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=2.540e^-4)
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

Covariate	χ²	p-value	Significance
wolba	2.8807	0.0896

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2050 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	4331250	3R_4331250_SNP [dm3] 3R_8505528_SNP [dm6]	T	G	3.274e^-7	0.323	INTERGENIC	TF binding site mE1_TFBS_cad
3L	12131257	3L_12131257_SNP [dm3] 3L_12138157_SNP [dm6]	G	A	3.552e^-7	0.323	SYNONYMOUS_CODING l_3_neo18 UPSTREAM RhoGAP68F DOWNSTREAM Atg12	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_sens mE1_TFBS_Ubx
2L	8781605	2L_8781605_SNP [dm3] 2L_8781605_SNP [dm6]	A	G	1.059e^-6	0.553	UPSTREAM CG9468 DOWNSTREAM CG42710 INTERGENIC
X	2611629	X_2611629_SNP [dm3] X_2717596_SNP [dm6]	T	C	1.455e^-6	0.553	UTR_3_PRIME CG2694 DOWNSTREAM CG2701
3L	15285419	3L_15285419_SNP [dm3] 3L_15292319_SNP [dm6]	C	G	2.704e^-6	0.553	INTERGENIC
3L	19217897	3L_19217897_SNP [dm3] 3L_19224797_SNP [dm6]	G	A	2.993e^-6	0.553	INTRON fz2
3L	19217913	3L_19217913_SNP [dm3] 3L_19224813_SNP [dm6]	A	G	2.993e^-6	0.553	INTRON fz2
3L	12131675	3L_12131675_SNP [dm3] 3L_12138575_SNP [dm6]	T	A	2.994e^-6	0.553	UTR_5_PRIME l_3_neo18 UPSTREAM RhoGAP68F & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_run mE1_TFBS_Ubx
3L	12133468	3L_12133468_SNP [dm3] 3L_12140368_SNP [dm6]	G	A	3.671e^-6	0.553	INTRON RhoGAP68F
2R	20238838	2R_20238838_SNP [dm3] 2R_24351315_SNP [dm6]	C	T	3.746e^-6	0.553	DOWNSTREAM CR44811 INTRON bs & 1 other	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
X	2893998	X_2893998_SNP [dm3] X_2999965_SNP [dm6]	T	A	3.897e^-6	0.553	INTRON kirre
3R	27355717	3R_27355717_SNP [dm3] 3R_31529995_SNP [dm6]	T	A	4.177e^-6	0.553	INTERGENIC
3R	24579641	3R_24579641_SNP [dm3] 3R_28753919_SNP [dm6]	C	A	5.751e^-6	0.553	INTERGENIC	TF binding site mE1_TFBS_inv
2L	19818313	2L_19818313_SNP [dm3] 2L_19818313_SNP [dm6]	A	T	5.876e^-6	0.553	INTRON sick	transposable element FlyBase
2R	16457507	2R_16457507_SNP [dm3] 2R_20570002_SNP [dm6]	A	T	6.078e^-6	0.553	INTRON qsm	TF binding site BDTNP1_TFBS_prd mE1_TFBS_HSA
3L	6496851	3L_6496851_SNP [dm3] 3L_6503751_SNP [dm6]	C	T	6.119e^-6	0.553	INTRON sfl	TF binding site BDTNP1_TFBS_dl
3R	26396664	3R_26396664_DEL [dm3] 3R_30570942_DEL [dm6]	TGACT	T	6.275e^-6	0.553	UPSTREAM tmod INTRON tmod
2L	8769220	2L_8769220_SNP [dm3] 2L_8769220_SNP [dm6]	T	A	6.787e^-6	0.553	SYNONYMOUS_CODING CG9465 UPSTREAM CG9463
2R	9740764	2R_9740764_SNP [dm3] 2R_13853259_SNP [dm6]	C	G	7.070e^-6	0.553	SYNONYMOUS_CODING CG6543 DOWNSTREAM CG30485	TF binding site BDTNP1_TFBS_gt BDTNP1_TFBS_sna mE1_TFBS_inv
2R	11156104	2R_11156104_SNP [dm3] 2R_15268599_SNP [dm6]	T	G	7.241e^-6	0.553	INTRON Trpm
3R	27355855	3R_27355855_SNP [dm3] 3R_31530133_SNP [dm6]	T	C	7.653e^-6	0.553	INTERGENIC
2R	16295473	2R_16295473_SNP [dm3] 2R_20407968_SNP [dm6]	C	T	7.781e^-6	0.553	INTERGENIC
3R	18467494	3R_18467494_SNP [dm3] 3R_22641772_SNP [dm6]	C	T	7.851e^-6	0.553	INTRON CG45058
3R	18467505	3R_18467505_SNP [dm3] 3R_22641783_SNP [dm6]	A	T	7.851e^-6	0.553	INTRON CG45058
2L	12959894	2L_12959894_SNP [dm3] 2L_12959894_SNP [dm6]	A	G	7.980e^-6	0.553	INTERGENIC
2L	22322229	2L_22322229_SNP [dm3] 2L_22322229_SNP [dm6]	T	C	8.212e^-6	0.553	INTRON CG17018
2L	12961924	2L_12961924_SNP [dm3] 2L_12961924_SNP [dm6]	A	C	8.605e^-6	0.553	INTERGENIC
3R	6906223	3R_6906223_SNP [dm3] 3R_11080501_SNP [dm6]	A	C	8.807e^-6	0.553	INTERGENIC
X	8113500	X_8113500_SNP [dm3] X_8219467_SNP [dm6]	T	A	9.045e^-6	0.553	INTRON sdt	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_twi
3L	19180226	3L_19180226_SNP [dm3] 3L_19187126_SNP [dm6]	G	T	9.130e^-6	0.553	INTRON fz2
2L	4204566	2L_4204566_SNP [dm3] 2L_4204566_SNP [dm6]	C	T	1.035e^-5	0.554	NON_SYNONYMOUS_CODING ft	TF binding site mE1_TFBS_sens
3L	12128964	3L_12128964_SNP [dm3] 3L_12135864_SNP [dm6]	C	T	1.067e^-5	0.554	SYNONYMOUS_CODING CG5645	TF binding site mE1_TFBS_cad mE1_TFBS_sens
3L	12129837	3L_12129837_SNP [dm3] 3L_12136737_SNP [dm6]	A	T	1.067e^-5	0.554	UPSTREAM Atg12 & 1 other DOWNSTREAM l_3_neo18 INTERGENIC	TF binding site mE1_TFBS_cad
3L	12130109	3L_12130109_SNP [dm3] 3L_12137009_SNP [dm6]	C	A	1.067e^-5	0.554	UTR_5_PRIME Atg12 UPSTREAM CG5645 DOWNSTREAM l_3_neo18
3L	12130243	3L_12130243_DEL [dm3] 3L_12137143_DEL [dm6]	CTT	C	1.067e^-5	0.554	UPSTREAM CG5645 DOWNSTREAM l_3_neo18 INTRON Atg12
3L	17853328	3L_17853328_SNP [dm3] 3L_17860228_SNP [dm6]	T	G	1.121e^-5	0.566	SYNONYMOUS_CODING CG34002
2R	16611878	2R_16611878_SNP [dm3] 2R_20724373_SNP [dm6]	A	T	1.172e^-5	0.575	INTRON dpr	TF binding site mE1_TFBS_sbb
3L	2858594	3L_2858594_DEL [dm3] 3L_2858594_DEL [dm6]	ATA	A	1.215e^-5	0.581	INTRON CG43444	insulator Insulator_Class_II.mE01
3L	17850683	3L_17850683_SNP [dm3] 3L_17857583_SNP [dm6]	C	T	1.345e^-5	0.604	UPSTREAM CG5535 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_Trl
2R	9805525	2R_9805525_SNP [dm3] 2R_13918020_SNP [dm6]	A	G	1.352e^-5	0.604	INTRON shot
3L	3493158	3L_3493158_SNP [dm3] 3L_3493158_SNP [dm6]	T	C	1.412e^-5	0.604	INTRON CG42324
2L	12961774	2L_12961774_INS [dm3] 2L_12961774_INS [dm6]	A	AA	1.419e^-5	0.604	INTERGENIC	TF binding site mE1_TFBS_HSA
2R	15294571	2R_15294571_SNP [dm3] 2R_19407066_SNP [dm6]	T	G	1.429e^-5	0.604	UTR_3_PRIME hts INTRON hts
3L	12128460	3L_12128460_SNP [dm3] 3L_12135360_SNP [dm6]	G	A	1.638e^-5	0.673	SYNONYMOUS_CODING CG5645	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
X	4433154	X_4433154_SNP [dm3] X_4539121_SNP [dm6]	C	T	1.666e^-5	0.673	SYNONYMOUS_CODING rb INTRON CR32773	TF binding site mE1_TFBS_sens
2R	16690130	2R_16690130_SNP [dm3] 2R_20802625_SNP [dm6]	A	C	1.709e^-5	0.675	INTERGENIC
2R	20006383	2R_20006383_SNP [dm3] 2R_24118860_SNP [dm6]	T	A	1.989e^-5	0.76	INTRON CG3257	TF binding site mE1_TFBS_chinmo mE1_TFBS_inv
3L	10115037	3L_10115037_SNP [dm3] 3L_10121937_SNP [dm6]	C	T	2.125e^-5	0.76	INTRON dpr6
2R	11304765	2R_11304765_SNP [dm3] 2R_15417260_SNP [dm6]	T	C	2.190e^-5	0.76	INTRON CG43729
X	5468501	X_5468501_SNP [dm3] X_5574468_SNP [dm6]	C	T	2.252e^-5	0.76	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	4659296	3L_4659296_SNP [dm3] 3L_4659296_SNP [dm6]	T	C	2.254e^-5	0.76	INTRON axo
3L	4659302	3L_4659302_SNP [dm3] 3L_4659302_SNP [dm6]	A	G	2.254e^-5	0.76	INTRON axo
3L	4659304	3L_4659304_SNP [dm3] 3L_4659304_SNP [dm6]	A	T	2.254e^-5	0.76	INTRON axo
3L	8673546	3L_8673546_SNP [dm3] 3L_8680446_SNP [dm6]	G	A	2.332e^-5	0.76	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_prd mE1_TFBS_HSA mE1_TFBS_sens
2L	19580071	2L_19580071_SNP [dm3] 2L_19580071_SNP [dm6]	C	A	2.353e^-5	0.76	NON_SYNONYMOUS_CODING CG10268 DOWNSTREAM msb1l & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
X	5242341	X_5242341_INS [dm3] X_5348308_INS [dm6]	T	TT	2.679e^-5	0.76	INTRON SK
2R	17750945	2R_17750945_SNP [dm3] 2R_21863440_SNP [dm6]	A	C	2.685e^-5	0.76	INTERGENIC
3L	2985251	3L_2985251_SNP [dm3] 3L_2985251_SNP [dm6]	T	G	2.728e^-5	0.76	INTERGENIC
3L	11551811	3L_11551811_SNP [dm3] 3L_11558711_SNP [dm6]	G	A	2.729e^-5	0.76	UTR_5_PRIME Mob2 INTRON Mob2	TF binding site mE1_TFBS_cad
3R	3703864	3R_3703864_SNP [dm3] 3R_7878142_SNP [dm6]	A	G	2.742e^-5	0.76	INTRON CG17816
2L	4148869	2L_4148869_SNP [dm3] 2L_4148869_SNP [dm6]	C	T	2.786e^-5	0.76	UPSTREAM CG2955 INTERGENIC
3R	10567761	3R_10567761_SNP [dm3] 3R_14742039_SNP [dm6]	T	C	2.811e^-5	0.76	UTR_5_PRIME jvl UPSTREAM eff	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_sens
3L	4659310	3L_4659310_SNP [dm3] 3L_4659310_SNP [dm6]	G	A	2.885e^-5	0.76	INTRON axo
X	6007635	X_6007635_SNP [dm3] X_6113602_SNP [dm6]	G	A	2.924e^-5	0.76	SYNONYMOUS_CODING Ca-alpha1T	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_chinmo mE1_TFBS_HSA
2R	11688234	2R_11688234_SNP [dm3] 2R_15800729_SNP [dm6]	C	A	2.945e^-5	0.76	INTRON Zasp52 & 1 other
3L	6565578	3L_6565578_SNP [dm3] 3L_6572478_SNP [dm6]	A	G	3.060e^-5	0.76	INTRON CG18769 & 1 other
2L	9151139	2L_9151139_INS [dm3] 2L_9151139_INS [dm6]	A	AA	3.241e^-5	0.76	UPSTREAM CG32982 INTRON CG32982	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad
3L	4659254	3L_4659254_SNP [dm3] 3L_4659254_SNP [dm6]	A	T	3.249e^-5	0.76	INTRON axo
3L	11000608	3L_11000608_SNP [dm3] 3L_11007508_SNP [dm6]	C	T	3.261e^-5	0.76	INTRON klu	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
2L	14359397	2L_14359397_SNP [dm3] 2L_14359397_SNP [dm6]	C	G	3.346e^-5	0.76	SYNONYMOUS_CODING Pgant35A DOWNSTREAM Rab14 EXON CR43463	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_Ubx
3R	968557	3R_968557_SNP [dm3] 3R_5142835_SNP [dm6]	C	T	3.352e^-5	0.76	INTERGENIC
3L	16019910	3L_16019910_SNP [dm3] 3L_16026810_SNP [dm6]	T	G	3.502e^-5	0.76	INTRON Notum	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
3L	14987444	3L_14987444_SNP [dm3] 3L_14994344_SNP [dm6]	C	T	3.512e^-5	0.76	INTRON Zip71B	TF binding site mE1_TFBS_cad
2R	6343862	2R_6343862_INS [dm3] 2R_10456357_INS [dm6]	A	ACCCCC	3.534e^-5	0.76	INTRON Galphao & 1 other	TF binding site mE1_TFBS_inv
2R	6343863	2R_6343863_SNP [dm3] 2R_10456358_SNP [dm6]	T	C	3.534e^-5	0.76	INTRON Galphao & 1 other	TF binding site mE1_TFBS_inv
3L	6535050	3L_6535050_SNP [dm3] 3L_6541950_SNP [dm6]	T	C	3.540e^-5	0.76	INTRON sfl	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	21328967	3L_21328967_SNP [dm3] 3L_21335867_SNP [dm6]	C	A	3.559e^-5	0.76	NON_SYNONYMOUS_CODING CG7338 DOWNSTREAM Rab26	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3L	21329575	3L_21329575_SNP [dm3] 3L_21336475_SNP [dm6]	C	G	3.559e^-5	0.76	NON_SYNONYMOUS_CODING CG7338	TF binding site mE1_TFBS_cad mE1_TFBS_sens
3L	11383402	3L_11383402_SNP [dm3] 3L_11390302_SNP [dm6]	A	C	3.607e^-5	0.76	INTERGENIC
2R	7888285	2R_7888285_SNP [dm3] 2R_12000780_SNP [dm6]	T	A	3.731e^-5	0.76	DOWNSTREAM otk INTERGENIC
3L	19034475	3L_19034475_SNP [dm3] 3L_19041375_SNP [dm6]	T	C	3.738e^-5	0.76	INTRON nkd	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	11830598	2R_11830598_SNP [dm3] 2R_15943093_SNP [dm6]	G	A	3.747e^-5	0.76	UPSTREAM CG30093 INTRON Cyp4aa1
3L	11383403	3L_11383403_SNP [dm3] 3L_11390303_SNP [dm6]	A	G	3.768e^-5	0.76	INTERGENIC
3L	17853812	3L_17853812_SNP [dm3] 3L_17860712_SNP [dm6]	C	G	3.772e^-5	0.76	DOWNSTREAM CG34002 INTERGENIC
2L	22322001	2L_22322001_SNP [dm3] 2L_22322001_SNP [dm6]	C	T	3.798e^-5	0.76	INTRON CG17018	transposable element FlyBase
3L	7628925	3L_7628925_SNP [dm3] 3L_7635825_SNP [dm6]	G	A	3.914e^-5	0.76	INTRON CG33275	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3L	747174	3L_747174_SNP [dm3] 3L_747174_SNP [dm6]	T	C	3.949e^-5	0.76	INTRON hng3	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
2L	920946	2L_920946_SNP [dm3] 2L_920946_SNP [dm6]	T	C	3.981e^-5	0.76	INTERGENIC
3L	4659206	3L_4659206_SNP [dm3] 3L_4659206_SNP [dm6]	G	T	4.013e^-5	0.76	INTRON axo
2L	21730347	2L_21730347_SNP [dm3] 2L_21730347_SNP [dm6]	T	C	4.070e^-5	0.76	INTERGENIC	transposable element FlyBase
2R	16619549	2R_16619549_SNP [dm3] 2R_20732044_SNP [dm6]	T	A	4.140e^-5	0.76	INTRON dpr
3L	12129240	3L_12129240_SNP [dm3] 3L_12136140_SNP [dm6]	C	A	4.210e^-5	0.76	NON_SYNONYMOUS_CODING CG5645 UPSTREAM Atg12	TF binding site mE1_TFBS_cad mE1_TFBS_sens
3L	6606854	3L_6606854_SNP [dm3] 3L_6613754_SNP [dm6]	A	G	4.272e^-5	0.76	UTR_5_PRIME CG8398 INTRON CG8398
3R	26982549	3R_26982549_SNP [dm3] 3R_31156827_SNP [dm6]	A	G	4.274e^-5	0.76	INTRON Gycbeta100B
3L	11663985	3L_11663985_SNP [dm3] 3L_11670885_SNP [dm6]	G	A	4.323e^-5	0.76	INTRON CG32085
X	1354610	X_1354610_INS [dm3] X_1460577_INS [dm6]	T	TA	4.382e^-5	0.76	UTR_5_PRIME CG14786 DOWNSTREAM CG14787	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_ftz mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_run
X	13817436	X_13817436_SNP [dm3] X_13923403_SNP [dm6]	C	T	4.414e^-5	0.76	INTRON mamo
3L	4659205	3L_4659205_SNP [dm3] 3L_4659205_SNP [dm6]	G	T	4.417e^-5	0.76	INTRON axo
3L	4659225	3L_4659225_SNP [dm3] 3L_4659225_SNP [dm6]	G	C	4.417e^-5	0.76	INTRON axo
3L	4659235	3L_4659235_SNP [dm3] 3L_4659235_SNP [dm6]	T	C	4.417e^-5	0.76	INTRON axo

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Missing results

By genomic position
Variant impact
Gene name

pc_KP_PElem_GS phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results