_SNP [dm3] 3L_9570101_SNP [dm6]	C	T	2.113e^-5	0.632	INTRON CG42673
2R	19049526	2R_19049526_SNP [dm3] 2R_23162003_SNP [dm6]	T	A	2.196e^-5	0.632	SYNONYMOUS_CODING CG9899
2L	3954063	2L_3954063_SNP [dm3] 2L_3954063_SNP [dm6]	G	A	2.206e^-5	0.632	INTRON fred
3L	10561289	3L_10561289_SNP [dm3] 3L_10568189_SNP [dm6]	C	G	2.209e^-5	0.632	NON_SYNONYMOUS_CODING A2bp1 INTRON A2bp1
2L	3954062	2L_3954062_SNP [dm3] 2L_3954062_SNP [dm6]	G	A	2.218e^-5	0.632	INTRON fred
X	10588055	X_10588055_SNP [dm3] X_10694022_SNP [dm6]	A	G	2.230e^-5	0.632	INTRON X11Lbeta
2L	10830936	2L_10830936_DEL [dm3] 2L_10830936_DEL [dm6]	TC	T	2.234e^-5	0.632	INTRON Nos
3L	11837424	3L_11837424_SNP [dm3] 3L_11844324_SNP [dm6]	G	T	2.241e^-5	0.632	INTERGENIC
3R	26712976	3R_26712976_SNP [dm3] 3R_30887254_SNP [dm6]	A	T	2.291e^-5	0.632	INTRON Sap-r
3R	21513204	3R_21513204_SNP [dm3] 3R_25687482_SNP [dm6]	A	C	2.399e^-5	0.632	UPSTREAM CLS INTERGENIC	TF binding site mE1_TFBS_cad
X	17176893	X_17176893_SNP [dm3] X_17282860_SNP [dm6]	A	G	2.426e^-5	0.632	UPSTREAM CG8664 DOWNSTREAM CG8661 INTRON CG5445	TF binding site mE1_TFBS_inv
3L	7755554	3L_7755554_SNP [dm3] 3L_7762454_SNP [dm6]	C	T	2.456e^-5	0.632	SYNONYMOUS_CODING Hn DOWNSTREAM Clk
X	17179596	X_17179596_SNP [dm3] X_17285563_SNP [dm6]	G	A	2.500e^-5	0.632	DOWNSTREAM Fim INTRON CG5445	TF binding site BDTNP1_TFBS_dl
3L	4957037	3L_4957037_SNP [dm3] 3L_4957037_SNP [dm6]	C	T	2.504e^-5	0.632	INTRON Con
3L	12844018	3L_12844018_SNP [dm3] 3L_12850918_SNP [dm6]	T	C	2.550e^-5	0.632	SYNONYMOUS_CODING Wbp2 UPSTREAM CG10948	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
3L	16399527	3L_16399527_SNP [dm3] 3L_16406427_SNP [dm6]	A	T	2.570e^-5	0.632	INTRON fax
2L	5509172	2L_5509172_SNP [dm3] 2L_5509172_SNP [dm6]	G	T	2.658e^-5	0.632	INTERGENIC
X	18537891	X_18537891_SNP [dm3] X_18643858_SNP [dm6]	T	C	2.665e^-5	0.632	INTRON Rip11	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3R	7794857	3R_7794857_SNP [dm3] 3R_11969135_SNP [dm6]	A	C	2.714e^-5	0.632	INTRON GC1
2L	11372106	2L_11372106_SNP [dm3] 2L_11372106_SNP [dm6]	C	T	2.737e^-5	0.632	SYNONYMOUS_CODING salr	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3L	4932450	3L_4932450_SNP [dm3] 3L_4932450_SNP [dm6]	A	G	2.800e^-5	0.632	INTERGENIC	regulatory region REDfly_CRMs
3R	19723072	3R_19723072_SNP [dm3] 3R_23897350_SNP [dm6]	C	T	2.855e^-5	0.632	SPLICE_SITE_REGION sba INTRON sba
3L	11837443	3L_11837443_SNP [dm3] 3L_11844343_SNP [dm6]	C	T	2.871e^-5	0.632	INTERGENIC
3L	14368641	3L_14368641_SNP [dm3] 3L_14375541_SNP [dm6]	T	A	2.913e^-5	0.632	INTERGENIC
3R	17735740	3R_17735740_SNP [dm3] 3R_21910018_SNP [dm6]	A	T	2.921e^-5	0.632	INTERGENIC
X	14566536	X_14566536_SNP [dm3] X_14672503_SNP [dm6]	T	G	2.930e^-5	0.632	INTERGENIC
2L	6088913	2L_6088913_SNP [dm3] 2L_6088913_SNP [dm6]	C	T	2.997e^-5	0.632	INTRON Kr-h1	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_run mE1_TFBS_sens mE1_TFBS_Trl
X	18544669	X_18544669_SNP [dm3] X_18650636_SNP [dm6]	C	T	3.020e^-5	0.632	UPSTREAM CG6617 DOWNSTREAM Ing3 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_chinmo
3R	25741574	3R_25741574_SNP [dm3] 3R_29915852_SNP [dm6]	A	G	3.025e^-5	0.632	SYNONYMOUS_CODING trp UTR_3_PRIME trp	TF binding site mE1_TFBS_chinmo
2L	924818	2L_924818_SNP [dm3] 2L_924818_SNP [dm6]	G	A	3.040e^-5	0.632	INTRON CG4341
2L	13501584	2L_13501584_SNP [dm3] 2L_13501584_SNP [dm6]	G	T	3.084e^-5	0.632	UTR_3_PRIME B4
X	3793894	X_3793894_SNP [dm3] X_3899861_SNP [dm6]	G	C	3.266e^-5	0.632	INTRON CG42541
3R	25524290	3R_25524290_INS [dm3] 3R_29698568_INS [dm6]	G	GAG	3.303e^-5	0.632	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	7213844	2R_7213844_SNP [dm3] 2R_11326339_SNP [dm6]	G	A	3.425e^-5	0.632	INTRON sha	TF binding site mE1_TFBS_Trl
X	3778948	X_3778948_INS [dm3] X_3884915_INS [dm6]	T	TCG	3.448e^-5	0.632	INTRON CG15239
X	17175125	X_17175125_SNP [dm3] X_17281092_SNP [dm6]	A	G	3.537e^-5	0.632	UTR_3_PRIME CG8664 DOWNSTREAM CG8664 & 1 other	transposable element FlyBase
2L	20476118	2L_20476118_SNP [dm3] 2L_20476118_SNP [dm6]	C	T	3.543e^-5	0.632	DOWNSTREAM CR43234 INTRON CR44980	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi
3R	22994718	3R_22994718_SNP [dm3] 3R_27168996_SNP [dm6]	G	A	3.545e^-5	0.632	INTERGENIC	regulatory region REDfly_CRMs
3L	16399528	3L_16399528_SNP [dm3] 3L_16406428_SNP [dm6]	G	A	3.559e^-5	0.632	INTRON fax
X	18546216	X_18546216_SNP [dm3] X_18652183_SNP [dm6]	G	A	3.612e^-5	0.632	SYNONYMOUS_CODING Ing3	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	908421	2L_908421_INS [dm3] 2L_908421_INS [dm6]	T	TGTCATATCATGATATCA...	3.684e^-5	0.632	INTERGENIC
3R	3735139	3R_3735139_SNP [dm3] 3R_7909417_SNP [dm6]	T	A	3.694e^-5	0.632	UTR_3_PRIME Taf7 DOWNSTREAM Prat & 1 other
X	12096109	X_12096109_SNP [dm3] X_12202076_SNP [dm6]	A	G	3.702e^-5	0.632	INTRON Ten-a
2L	5899820	2L_5899820_SNP [dm3] 2L_5899820_SNP [dm6]	A	C	3.715e^-5	0.632	DOWNSTREAM CR44579 INTERGENIC
X	20839875	X_20839875_SNP [dm3] X_20968848_SNP [dm6]	C	A	3.727e^-5	0.632	INTERGENIC

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By genomic position
Variant impact
Gene name

Baseline_mean phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results