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=2.822e^-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

Covariate	p-value	Significance
In_2L_t	0.05229

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	5.1564	0.0759

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1304 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	10346507	2R_10346507_SNP [dm3] 2R_14459002_SNP [dm6]	C	T	4.294e^-6	0.946	INTRON Oaz	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3L	6024547	3L_6024547_SNP [dm3] 3L_6031447_SNP [dm6]	G	C	1.001e^-5	0.946	INTERGENIC
2L	4130306	2L_4130306_SNP [dm3] 2L_4130306_SNP [dm6]	T	A	1.274e^-5	0.946	INTERGENIC
3L	9177435	3L_9177435_SNP [dm3] 3L_9184335_SNP [dm6]	A	G	1.301e^-5	0.946	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3R	10855498	3R_10855498_SNP [dm3] 3R_15029776_SNP [dm6]	T	G	1.410e^-5	0.946	INTERGENIC
3L	9177462	3L_9177462_SNP [dm3] 3L_9184362_SNP [dm6]	G	T	1.430e^-5	0.946	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3R	3893262	3R_3893262_SNP [dm3] 3R_8067540_SNP [dm6]	T	C	1.518e^-5	0.946	INTRON mAChR-B
3L	7982920	3L_7982920_DEL [dm3] 3L_7989820_DEL [dm6]	TA	G	1.520e^-5	0.946	INTRON nmo	TF binding site mE1_TFBS_HSA
2L	4049383	2L_4049383_SNP [dm3] 2L_4049383_SNP [dm6]	C	A	1.692e^-5	0.946	INTRON ed
2L	3384823	2L_3384823_SNP [dm3] 2L_3384823_SNP [dm6]	C	G	1.987e^-5	0.946	INTERGENIC
X	6129486	X_6129486_SNP [dm3] X_6235453_SNP [dm6]	T	A	2.534e^-5	0.946	UTR_3_PRIME CG14446
2R	10346503	2R_10346503_SNP [dm3] 2R_14458998_SNP [dm6]	C	T	2.571e^-5	0.946	INTRON Oaz	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
2R	10346504	2R_10346504_SNP [dm3] 2R_14458999_SNP [dm6]	A	T	2.578e^-5	0.946	INTRON Oaz	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
2R	10346508	2R_10346508_SNP [dm3] 2R_14459003_SNP [dm6]	A	T	2.578e^-5	0.946	INTRON Oaz	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
2R	10346542	2R_10346542_SNP [dm3] 2R_14459037_SNP [dm6]	C	T	2.578e^-5	0.946	INTRON Oaz	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
X	6136486	X_6136486_SNP [dm3] X_6242453_SNP [dm6]	G	A	2.798e^-5	0.946	SYNONYMOUS_CODING Rbcn-3A	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_inv
3R	10855717	3R_10855717_SNP [dm3] 3R_15029995_SNP [dm6]	A	C	2.868e^-5	0.946	INTERGENIC
2R	6527136	2R_6527136_SNP [dm3] 2R_10639631_SNP [dm6]	C	T	2.961e^-5	0.946	SYNONYMOUS_CODING CG11883	TF binding site mE1_TFBS_cad
3L	9343849	3L_9343849_SNP [dm3] 3L_9350749_SNP [dm6]	A	T	3.223e^-5	0.946	NON_SYNONYMOUS_CODING PGRP-LF DOWNSTREAM UGP
2R	18669410	2R_18669410_SNP [dm3] 2R_22781905_SNP [dm6]	A	G	3.343e^-5	0.946	INTRON CG42260
2R	17118011	2R_17118011_SNP [dm3] 2R_21230506_SNP [dm6]	G	T	3.520e^-5	0.946	INTRON ASPP	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sbb
3R	6572823	3R_6572823_SNP [dm3] 3R_10747101_SNP [dm6]	T	A	3.694e^-5	0.946	INTRON TkR86C
3R	12728815	3R_12728815_SNP [dm3] 3R_16903093_SNP [dm6]	T	C	3.805e^-5	0.946	INTRON iab-8
2R	10814468	2R_10814468_SNP [dm3] 2R_14926963_SNP [dm6]	G	T	4.010e^-5	0.946	INTRON CG10249	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	9638486	2R_9638486_SNP [dm3] 2R_13750981_SNP [dm6]	A	G	4.061e^-5	0.946	INTERGENIC
2L	3703499	2L_3703499_SNP [dm3] 2L_3703499_SNP [dm6]	G	A	4.065e^-5	0.946	UPSTREAM CG2816 DOWNSTREAM CR44311 & 1 other INTERGENIC
X	3020302	X_3020302_SNP [dm3] X_3126269_SNP [dm6]	A	G	4.066e^-5	0.946	INTRON kirre
3L	17985935	3L_17985935_SNP [dm3] 3L_17992835_SNP [dm6]	C	A	4.155e^-5	0.946	INTRON Eip75B	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
3R	13943443	3R_13943443_SNP [dm3] 3R_18117721_SNP [dm6]	T	C	4.214e^-5	0.946	INTRON sr
2R	11364164	2R_11364164_SNP [dm3] 2R_15476659_SNP [dm6]	C	T	4.293e^-5	0.946	INTRON CG8180
3L	14643576	3L_14643576_SNP [dm3] 3L_14650476_SNP [dm6]	A	C	4.361e^-5	0.946	INTRON dlp	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_prd mE1_TFBS_HSA
X	4285635	X_4285635_SNP [dm3] X_4391602_SNP [dm6]	C	G	4.564e^-5	0.946	INTRON CR32773	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3L	21649465	3L_21649465_SNP [dm3] 3L_21656365_SNP [dm6]	G	C	4.585e^-5	0.946	INTRON CG43980
3L	11407095	3L_11407095_SNP [dm3] 3L_11413995_SNP [dm6]	A	C	4.588e^-5	0.946	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl
X	5380170	X_5380170_SNP [dm3] X_5486137_SNP [dm6]	G	T	4.597e^-5	0.946	INTRON SPR	TF binding site BDTNP1_TFBS_da
3L	9339806	3L_9339806_SNP [dm3] 3L_9346706_SNP [dm6]	A	T	4.839e^-5	0.946	SYNONYMOUS_CODING PGRP-LC UTR_3_PRIME PGRP-LC DOWNSTREAM PGRP-LC INTRON PGRP-LC
2R	11343848	2R_11343848_SNP [dm3] 2R_15456343_SNP [dm6]	T	C	4.840e^-5	0.946	INTRON CG43729	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2R	10346553	2R_10346553_SNP [dm3] 2R_14459048_SNP [dm6]	C	T	5.101e^-5	0.946	INTRON Oaz	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3L	2962491	3L_2962491_SNP [dm3] 3L_2962491_SNP [dm6]	A	T	5.229e^-5	0.946	STOP_LOST Or63a SPLICE_SITE_REGION Or63a INTRON Or63a
3L	2962513	3L_2962513_SNP [dm3] 3L_2962513_SNP [dm6]	T	C	5.229e^-5	0.946	UTR_3_PRIME Or63a INTRON Or63a
X	15327511	X_15327511_SNP [dm3] X_15433478_SNP [dm6]	C	A	5.286e^-5	0.946	INTRON Cngl	transposable element FlyBase
2R	11342370	2R_11342370_SNP [dm3] 2R_15454865_SNP [dm6]	C	G	5.355e^-5	0.946	INTRON CG43729
3L	9343847	3L_9343847_SNP [dm3] 3L_9350747_SNP [dm6]	T	C	5.368e^-5	0.946	SYNONYMOUS_CODING PGRP-LF DOWNSTREAM UGP
X	20494068	X_20494068_SNP [dm3] X_20623041_SNP [dm6]	A	G	5.453e^-5	0.946	INTRON RunxA
X	18637172	X_18637172_SNP [dm3] X_18743139_SNP [dm6]	C	T	5.524e^-5	0.946	INTERGENIC
2R	11342386	2R_11342386_SNP [dm3] 2R_15454881_SNP [dm6]	G	T	5.615e^-5	0.946	INTRON CG43729
3L	2083118	3L_2083118_SNP [dm3] 3L_2083118_SNP [dm6]	C	T	5.817e^-5	0.946	SYNONYMOUS_CODING sls INTRON sls	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	6342541	3L_6342541_INS [dm3] 3L_6349441_INS [dm6]	A	AA	6.115e^-5	0.946	UPSTREAM Sfp65A INTRON CG13300	TF binding site BDTNP1_TFBS_z mE1_TFBS_HSA
2R	18674126	2R_18674126_SNP [dm3] 2R_22786621_SNP [dm6]	C	A	6.166e^-5	0.946	INTRON CG42260
2R	2673987	2R_2673987_SNP [dm3] 2R_6786482_SNP [dm6]	G	A	6.251e^-5	0.946	INTRON Epac
3L	11849972	3L_11849972_SNP [dm3] 3L_11856872_SNP [dm6]	A	T	6.282e^-5	0.946	INTRON CG44837
3L	9177444	3L_9177444_SNP [dm3] 3L_9184344_SNP [dm6]	A	C	6.458e^-5	0.946	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3L	9352978	3L_9352978_SNP [dm3] 3L_9359878_SNP [dm6]	T	G	6.622e^-5	0.946	UTR_3_PRIME CG32039 UPSTREAM UGP & 1 other DOWNSTREAM CG32039	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_inv
2R	16652875	2R_16652875_SNP [dm3] 2R_20765370_SNP [dm6]	C	T	6.826e^-5	0.946	INTERGENIC
3R	4915662	3R_4915662_SNP [dm3] 3R_9089940_SNP [dm6]	C	T	6.996e^-5	0.946	INTRON pum
2L	3703331	2L_3703331_SNP [dm3] 2L_3703331_SNP [dm6]	T	C	7.154e^-5	0.946	UPSTREAM CG2816 DOWNSTREAM CR44311 & 1 other INTERGENIC
3R	22466299	3R_22466299_SNP [dm3] 3R_26640577_SNP [dm6]	A	G	7.275e^-5	0.946	SYNONYMOUS_CODING TwdlD
3L	2959849	3L_2959849_SNP [dm3] 3L_2959849_SNP [dm6]	A	G	7.374e^-5	0.946	UTR_3_PRIME CG34025 DOWNSTREAM Shab
2L	5809499	2L_5809499_SNP [dm3] 2L_5809499_SNP [dm6]	T	G	7.411e^-5	0.946	UPSTREAM CR44575 & 1 other DOWNSTREAM CG11034 INTERGENIC
3R	4326804	3R_4326804_SNP [dm3] 3R_8501082_SNP [dm6]	A	T	7.439e^-5	0.946	INTERGENIC
3R	12728942	3R_12728942_SNP [dm3] 3R_16903220_SNP [dm6]	A	T	7.504e^-5	0.946	INTRON iab-8
2R	16861967	2R_16861967_SNP [dm3] 2R_20974462_SNP [dm6]	G	A	7.711e^-5	0.946	UPSTREAM CG15649 INTERGENIC
2R	802575	2R_802575_SNP [dm3] 2R_4915070_SNP [dm6]	T	A	7.863e^-5	0.946	INTERGENIC
2R	802586	2R_802586_SNP [dm3] 2R_4915081_SNP [dm6]	T	A	7.863e^-5	0.946	INTERGENIC
3R	3884282	3R_3884282_SNP [dm3] 3R_8058560_SNP [dm6]	G	C	8.097e^-5	0.946	UPSTREAM mAChR-B INTERGENIC
3R	3893362	3R_3893362_SNP [dm3] 3R_8067640_SNP [dm6]	T	A	8.131e^-5	0.946	INTRON mAChR-B
2L	2832191	2L_2832191_SNP [dm3] 2L_2832191_SNP [dm6]	C	A	8.223e^-5	0.946	INTERGENIC
2R	17243378	2R_17243378_SNP [dm3] 2R_21355873_SNP [dm6]	G	A	8.263e^-5	0.946	UTR_3_PRIME cv-2	TF binding site mE1_TFBS_cad
2R	10001604	2R_10001604_SNP [dm3] 2R_14114099_SNP [dm6]	A	G	8.369e^-5	0.946	INTRON Prosap	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_eve mE1_TFBS_HSA
X	4285668	X_4285668_SNP [dm3] X_4391635_SNP [dm6]	A	G	8.432e^-5	0.946	INTRON CR32773	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
X	15684796	X_15684796_SNP [dm3] X_15790763_SNP [dm6]	C	T	8.692e^-5	0.946	SYNONYMOUS_CODING Rhp
2R	11393388	2R_11393388_SNP [dm3] 2R_15505883_SNP [dm6]	G	A	8.742e^-5	0.946	SYNONYMOUS_CODING Ir52c UPSTREAM Ir52d
X	8473181	X_8473181_SNP [dm3] X_8579148_SNP [dm6]	A	T	8.832e^-5	0.946	INTRON CG12065
X	15327555	X_15327555_SNP [dm3] X_15433522_SNP [dm6]	G	A	8.840e^-5	0.946	INTRON Cngl	transposable element FlyBase
3R	13943448	3R_13943448_SNP [dm3] 3R_18117726_SNP [dm6]	T	C	8.987e^-5	0.946	INTRON sr
3L	2376438	3L_2376438_INS [dm3] 3L_2376438_INS [dm6]	A	AATAATAATAATAATAATAA...	9.063e^-5	0.946	UTR_3_PRIME CG9004 DOWNSTREAM CG15877
2R	18669470	2R_18669470_SNP [dm3] 2R_22781965_SNP [dm6]	A	T	9.419e^-5	0.946	INTRON CG42260
3L	9345653	3L_9345653_SNP [dm3] 3L_9352553_SNP [dm6]	A	G	9.488e^-5	0.946	INTRON UGP
3L	7982980	3L_7982980_SNP [dm3] 3L_7989880_SNP [dm6]	T	C	9.520e^-5	0.946	INTRON nmo
3R	22466323	3R_22466323_SNP [dm3] 3R_26640601_SNP [dm6]	T	C	9.550e^-5	0.946	SYNONYMOUS_CODING TwdlD
2R	15042218	2R_15042218_SNP [dm3] 2R_19154713_SNP [dm6]	T	A	9.866e^-5	0.946	UPSTREAM ena INTRON ena	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
2R	15042226	2R_15042226_SNP [dm3] 2R_19154721_SNP [dm6]	A	C	9.866e^-5	0.946	UPSTREAM ena INTRON ena	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
3R	4699131	3R_4699131_SNP [dm3] 3R_8873409_SNP [dm6]	G	T	9.898e^-5	0.946	INTRON pyd
X	20494044	X_20494044_SNP [dm3] X_20623017_SNP [dm6]	A	G	1.042e^-4	0.946	INTRON RunxA
3L	2082777	3L_2082777_SNP [dm3] 3L_2082777_SNP [dm6]	T	G	1.047e^-4	0.946	NON_SYNONYMOUS_CODING sls INTRON sls
X	12434553	X_12434553_SNP [dm3] X_12540520_SNP [dm6]	T	C	1.074e^-4	0.946	INTRON CG43921	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	11384563	3R_11384563_SNP [dm3] 3R_15558841_SNP [dm6]	C	T	1.080e^-4	0.946	INTERGENIC
3L	7982902	3L_7982902_SNP [dm3] 3L_7989802_SNP [dm6]	G	A	1.086e^-4	0.946	INTRON nmo	TF binding site mE1_TFBS_HSA
2L	4225535	2L_4225535_SNP [dm3] 2L_4225535_SNP [dm6]	C	A	1.114e^-4	0.946	SYNONYMOUS_CODING CG3702	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	20495660	3R_20495660_SNP [dm3] 3R_24669938_SNP [dm6]	A	T	1.164e^-4	0.946	INTRON slo
2R	17117951	2R_17117951_SNP [dm3] 2R_21230446_SNP [dm6]	G	A	1.165e^-4	0.946	INTRON ASPP	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sbb
2R	10345388	2R_10345388_DEL [dm3] 2R_14457883_DEL [dm6]	TGTGCACAT	T	1.169e^-4	0.946	UPSTREAM Oaz INTRON Oaz	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl mE1_TFBS_zfh1
2L	10969232	2L_10969232_SNP [dm3] 2L_10969232_SNP [dm6]	T	G	1.180e^-4	0.946	SYNONYMOUS_CODING CG33129	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
2L	10969262	2L_10969262_SNP [dm3] 2L_10969262_SNP [dm6]	A	G	1.180e^-4	0.946	SYNONYMOUS_CODING CG33129	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
2L	10969274	2L_10969274_SNP [dm3] 2L_10969274_SNP [dm6]	G	A	1.180e^-4	0.946	SYNONYMOUS_CODING CG33129	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
3L	16366902	3L_16366902_SNP [dm3] 3L_16373802_SNP [dm6]	G	T	1.188e^-4	0.946	UTR_3_PRIME roq
3L	1469004	3L_1469004_SNP [dm3] 3L_1469004_SNP [dm6]	T	C	1.213e^-4	0.946	DOWNSTREAM rho INTRON Ptp61F
3L	14354197	3L_14354197_SNP [dm3] 3L_14361097_SNP [dm6]	G	C	1.220e^-4	0.946	INTRON fz
3L	2376565	3L_2376565_SNP [dm3] 3L_2376565_SNP [dm6]	A	G	1.232e^-4	0.946	SYNONYMOUS_CODING CG15877 DOWNSTREAM CG9004
3R	4107003	3R_4107003_SNP [dm3] 3R_8281281_SNP [dm6]	T	A	1.236e^-4	0.946	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_gt mE1_TFBS_HSA

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By genomic position
Variant impact
Gene name

pc_Remating_Female phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results