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=5.149e^-2)
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_2R_NS	0.03367

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2R_NS	7.9018	0.0192

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1541 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	21749580	3R_21749580_SNP [dm3] 3R_25923858_SNP [dm6]	T	C	1.074e^-6	1	UTR_3_PRIME CCAP-R
3L	15210888	3L_15210888_SNP [dm3] 3L_15217788_SNP [dm6]	C	T	1.677e^-6	1	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	11397687	2L_11397687_SNP [dm3] 2L_11397687_SNP [dm6]	A	G	1.960e^-6	1	INTERGENIC	regulatory region REDfly_CRMs
2R	7327863	2R_7327863_SNP [dm3] 2R_11440358_SNP [dm6]	A	T	2.797e^-6	1	INTRON CG7777
X	6829581	X_6829581_SNP [dm3] X_6935548_SNP [dm6]	G	T	3.538e^-6	1	INTRON CG14431
2L	16564816	2L_16564816_DEL [dm3] 2L_16564816_DEL [dm6]	ACTGCAGTTGTCA...	A	3.651e^-6	1	INTRON CG42389
3R	13856596	3R_13856596_DEL [dm3] 3R_18030874_DEL [dm6]	GA	G	4.391e^-6	1	INTERGENIC
3L	6567577	3L_6567577_SNP [dm3] 3L_6574477_SNP [dm6]	T	C	4.415e^-6	1	INTRON CG18769 & 1 other
2L	16564834	2L_16564834_SNP [dm3] 2L_16564834_SNP [dm6]	A	C	5.681e^-6	1	INTRON CG42389
X	6414560	X_6414560_SNP [dm3] X_6520527_SNP [dm6]	T	C	6.419e^-6	1	INTRON CG42340
2L	11397732	2L_11397732_SNP [dm3] 2L_11397732_SNP [dm6]	A	T	7.049e^-6	1	INTERGENIC	regulatory region REDfly_CRMs
X	2320172	X_2320172_SNP [dm3] X_2426139_SNP [dm6]	C	A	8.611e^-6	1	UPSTREAM CG32797 DOWNSTREAM gt INTERGENIC	transposable element FlyBase
3L	6635579	3L_6635579_SNP [dm3] 3L_6642479_SNP [dm6]	G	A	8.836e^-6	1	DOWNSTREAM CR45238 EXON CR45239
2R	17598285	2R_17598285_SNP [dm3] 2R_21710780_SNP [dm6]	T	C	9.614e^-6	1	INTRON HmgD & 1 other	TF binding site BDTNP1_TFBS_dl
2R	11246933	2R_11246933_SNP [dm3] 2R_15359428_SNP [dm6]	C	A	1.113e^-5	1	INTRON unc-5
2R	19475645	2R_19475645_SNP [dm3] 2R_23588122_SNP [dm6]	G	T	1.144e^-5	1	INTRON apt	TF binding site BDTNP1_TFBS_dl
3R	18141396	3R_18141396_SNP [dm3] 3R_22315674_SNP [dm6]	C	A	1.167e^-5	1	SYNONYMOUS_CODING CG34377
2R	13186615	2R_13186615_SNP [dm3] 2R_17299110_SNP [dm6]	C	T	1.185e^-5	1	INTRON mbl
3L	6650340	3L_6650340_SNP [dm3] 3L_6657240_SNP [dm6]	T	C	1.214e^-5	1	INTERGENIC
2R	19085373	2R_19085373_SNP [dm3] 2R_23197850_SNP [dm6]	T	G	1.241e^-5	1	INTRON CG34371
2R	17598259	2R_17598259_SNP [dm3] 2R_21710754_SNP [dm6]	A	C	1.299e^-5	1	INTRON HmgD & 1 other	TF binding site BDTNP1_TFBS_dl
3L	15211034	3L_15211034_SNP [dm3] 3L_15217934_SNP [dm6]	G	A	1.306e^-5	1	INTERGENIC	TF binding site mE1_TFBS_HSA
2R	17623111	2R_17623111_DEL [dm3] 2R_21735606_DEL [dm6]	CCC	C	1.474e^-5	1	INTERGENIC
2R	10580250	2R_10580250_SNP [dm3] 2R_14692745_SNP [dm6]	T	G	1.798e^-5	1	INTRON mspo
3R	18818785	3R_18818785_SNP [dm3] 3R_22993063_SNP [dm6]	G	T	1.842e^-5	1	INTRON Nha2
X	7195683	X_7195683_SNP [dm3] X_7301650_SNP [dm6]	G	A	1.847e^-5	1	INTRON CR44357 & 1 other	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_shn mE1_TFBS_bab1 mE1_TFBS_HSA
2R	9632060	2R_9632060_SNP [dm3] 2R_13744555_SNP [dm6]	A	T	1.959e^-5	1	INTRON fas
2L	7353392	2L_7353392_SNP [dm3] 2L_7353392_SNP [dm6]	A	C	2.042e^-5	1	DOWNSTREAM Wnt6 INTERGENIC
3R	25478818	3R_25478818_SNP [dm3] 3R_29653096_SNP [dm6]	A	G	2.086e^-5	1	INTRON Dop1R2
3L	2579832	3L_2579832_SNP [dm3] 3L_2579832_SNP [dm6]	C	T	2.130e^-5	1	INTRON msn	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	2062609	2L_2062609_SNP [dm3] 2L_2062609_SNP [dm6]	C	T	2.179e^-5	1	INTRON dpr3	TF binding site mE1_TFBS_chinmo
2R	17576027	2R_17576027_SNP [dm3] 2R_21688522_SNP [dm6]	C	G	2.226e^-5	1	UTR_5_PRIME CG30285 UPSTREAM Tbp & 1 other	TF binding site BDTNP1_TFBS_dl
3L	10214960	3L_10214960_SNP [dm3] 3L_10221860_SNP [dm6]	C	A	2.291e^-5	1	SYNONYMOUS_CODING scramb1	TF binding site mE1_TFBS_cad
3R	5352797	3R_5352797_SNP [dm3] 3R_9527075_SNP [dm6]	A	G	2.356e^-5	1	UTR_3_PRIME CG8176
2R	17598378	2R_17598378_SNP [dm3] 2R_21710873_SNP [dm6]	G	A	2.365e^-5	1	INTRON HmgD & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
2L	13146439	2L_13146439_SNP [dm3] 2L_13146439_SNP [dm6]	C	G	2.456e^-5	1	UPSTREAM CR44199 INTERGENIC
2R	16281405	2R_16281405_SNP [dm3] 2R_20393900_SNP [dm6]	A	G	2.633e^-5	1	INTERGENIC	TF binding site mE1_TFBS_chinmo
2L	4855638	2L_4855638_SNP [dm3] 2L_4855638_SNP [dm6]	A	T	2.679e^-5	1	INTRON pog
X	2201307	X_2201307_DEL [dm3] X_2307274_DEL [dm6]	CTTATCC	C	2.847e^-5	1	INTRON phl	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_sens mE1_TFBS_Trl
2R	16281417	2R_16281417_SNP [dm3] 2R_20393912_SNP [dm6]	G	A	2.966e^-5	1	INTERGENIC	TF binding site mE1_TFBS_chinmo
2R	16281419	2R_16281419_DEL [dm3] 2R_20393914_DEL [dm6]	AG	A	2.966e^-5	1	INTERGENIC	TF binding site mE1_TFBS_chinmo
2R	16281465	2R_16281465_SNP [dm3] 2R_20393960_SNP [dm6]	T	A	2.966e^-5	1	INTERGENIC
2R	17575071	2R_17575071_SNP [dm3] 2R_21687566_SNP [dm6]	T	A	3.032e^-5	1	UTR_5_PRIME Tbp DOWNSTREAM CG30285	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
X	16918901	X_16918901_SNP [dm3] X_17024868_SNP [dm6]	G	C	3.333e^-5	1	DOWNSTREAM CG43997 INTRON CG45002
3R	17662696	3R_17662696_SNP [dm3] 3R_21836974_SNP [dm6]	A	T	3.356e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_dl
2R	8911622	2R_8911622_SNP [dm3] 2R_13024117_SNP [dm6]	A	C	3.410e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_dl
3L	449067	3L_449067_SNP [dm3] 3L_449067_SNP [dm6]	G	A	3.551e^-5	1	UPSTREAM klar INTRON klar
3R	10284827	3R_10284827_SNP [dm3] 3R_14459105_SNP [dm6]	A	G	3.592e^-5	1	INTRON cv-c
2R	2876669	2R_2876669_SNP [dm3] 2R_6989164_SNP [dm6]	A	G	3.622e^-5	1	DOWNSTREAM CG17002 INTERGENIC	transposable element FlyBase
2L	17614300	2L_17614300_SNP [dm3] 2L_17614300_SNP [dm6]	C	G	3.658e^-5	1	INTERGENIC
3L	16004825	3L_16004825_SNP [dm3] 3L_16011725_SNP [dm6]	A	G	3.691e^-5	1	UTR_5_PRIME mib1	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_sens
2R	16281418	2R_16281418_SNP [dm3] 2R_20393913_SNP [dm6]	A	T	3.722e^-5	1	INTERGENIC	TF binding site mE1_TFBS_chinmo
3R	25289493	3R_25289493_SNP [dm3] 3R_29463771_SNP [dm6]	C	T	3.746e^-5	1	INTRON Ptp99A	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	18876720	3L_18876720_SNP [dm3] 3L_18883620_SNP [dm6]	G	A	3.894e^-5	1	INTRON CG3961
2R	15573726	2R_15573726_INS [dm3] 2R_19686221_INS [dm6]	A	AA	4.090e^-5	1	INTRON CG15128	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_dl BDTNP1_TFBS_twi
2R	17576024	2R_17576024_DEL [dm3] 2R_21688519_DEL [dm6]	TT	T	4.188e^-5	1	UTR_5_PRIME CG30285 UPSTREAM Tbp & 1 other	TF binding site BDTNP1_TFBS_dl
3L	13885333	3L_13885333_SNP [dm3] 3L_13892233_SNP [dm6]	C	T	4.253e^-5	1	INTRON dysc
2R	7673484	2R_7673484_SNP [dm3] 2R_11785979_SNP [dm6]	A	C	4.321e^-5	1	INTRON ths
3L	6656004	3L_6656004_SNP [dm3] 3L_6662904_SNP [dm6]	C	G	4.379e^-5	1	INTERGENIC
3R	24358105	3R_24358105_SNP [dm3] 3R_28532383_SNP [dm6]	T	G	4.570e^-5	1	INTRON Ppn	TF binding site mE1_TFBS_chinmo
2R	10111160	2R_10111160_SNP [dm3] 2R_14223655_SNP [dm6]	A	C	4.685e^-5	1	INTRON CG8468	TF binding site BDTNP1_TFBS_twi
3L	5156857	3L_5156857_SNP [dm3] 3L_5163757_SNP [dm6]	C	A	4.734e^-5	1	INTRON shep
X	7886212	X_7886212_SNP [dm3] X_7992179_SNP [dm6]	G	A	4.868e^-5	1	INTERGENIC
2L	16322471	2L_16322471_SNP [dm3] 2L_16322471_SNP [dm6]	C	T	4.941e^-5	1	INTRON cact	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_sna
2L	12869258	2L_12869258_SNP [dm3] 2L_12869258_SNP [dm6]	G	C	4.948e^-5	1	INTERGENIC
X	10966750	X_10966750_SNP [dm3] X_11072717_SNP [dm6]	A	G	5.084e^-5	1	SYNONYMOUS_CODING sev	TF binding site mE1_TFBS_chinmo
3L	5171782	3L_5171782_SNP [dm3] 3L_5178682_SNP [dm6]	C	T	5.108e^-5	1	INTRON shep
3L	12310530	3L_12310530_SNP [dm3] 3L_12317430_SNP [dm6]	A	C	5.301e^-5	1	INTERGENIC
2R	6262197	2R_6262197_SNP [dm3] 2R_10374692_SNP [dm6]	A	G	5.341e^-5	1	INTRON CG42732
3R	26742576	3R_26742576_DEL [dm3] 3R_30916854_DEL [dm6]	TT	T	5.507e^-5	1	INTRON Ptx1	TF binding site BDTNP1_TFBS_da
3L	12015931	3L_12015931_SNP [dm3] 3L_12022831_SNP [dm6]	T	C	5.658e^-5	1	INTRON rols
3L	464743	3L_464743_SNP [dm3] 3L_464743_SNP [dm6]	G	T	5.691e^-5	1	INTRON klar
3L	16004899	3L_16004899_SNP [dm3] 3L_16011799_SNP [dm6]	C	T	5.703e^-5	1	UTR_5_PRIME mib1	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_sens
2L	775604	2L_775604_SNP [dm3] 2L_775604_SNP [dm6]	C	T	5.725e^-5	1	UPSTREAM CG13946 INTERGENIC
3L	9917433	3L_9917433_SNP [dm3] 3L_9924333_SNP [dm6]	T	C	5.755e^-5	1	INTRON CG34356
X	17567296	X_17567296_SNP [dm3] X_17673263_SNP [dm6]	G	A	5.988e^-5	1	SYNONYMOUS_CODING chas	TF binding site mE1_TFBS_chinmo
3R	18684318	3R_18684318_SNP [dm3] 3R_22858596_SNP [dm6]	G	A	6.051e^-5	1	INTERGENIC
3R	8790593	3R_8790593_SNP [dm3] 3R_12964871_SNP [dm6]	A	G	6.081e^-5	1	NON_SYNONYMOUS_CODING Cyp304a1 INTRON grsm	TF binding site mE1_TFBS_cad
3L	10902642	3L_10902642_SNP [dm3] 3L_10909542_SNP [dm6]	G	T	6.088e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_dl
2L	12120038	2L_12120038_SNP [dm3] 2L_12120038_SNP [dm6]	C	A	6.097e^-5	1	INTRON CG17211
3L	12310521	3L_12310521_DEL [dm3] 3L_12317421_DEL [dm6]	ATTGCAA	A	6.139e^-5	1	INTERGENIC
3R	12194572	3R_12194572_DEL [dm3] 3R_16368850_DEL [dm6]	TTTACGT	T	6.206e^-5	1	UTR_3_PRIME CG10317 UPSTREAM CG14880 DOWNSTREAM CG10317 INTRAGENIC CG10317 INTERGENIC	regulatory region REDfly_CRMs
3L	6650211	3L_6650211_SNP [dm3] 3L_6657111_SNP [dm6]	C	A	6.237e^-5	1	INTERGENIC
3L	2802260	3L_2802260_SNP [dm3] 3L_2802260_SNP [dm6]	T	C	6.349e^-5	1	INTRON CG43444
3L	454489	3L_454489_SNP [dm3] 3L_454489_SNP [dm6]	C	G	6.458e^-5	1	INTRON klar
X	8710065	X_8710065_SNP [dm3] X_8816032_SNP [dm6]	A	T	6.482e^-5	1	INTERGENIC
2R	10580283	2R_10580283_SNP [dm3] 2R_14692778_SNP [dm6]	T	C	6.666e^-5	1	INTRON mspo
2L	8316116	2L_8316116_SNP [dm3] 2L_8316116_SNP [dm6]	T	C	6.777e^-5	1	SYNONYMOUS_CODING CG7806 DOWNSTREAM mtsh
2L	12860002	2L_12860002_SNP [dm3] 2L_12860002_SNP [dm6]	G	T	6.787e^-5	1	INTERGENIC	TF binding site mE1_TFBS_inv
3L	2313500	3L_2313500_SNP [dm3] 3L_2313500_SNP [dm6]	G	C	6.795e^-5	1	INTERGENIC
3L	10473717	3L_10473717_SNP [dm3] 3L_10480617_SNP [dm6]	A	G	6.802e^-5	1	UPSTREAM A2bp1 INTERGENIC
3L	9432779	3L_9432779_SNP [dm3] 3L_9439679_SNP [dm6]	C	A	6.896e^-5	1	DOWNSTREAM MTF-1 & 1 other INTRON Bet3
2R	16281341	2R_16281341_SNP [dm3] 2R_20393836_SNP [dm6]	A	T	7.064e^-5	1	INTERGENIC	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
X	1876052	X_1876052_SNP [dm3] X_1982019_SNP [dm6]	G	A	7.259e^-5	1	INTRON Hr4	TF binding site mE1_TFBS_chinmo
3R	5352892	3R_5352892_SNP [dm3] 3R_9527170_SNP [dm6]	A	G	7.370e^-5	1	UTR_3_PRIME CG8176
2R	19317385	2R_19317385_SNP [dm3] 2R_23429862_SNP [dm6]	A	G	7.437e^-5	1	INTRON CG9815
2L	14105441	2L_14105441_SNP [dm3] 2L_14105441_SNP [dm6]	T	A	7.609e^-5	1	INTRON CG16879	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2L	13149426	2L_13149426_INS [dm3] 2L_13149426_INS [dm6]	G	GT	7.963e^-5	1	INTERGENIC
3R	6404252	3R_6404252_SNP [dm3] 3R_10578530_SNP [dm6]	A	G	7.984e^-5	1	INTRON hth	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb mE1_TFBS_HSA
2L	11233049	2L_11233049_SNP [dm3] 2L_11233049_SNP [dm6]	A	T	8.020e^-5	1	INTRON ab

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By genomic position
Variant impact
Gene name

mn_Glycogen_Pooled phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results