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=4.376e^-1)
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
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1881 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	12687447	2R_12687447_SNP [dm3] 2R_16799942_SNP [dm6]	T	A	5.040e^-7	0.878	INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_zfh1
2L	10885834	2L_10885834_SNP [dm3] 2L_10885834_SNP [dm6]	A	G	1.110e^-6	0.878	UPSTREAM CR44490 INTERGENIC
3R	12888013	3R_12888013_SNP [dm3] 3R_17062291_SNP [dm6]	C	T	3.487e^-6	0.878	INTRON Dad	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	12687356	2R_12687356_DEL [dm3] 2R_16799851_DEL [dm6]	TGGTGAATT	T	3.739e^-6	0.878	INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_zfh1
2R	12687436	2R_12687436_SNP [dm3] 2R_16799931_SNP [dm6]	G	A	4.169e^-6	0.878	INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_zfh1
2R	12111465	2R_12111465_SNP [dm3] 2R_16223960_SNP [dm6]	G	T	4.475e^-6	0.878	SYNONYMOUS_CODING CG15706 DOWNSTREAM CR43898	TF binding site mE1_TFBS_HSA
2R	12687446	2R_12687446_SNP [dm3] 2R_16799941_SNP [dm6]	T	C	4.582e^-6	0.878	INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_zfh1
3L	11847029	3L_11847029_SNP [dm3] 3L_11853929_SNP [dm6]	A	C	5.315e^-6	0.878	INTRON CG44837
2R	12687371	2R_12687371_SNP [dm3] 2R_16799866_SNP [dm6]	A	G	5.526e^-6	0.878	INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_zfh1
2R	12687403	2R_12687403_SNP [dm3] 2R_16799898_SNP [dm6]	T	G	5.918e^-6	0.878	INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_zfh1
3R	26255759	3R_26255759_SNP [dm3] 3R_30430037_SNP [dm6]	T	A	5.934e^-6	0.878	INTRON CG15533	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2R	12687965	2R_12687965_SNP [dm3] 2R_16800460_SNP [dm6]	T	C	7.977e^-6	0.878	INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_zfh1
X	16819682	X_16819682_SNP [dm3] X_16925649_SNP [dm6]	G	C	8.067e^-6	0.878	INTRON CG4928
3R	12888003	3R_12888003_SNP [dm3] 3R_17062281_SNP [dm6]	T	A	9.095e^-6	0.878	INTRON Dad	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	14493569	2R_14493569_SNP [dm3] 2R_18606064_SNP [dm6]	T	A	1.113e^-5	0.878	INTRON GEFmeso
3R	6743400	3R_6743400_SNP [dm3] 3R_10917678_SNP [dm6]	C	T	1.158e^-5	0.878	INTERGENIC
3L	11846981	3L_11846981_SNP [dm3] 3L_11853881_SNP [dm6]	G	T	1.348e^-5	0.878	INTRON CG44837
3R	26255757	3R_26255757_INS [dm3] 3R_30430035_INS [dm6]	T	TC	1.454e^-5	0.878	INTRON CG15533	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2R	7874300	2R_7874300_DEL [dm3] 2R_11986795_DEL [dm6]	AGCGTAGTGCTACT...	A	1.574e^-5	0.878	UTR_3_PRIME rho-7 & 1 other	TF binding site mE1_TFBS_sens
2L	4080642	2L_4080642_SNP [dm3] 2L_4080642_SNP [dm6]	C	G	1.583e^-5	0.878	INTRON ed	TF binding site BDTNP1_TFBS_dl
3R	22818632	3R_22818632_SNP [dm3] 3R_26992910_SNP [dm6]	A	T	1.589e^-5	0.878	INTERGENIC
3L	1007912	3L_1007912_SNP [dm3] 3L_1007912_SNP [dm6]	G	A	1.618e^-5	0.878	UPSTREAM trio INTRON trio	TF binding site mE1_TFBS_inv
3R	4362491	3R_4362491_SNP [dm3] 3R_8536769_SNP [dm6]	A	G	1.644e^-5	0.878	INTERGENIC
2L	9179605	2L_9179605_DEL [dm3] 2L_9179605_DEL [dm6]	TT	A	1.671e^-5	0.878	INTRON tai	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
2L	9035324	2L_9035324_SNP [dm3] 2L_9035324_SNP [dm6]	G	T	1.702e^-5	0.878	INTERGENIC
3R	12605734	3R_12605734_SNP [dm3] 3R_16780012_SNP [dm6]	T	C	1.707e^-5	0.878	INTERGENIC
2R	12687558	2R_12687558_INS [dm3] 2R_16800053_INS [dm6]	A	ATTTTTTACATTAA...	1.768e^-5	0.878	INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_zfh1
2R	15591974	2R_15591974_DEL [dm3] 2R_19704469_DEL [dm6]	ATATA	T	1.799e^-5	0.878	UPSTREAM Obp56d INTERGENIC	regulatory region REDfly_CRMs
2R	12687381	2R_12687381_SNP [dm3] 2R_16799876_SNP [dm6]	T	A	1.808e^-5	0.878	INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_zfh1
3R	12888015	3R_12888015_SNP [dm3] 3R_17062293_SNP [dm6]	C	T	1.822e^-5	0.878	INTRON Dad	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	16740735	3L_16740735_SNP [dm3] 3L_16747635_SNP [dm6]	C	G	1.832e^-5	0.878	INTERGENIC
2R	14322014	2R_14322014_SNP [dm3] 2R_18434509_SNP [dm6]	T	G	1.885e^-5	0.878	INTRON CG30118
3R	12520991	3R_12520991_SNP [dm3] 3R_16695269_SNP [dm6]	A	T	2.009e^-5	0.878	INTRON Ubx	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl
3L	3979048	3L_3979048_DEL [dm3] 3L_3979048_DEL [dm6]	ACA	A	2.031e^-5	0.878	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_sens
2R	12687476	2R_12687476_SNP [dm3] 2R_16799971_SNP [dm6]	A	T	2.240e^-5	0.878	INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_zfh1
2R	12687465	2R_12687465_DEL [dm3] 2R_16799960_DEL [dm6]	TG	T	2.399e^-5	0.878	INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_zfh1
2L	16700783	2L_16700783_INS [dm3] 2L_16700783_INS [dm6]	G	GAT	2.479e^-5	0.878	DOWNSTREAM grp & 1 other EXON CR43669
2R	12687477	2R_12687477_SNP [dm3] 2R_16799972_SNP [dm6]	A	G	2.480e^-5	0.878	INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_zfh1
2R	13398371	2R_13398371_SNP [dm3] 2R_17510866_SNP [dm6]	G	A	2.481e^-5	0.878	UTR_3_PRIME CG34193 UPSTREAM CG4847 DOWNSTREAM CG34193
2R	12927738	2R_12927738_SNP [dm3] 2R_17040233_SNP [dm6]	C	A	2.503e^-5	0.878	INTRON RhoGEF2 EXON CR45145
3L	11846806	3L_11846806_SNP [dm3] 3L_11853706_SNP [dm6]	T	G	2.521e^-5	0.878	INTRON CG44837
2R	12687473	2R_12687473_INS [dm3] 2R_16799968_INS [dm6]	A	AT	2.544e^-5	0.878	INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_zfh1
3L	11846459	3L_11846459_SNP [dm3] 3L_11853359_SNP [dm6]	A	G	2.559e^-5	0.878	INTRON CG44837
X	20515241	X_20515241_SNP [dm3] X_20644214_SNP [dm6]	A	G	2.592e^-5	0.878	INTERGENIC	enhancer mE1_CBP_Enhancers silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_hkb mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_Trl
3L	8579762	3L_8579762_SNP [dm3] 3L_8586662_SNP [dm6]	G	C	2.656e^-5	0.878	SYNONYMOUS_CODING CG43078 UTR_5_PRIME CG43078	TF binding site mE1_TFBS_chinmo
2R	12687908	2R_12687908_SNP [dm3] 2R_16800403_SNP [dm6]	C	T	2.690e^-5	0.878	INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_zfh1
2R	12687426	2R_12687426_SNP [dm3] 2R_16799921_SNP [dm6]	A	T	2.709e^-5	0.878	INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_zfh1
2R	7874315	2R_7874315_SNP [dm3] 2R_11986810_SNP [dm6]	G	A	2.754e^-5	0.878	UTR_3_PRIME rho-7 & 1 other	TF binding site mE1_TFBS_sens
2R	13472400	2R_13472400_SNP [dm3] 2R_17584895_SNP [dm6]	A	G	2.799e^-5	0.878	UPSTREAM CG6484 & 1 other DOWNSTREAM CG14483 & 1 other INTERGENIC
2L	9035277	2L_9035277_SNP [dm3] 2L_9035277_SNP [dm6]	G	T	2.882e^-5	0.878	INTERGENIC
2R	1251733	2R_1251733_SNP [dm3] 2R_5364228_SNP [dm6]	G	A	2.887e^-5	0.878	INTRON CR42646 EXON CR42646
2R	1260892	2R_1260892_SNP [dm3] 2R_5373387_SNP [dm6]	G	A	2.887e^-5	0.878	INTERGENIC	transposable element FlyBase
2R	1263229	2R_1263229_SNP [dm3] 2R_5375724_SNP [dm6]	A	G	2.887e^-5	0.878	INTERGENIC	transposable element FlyBase
2R	1264160	2R_1264160_DEL [dm3] 2R_5376655_DEL [dm6]	TCTTGTA	GG	2.887e^-5	0.878	INTERGENIC	transposable element FlyBase
2R	1264168	2R_1264168_SNP [dm3] 2R_5376663_SNP [dm6]	A	G	2.887e^-5	0.878	INTERGENIC	transposable element FlyBase
2R	1264180	2R_1264180_SNP [dm3] 2R_5376675_SNP [dm6]	T	A	2.887e^-5	0.878	INTERGENIC	transposable element FlyBase
2R	1253433	2R_1253433_SNP [dm3] 2R_5365928_SNP [dm6]	C	T	2.889e^-5	0.878	EXON CR42646
2R	1264792	2R_1264792_SNP [dm3] 2R_5377287_SNP [dm6]	C	A	2.901e^-5	0.878	INTERGENIC	transposable element FlyBase
3R	12510232	3R_12510232_SNP [dm3] 3R_16684510_SNP [dm6]	G	A	2.927e^-5	0.878	INTRON Ubx	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_sbb
X	15288048	X_15288048_SNP [dm3] X_15394015_SNP [dm6]	T	C	3.046e^-5	0.878	SYNONYMOUS_CODING Cngl	TF binding site mE1_TFBS_chinmo
2L	3413976	2L_3413976_SNP [dm3] 2L_3413976_SNP [dm6]	T	C	3.139e^-5	0.878	INTRON pgant2	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2L	3413986	2L_3413986_SNP [dm3] 2L_3413986_SNP [dm6]	T	C	3.139e^-5	0.878	INTRON pgant2	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2R	14322005	2R_14322005_SNP [dm3] 2R_18434500_SNP [dm6]	C	T	3.142e^-5	0.878	INTRON CG30118
2R	7874247	2R_7874247_DEL [dm3] 2R_11986742_DEL [dm6]	TT	T	3.145e^-5	0.878	UTR_3_PRIME rho-7 & 1 other	TF binding site mE1_TFBS_sens
2R	12687376	2R_12687376_SNP [dm3] 2R_16799871_SNP [dm6]	T	C	3.171e^-5	0.878	INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_zfh1
2R	1264120	2R_1264120_SNP [dm3] 2R_5376615_SNP [dm6]	A	C	3.202e^-5	0.878	INTERGENIC	transposable element FlyBase
3R	13551918	3R_13551918_SNP [dm3] 3R_17726196_SNP [dm6]	T	C	3.259e^-5	0.878	INTRON Lgr1	TF binding site BDTNP1_TFBS_gt BDTNP1_TFBS_sna mE1_TFBS_HSA
3L	18185165	3L_18185165_SNP [dm3] 3L_18192065_SNP [dm6]	A	T	3.268e^-5	0.878	INTERGENIC
3R	23856598	3R_23856598_SNP [dm3] 3R_28030876_SNP [dm6]	G	T	3.348e^-5	0.878	NON_SYNONYMOUS_CODING CG34362	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3L	11730428	3L_11730428_SNP [dm3] 3L_11737328_SNP [dm6]	G	A	3.391e^-5	0.878	INTRON CG6024	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2R	19202958	2R_19202958_SNP [dm3] 2R_23315435_SNP [dm6]	A	G	3.399e^-5	0.878	INTERGENIC
3R	12524393	3R_12524393_SNP [dm3] 3R_16698671_SNP [dm6]	A	G	3.426e^-5	0.878	INTRON Ubx	regulatory region REDfly_CRMs
3R	8066983	3R_8066983_SNP [dm3] 3R_12241261_SNP [dm6]	C	T	3.579e^-5	0.878	DOWNSTREAM CR44036 INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
3R	12510244	3R_12510244_SNP [dm3] 3R_16684522_SNP [dm6]	A	T	3.610e^-5	0.878	INTRON Ubx	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sbb
3L	16721156	3L_16721156_SNP [dm3] 3L_16728056_SNP [dm6]	C	T	3.616e^-5	0.878	UPSTREAM PGRP-SB1 DOWNSTREAM PGRP-SB2 & 1 other INTERGENIC	regulatory region REDfly_CRMs TF binding site mE1_TFBS_cad
2R	14530546	2R_14530546_SNP [dm3] 2R_18643041_SNP [dm6]	T	G	3.637e^-5	0.878	INTRON SP2637
2R	11612951	2R_11612951_SNP [dm3] 2R_15725446_SNP [dm6]	G	A	3.687e^-5	0.878	INTERGENIC
2R	12623697	2R_12623697_SNP [dm3] 2R_16736192_SNP [dm6]	T	C	3.721e^-5	0.878	DOWNSTREAM CG43104 INTERGENIC
3R	12509231	3R_12509231_SNP [dm3] 3R_16683509_SNP [dm6]	G	A	3.760e^-5	0.878	INTRON Ubx	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb
2L	15283143	2L_15283143_SNP [dm3] 2L_15283143_SNP [dm6]	A	T	3.799e^-5	0.878	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3L	11846811	3L_11846811_SNP [dm3] 3L_11853711_SNP [dm6]	T	G	3.836e^-5	0.878	INTRON CG44837
2L	1623493	2L_1623493_SNP [dm3] 2L_1623493_SNP [dm6]	G	A	3.843e^-5	0.878	UPSTREAM CR44603 EXON CR44603
3R	24829701	3R_24829701_SNP [dm3] 3R_29003979_SNP [dm6]	C	G	3.974e^-5	0.886	INTRON wat
2L	9035256	2L_9035256_SNP [dm3] 2L_9035256_SNP [dm6]	A	G	4.017e^-5	0.886	INTERGENIC
2R	1325991	2R_1325991_SNP [dm3] 2R_5438486_SNP [dm6]	G	C	4.076e^-5	0.886	INTRON laccase2
3R	22818557	3R_22818557_SNP [dm3] 3R_26992835_SNP [dm6]	A	T	4.364e^-5	0.886	INTERGENIC
2L	9035355	2L_9035355_SNP [dm3] 2L_9035355_SNP [dm6]	T	A	4.460e^-5	0.886	INTERGENIC
2L	3411205	2L_3411205_SNP [dm3] 2L_3411205_SNP [dm6]	C	A	4.505e^-5	0.886	DOWNSTREAM CG8840 INTRON pgant2
3L	14912246	3L_14912246_SNP [dm3] 3L_14919146_SNP [dm6]	A	T	4.583e^-5	0.886	INTRON DCX-EMAP
3R	13924370	3R_13924370_SNP [dm3] 3R_18098648_SNP [dm6]	G	A	4.627e^-5	0.886	INTRON sr
2R	17293376	2R_17293376_SNP [dm3] 2R_21405871_SNP [dm6]	T	C	4.684e^-5	0.886	INTRON Sdc
2R	17293389	2R_17293389_SNP [dm3] 2R_21405884_SNP [dm6]	G	A	4.684e^-5	0.886	INTRON Sdc
3R	26254722	3R_26254722_SNP [dm3] 3R_30429000_SNP [dm6]	C	T	4.702e^-5	0.886	SYNONYMOUS_CODING CG15533 UPSTREAM CG2218	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	11846446	3L_11846446_SNP [dm3] 3L_11853346_SNP [dm6]	A	T	4.756e^-5	0.886	INTRON CG44837
2L	4440203	2L_4440203_SNP [dm3] 2L_4440203_SNP [dm6]	A	T	4.843e^-5	0.886	UPSTREAM CG15431 INTRON CG15431
2R	1323727	2R_1323727_SNP [dm3] 2R_5436222_SNP [dm6]	A	T	4.875e^-5	0.886	SYNONYMOUS_CODING laccase2
3L	13298701	3L_13298701_SNP [dm3] 3L_13305601_SNP [dm6]	T	C	4.911e^-5	0.886	INTERGENIC
2L	9996671	2L_9996671_SNP [dm3] 2L_9996671_SNP [dm6]	T	A	4.948e^-5	0.886	UPSTREAM CG31875 DOWNSTREAM SoYb INTRON CG31875	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Ubx
3R	16186080	3R_16186080_SNP [dm3] 3R_20360358_SNP [dm6]	G	A	4.976e^-5	0.886	NON_SYNONYMOUS_CODING MtnC DOWNSTREAM CR45023
3R	16186107	3R_16186107_SNP [dm3] 3R_20360385_SNP [dm6]	G	A	4.976e^-5	0.886	DOWNSTREAM CR45023 INTRON MtnC

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By genomic position
Variant impact
Gene name

TyrR_CT phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results