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=2.002e^-14)
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

2626 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

Show entries

Search:

Chromosome	Position	ID	Reference	Variant	p-value	FDR_BH	Transcript annotation	Binding site annotation
X	16430681	X_16430681_SNP [dm3] X_16536648_SNP [dm6]	T	A	4.201e^-7	0.483	INTERGENIC
3L	1999062	3L_1999062_SNP [dm3] 3L_1999062_SNP [dm6]	T	C	7.229e^-7	0.483	INTERGENIC
2R	2051002	2R_2051002_SNP [dm3] 2R_6163497_SNP [dm6]	A	C	7.723e^-7	0.483	UPSTREAM tRNA:K2:42Ac DOWNSTREAM tRNA:N5:42Aa INTRON EcR	transposable element FlyBase
3L	9355412	3L_9355412_SNP [dm3] 3L_9362312_SNP [dm6]	C	T	1.087e^-6	0.508	SYNONYMOUS_CODING CG34456 DOWNSTREAM Klp67A & 1 other
3L	1999043	3L_1999043_SNP [dm3] 3L_1999043_SNP [dm6]	G	A	1.648e^-6	0.508	INTERGENIC
3R	19200773	3R_19200773_SNP [dm3] 3R_23375051_SNP [dm6]	C	T	1.926e^-6	0.508	DOWNSTREAM CG42828 & 1 other INTERGENIC
3R	19088328	3R_19088328_SNP [dm3] 3R_23262606_SNP [dm6]	G	A	1.934e^-6	0.508	UTR_3_PRIME orb
2L	20942131	2L_20942131_SNP [dm3] 2L_20942131_SNP [dm6]	G	A	2.169e^-6	0.508	INTERGENIC
3L	1999145	3L_1999145_SNP [dm3] 3L_1999145_SNP [dm6]	G	A	2.891e^-6	0.538	INTERGENIC
3L	9304488	3L_9304488_SNP [dm3] 3L_9311388_SNP [dm6]	G	C	3.207e^-6	0.538	INTERGENIC
3L	1997949	3L_1997949_SNP [dm3] 3L_1997949_SNP [dm6]	G	C	3.640e^-6	0.538	INTERGENIC
X	11349981	X_11349981_SNP [dm3] X_11455948_SNP [dm6]	C	A	3.933e^-6	0.538	NON_SYNONYMOUS_CODING HP5	TF binding site mE1_TFBS_sens
3L	2003168	3L_2003168_SNP [dm3] 3L_2003168_SNP [dm6]	C	A	3.975e^-6	0.538	UTR_3_PRIME CG42841
3L	2004455	3L_2004455_DEL [dm3] 3L_2004455_DEL [dm6]	TCG	A	4.076e^-6	0.538	DOWNSTREAM CG42841 INTRON CG42841
3L	2004922	3L_2004922_INS [dm3] 3L_2004922_INS [dm6]	T	TGGTGTGT	4.306e^-6	0.538	DOWNSTREAM CG42841 INTRON CG42841
3L	16471811	3L_16471811_SNP [dm3] 3L_16478711_SNP [dm6]	A	C	5.120e^-6	0.6	INTRON CG33158 & 1 other
3R	13964446	3R_13964446_SNP [dm3] 3R_18138724_SNP [dm6]	A	G	5.623e^-6	0.604	INTERGENIC
2L	10834243	2L_10834243_SNP [dm3] 2L_10834243_SNP [dm6]	C	T	6.189e^-6	0.604	INTRON Nos
2L	1140456	2L_1140456_SNP [dm3] 2L_1140456_SNP [dm6]	C	T	6.579e^-6	0.604	UTR_3_PRIME CG4577
3R	16534452	3R_16534452_SNP [dm3] 3R_20708730_SNP [dm6]	A	T	6.841e^-6	0.604	INTRON Oamb
3L	2004753	3L_2004753_SNP [dm3] 3L_2004753_SNP [dm6]	G	A	7.481e^-6	0.604	DOWNSTREAM CG42841 INTRON CG42841
2L	21065272	2L_21065272_SNP [dm3] 2L_21065272_SNP [dm6]	A	G	7.927e^-6	0.604	INTRON CG9265
2R	17204081	2R_17204081_SNP [dm3] 2R_21316576_SNP [dm6]	G	A	8.320e^-6	0.604	SYNONYMOUS_CODING CG9485	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2R	3902264	2R_3902264_SNP [dm3] 2R_8014759_SNP [dm6]	T	C	8.574e^-6	0.604	UPSTREAM mir-4981 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_bab1
3L	2004308	3L_2004308_SNP [dm3] 3L_2004308_SNP [dm6]	G	C	9.169e^-6	0.604	DOWNSTREAM CG42841 INTRON CG42841
X	3986496	X_3986496_SNP [dm3] X_4092463_SNP [dm6]	C	A	9.600e^-6	0.604	DOWNSTREAM CG43689 INTERGENIC
3R	19034837	3R_19034837_SNP [dm3] 3R_23209115_SNP [dm6]	A	T	9.942e^-6	0.604	INTRON cnc
3L	2005293	3L_2005293_SNP [dm3] 3L_2005293_SNP [dm6]	A	G	1.083e^-5	0.604	UTR_3_PRIME CG42841
3L	5600033	3L_5600033_SNP [dm3] 3L_5606933_SNP [dm6]	A	T	1.090e^-5	0.604	UTR_3_PRIME mthl2 DOWNSTREAM Eaf6
X	12407473	X_12407473_INS [dm3] X_12513440_INS [dm6]	T	TT	1.093e^-5	0.604	INTRON CG2556	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2L	10834245	2L_10834245_SNP [dm3] 2L_10834245_SNP [dm6]	G	A	1.192e^-5	0.604	INTRON Nos
3L	1999192	3L_1999192_SNP [dm3] 3L_1999192_SNP [dm6]	G	A	1.235e^-5	0.604	INTERGENIC
3L	18947292	3L_18947292_SNP [dm3] 3L_18954192_SNP [dm6]	A	C	1.289e^-5	0.604	INTRON CG6836
3L	2004298	3L_2004298_SNP [dm3] 3L_2004298_SNP [dm6]	T	A	1.335e^-5	0.604	DOWNSTREAM CG42841 INTRON CG42841
3R	25398180	3R_25398180_SNP [dm3] 3R_29572458_SNP [dm6]	A	G	1.348e^-5	0.604	INTERGENIC	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_Trl
3R	25398178	3R_25398178_SNP [dm3] 3R_29572456_SNP [dm6]	A	G	1.359e^-5	0.604	INTERGENIC	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_Trl
2R	10843629	2R_10843629_SNP [dm3] 2R_14956124_SNP [dm6]	G	A	1.364e^-5	0.604	INTRON aPKC
3L	10236960	3L_10236960_SNP [dm3] 3L_10243860_SNP [dm6]	A	T	1.406e^-5	0.604	UPSTREAM CR44541 INTRON Or67c
3R	25463438	3R_25463438_SNP [dm3] 3R_29637716_SNP [dm6]	A	G	1.442e^-5	0.604	INTRON Dop1R2
2L	9839036	2L_9839036_SNP [dm3] 2L_9839036_SNP [dm6]	G	C	1.447e^-5	0.604	INTRON nAChRalpha6
2R	12023859	2R_12023859_SNP [dm3] 2R_16136354_SNP [dm6]	T	C	1.465e^-5	0.604	SYNONYMOUS_CODING spin UTR_3_PRIME spin
3L	1996667	3L_1996667_SNP [dm3] 3L_1996667_SNP [dm6]	A	G	1.485e^-5	0.604	INTERGENIC
3R	14437361	3R_14437361_SNP [dm3] 3R_18611639_SNP [dm6]	T	A	1.585e^-5	0.604	INTRON qin & 1 other
3L	5600035	3L_5600035_SNP [dm3] 3L_5606935_SNP [dm6]	A	T	1.619e^-5	0.604	UTR_3_PRIME mthl2 DOWNSTREAM Eaf6
2L	21065275	2L_21065275_SNP [dm3] 2L_21065275_SNP [dm6]	C	T	1.629e^-5	0.604	INTRON CG9265
3R	14437375	3R_14437375_SNP [dm3] 3R_18611653_SNP [dm6]	T	A	1.631e^-5	0.604	INTRON qin & 1 other
3L	1273290	3L_1273290_SNP [dm3] 3L_1273290_SNP [dm6]	A	T	1.659e^-5	0.604	INTRON CG9134
3L	5600030	3L_5600030_DEL [dm3] 3L_5606930_DEL [dm6]	AC	A	1.692e^-5	0.604	UTR_3_PRIME mthl2 DOWNSTREAM Eaf6
3L	2835271	3L_2835271_SNP [dm3] 3L_2835271_SNP [dm6]	T	A	1.702e^-5	0.604	INTRON CG43444
3L	2000949	3L_2000949_SNP [dm3] 3L_2000949_SNP [dm6]	C	T	1.710e^-5	0.604	INTERGENIC
3R	13685496	3R_13685496_SNP [dm3] 3R_17859774_SNP [dm6]	C	A	1.720e^-5	0.604	INTRON tinc
3L	2835279	3L_2835279_SNP [dm3] 3L_2835279_SNP [dm6]	A	T	1.747e^-5	0.604	INTRON CG43444
3L	2002534	3L_2002534_SNP [dm3] 3L_2002534_SNP [dm6]	T	A	1.759e^-5	0.604	DOWNSTREAM CG42841 INTERGENIC
2L	13237450	2L_13237450_SNP [dm3] 2L_13237450_SNP [dm6]	G	A	1.794e^-5	0.604	INTRON CG5867
3L	5600037	3L_5600037_INS [dm3] 3L_5606937_INS [dm6]	G	GAA	1.829e^-5	0.604	UTR_3_PRIME mthl2 DOWNSTREAM Eaf6
3R	23382864	3R_23382864_DEL [dm3] 3R_27557142_DEL [dm6]	AGA	A	1.829e^-5	0.604	INTRON Klp98A	TF binding site BDTNP1_TFBS_z
3R	25220787	3R_25220787_SNP [dm3] 3R_29395065_SNP [dm6]	C	G	1.852e^-5	0.604	INTRON Ptp99A
2R	9420329	2R_9420329_SNP [dm3] 2R_13532824_SNP [dm6]	A	G	1.990e^-5	0.604	UTR_5_PRIME Vmat INTRON Vmat	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
3R	26024512	3R_26024512_SNP [dm3] 3R_30198790_SNP [dm6]	A	C	2.025e^-5	0.604	NON_SYNONYMOUS_CODING CG9743	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2R	17204093	2R_17204093_SNP [dm3] 2R_21316588_SNP [dm6]	A	C	2.034e^-5	0.604	SYNONYMOUS_CODING CG9485	TF binding site mE1_TFBS_cad mE1_TFBS_sens
3L	5992565	3L_5992565_SNP [dm3] 3L_5999465_SNP [dm6]	C	A	2.057e^-5	0.604	INTRON PVRAP
3R	20264189	3R_20264189_SNP [dm3] 3R_24438467_SNP [dm6]	A	T	2.068e^-5	0.604	INTRON nAChRalpha1
3R	22067020	3R_22067020_SNP [dm3] 3R_26241298_SNP [dm6]	C	G	2.102e^-5	0.604	INTRON CR42745
2L	9839039	2L_9839039_SNP [dm3] 2L_9839039_SNP [dm6]	A	G	2.138e^-5	0.604	INTRON nAChRalpha6
3L	1996694	3L_1996694_SNP [dm3] 3L_1996694_SNP [dm6]	T	C	2.149e^-5	0.604	INTERGENIC
3R	16534400	3R_16534400_SNP [dm3] 3R_20708678_SNP [dm6]	G	A	2.149e^-5	0.604	INTRON Oamb
X	6157570	X_6157570_SNP [dm3] X_6263537_SNP [dm6]	T	G	2.190e^-5	0.604	INTRON schlank
3R	18644615	3R_18644615_SNP [dm3] 3R_22818893_SNP [dm6]	G	A	2.216e^-5	0.604	INTERGENIC
2R	11788652	2R_11788652_SNP [dm3] 2R_15901147_SNP [dm6]	G	T	2.251e^-5	0.604	INTRON sli	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3L	13769604	3L_13769604_SNP [dm3] 3L_13776504_SNP [dm6]	C	A	2.302e^-5	0.604	INTRON bru-3
2L	9281511	2L_9281511_SNP [dm3] 2L_9281511_SNP [dm6]	C	A	2.313e^-5	0.604	INTRON Ggamma30A
3L	1996616	3L_1996616_SNP [dm3] 3L_1996616_SNP [dm6]	C	G	2.318e^-5	0.604	INTERGENIC
2L	12619533	2L_12619533_SNP [dm3] 2L_12619533_SNP [dm6]	G	A	2.430e^-5	0.608	INTRON Ref2 & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
2R	9385622	2R_9385622_SNP [dm3] 2R_13498117_SNP [dm6]	T	A	2.438e^-5	0.608	INTRON drk
3R	19034780	3R_19034780_SNP [dm3] 3R_23209058_SNP [dm6]	C	T	2.440e^-5	0.608	INTRON cnc
3L	11618712	3L_11618712_SNP [dm3] 3L_11625612_SNP [dm6]	C	T	2.498e^-5	0.608	SPLICE_SITE_REGION CG6083 UPSTREAM PCID2 INTRON CG6083
X	13844763	X_13844763_INS [dm3] X_13950730_INS [dm6]	C	ATGGA	2.517e^-5	0.608	INTRON mamo
2R	12807373	2R_12807373_SNP [dm3] 2R_16919868_SNP [dm6]	A	T	2.586e^-5	0.608	INTERGENIC
3L	11121264	3L_11121264_SNP [dm3] 3L_11128164_SNP [dm6]	C	G	2.614e^-5	0.608	INTRON CG42575
3R	16534441	3R_16534441_SNP [dm3] 3R_20708719_SNP [dm6]	C	T	2.635e^-5	0.608	INTRON Oamb
3L	6001607	3L_6001607_SNP [dm3] 3L_6008507_SNP [dm6]	T	C	2.683e^-5	0.608	DOWNSTREAM alphaKap4 INTRON PVRAP
2R	12807372	2R_12807372_SNP [dm3] 2R_16919867_SNP [dm6]	T	A	2.724e^-5	0.608	INTERGENIC
3L	1996691	3L_1996691_SNP [dm3] 3L_1996691_SNP [dm6]	G	C	2.753e^-5	0.608	INTERGENIC
3L	17280352	3L_17280352_SNP [dm3] 3L_17287252_SNP [dm6]	G	A	2.768e^-5	0.608	INTERGENIC
X	17204033	X_17204033_SNP [dm3] X_17310000_SNP [dm6]	A	C	2.860e^-5	0.608	INTERGENIC
3R	14841118	3R_14841118_SNP [dm3] 3R_19015396_SNP [dm6]	T	C	2.879e^-5	0.608	INTRON gukh	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Trl
2R	9548009	2R_9548009_DEL [dm3] 2R_13660504_DEL [dm6]	CA	C	3.082e^-5	0.608	DOWNSTREAM CG6209 INTRON fas	TF binding site BDTNP1_TFBS_twi mE1_TFBS_chinmo mE1_TFBS_HSA
2R	11575868	2R_11575868_SNP [dm3] 2R_15688363_SNP [dm6]	A	G	3.095e^-5	0.608	SYNONYMOUS_CODING Cep89 DOWNSTREAM Ranbp11	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	10534765	3L_10534765_SNP [dm3] 3L_10541665_SNP [dm6]	T	C	3.191e^-5	0.608	INTRON A2bp1
3R	24335719	3R_24335719_SNP [dm3] 3R_28509997_SNP [dm6]	T	A	3.233e^-5	0.608	INTRON Dhc98D	TF binding site mE1_TFBS_cad
3R	14437372	3R_14437372_SNP [dm3] 3R_18611650_SNP [dm6]	A	T	3.248e^-5	0.608	INTRON qin & 1 other
X	12407422	X_12407422_SNP [dm3] X_12513389_SNP [dm6]	A	T	3.259e^-5	0.608	INTRON CG2556	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2L	16870627	2L_16870627_SNP [dm3] 2L_16870627_SNP [dm6]	C	T	3.359e^-5	0.608	EXON CR31781
3L	13769605	3L_13769605_SNP [dm3] 3L_13776505_SNP [dm6]	T	A	3.394e^-5	0.608	INTRON bru-3
X	13844759	X_13844759_SNP [dm3] X_13950726_SNP [dm6]	C	A	3.397e^-5	0.608	INTRON mamo
3R	17003184	3R_17003184_DEL [dm3] 3R_21177462_DEL [dm6]	TGCGTAAGTAAGCTT...	T	3.410e^-5	0.608	INTRON SNF4Agamma
2L	17809011	2L_17809011_SNP [dm3] 2L_17809011_SNP [dm6]	T	C	3.432e^-5	0.608	INTRON CadN2
3L	10014295	3L_10014295_SNP [dm3] 3L_10021195_SNP [dm6]	T	C	3.451e^-5	0.608	INTRON dpr6
3L	10237066	3L_10237066_SNP [dm3] 3L_10243966_SNP [dm6]	C	G	3.514e^-5	0.608	NON_SYNONYMOUS_CODING Or67c UPSTREAM CR44541
3L	3928101	3L_3928101_SNP [dm3] 3L_3928101_SNP [dm6]	G	A	3.535e^-5	0.608	INTRON Eip63F-1

Showing 1 to 100 of 1,000 entries

Previous1 2 3 4 5…10Next

By genomic position
Variant impact
Gene name

Mitochon_Mapped_Read phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results