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=1.165e^-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_3R_K	0.09775

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1645 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
X	19324186	X_19324186_SNP [dm3] X_19430153_SNP [dm6]	G	C	1.477e^-6	1	INTRON kek5
X	14082999	X_14082999_SNP [dm3] X_14188966_SNP [dm6]	C	T	3.691e^-6	1	UPSTREAM CG11585 INTERGENIC
3R	23253202	3R_23253202_SNP [dm3] 3R_27427480_SNP [dm6]	C	T	4.301e^-6	1	INTRON side
2L	13335719	2L_13335719_SNP [dm3] 2L_13335719_SNP [dm6]	G	A	4.454e^-6	1	INTERGENIC
3L	13114743	3L_13114743_SNP [dm3] 3L_13121643_SNP [dm6]	T	G	4.599e^-6	1	INTERGENIC	TF binding site BDTNP1_TFBS_twi
X	7086346	X_7086346_INS [dm3] X_7192313_INS [dm6]	T	TCTT	7.048e^-6	1	INTRON CG9650 & 1 other	TF binding site mE1_TFBS_HSA mE1_TFBS_jumu mE1_TFBS_sbb
3L	12012553	3L_12012553_SNP [dm3] 3L_12019453_SNP [dm6]	G	A	9.973e^-6	1	INTRON rols
X	8466365	X_8466365_INS [dm3] X_8572332_INS [dm6]	G	GG	1.113e^-5	1	INTRON spirit	TF binding site mE1_TFBS_chinmo
2R	5901558	2R_5901558_SNP [dm3] 2R_10014053_SNP [dm6]	A	T	1.231e^-5	1	INTRON Pka-R2
2L	4185405	2L_4185405_SNP [dm3] 2L_4185405_SNP [dm6]	C	A	1.359e^-5	1	DOWNSTREAM CG31961 EXON CR44057
3L	7103628	3L_7103628_SNP [dm3] 3L_7110528_SNP [dm6]	G	T	1.508e^-5	1	INTRON form3
2L	8316116	2L_8316116_SNP [dm3] 2L_8316116_SNP [dm6]	T	C	1.529e^-5	1	SYNONYMOUS_CODING CG7806 DOWNSTREAM mtsh
3R	21491118	3R_21491118_SNP [dm3] 3R_25665396_SNP [dm6]	A	T	1.679e^-5	1	UTR_3_PRIME RASSF8 UPSTREAM Lgr3	TF binding site BDTNP1_TFBS_twi
2L	22188014	2L_22188014_SNP [dm3] 2L_22188014_SNP [dm6]	T	C	1.726e^-5	1	INTERGENIC	transposable element FlyBase
2L	4771233	2L_4771233_SNP [dm3] 2L_4771233_SNP [dm6]	A	G	1.756e^-5	1	INTRON CG15630
X	12403464	X_12403464_SNP [dm3] X_12509431_SNP [dm6]	A	G	1.778e^-5	1	INTRON CG2556
2R	2601019	2R_2601019_SNP [dm3] 2R_6713514_SNP [dm6]	G	A	1.875e^-5	1	INTRON CG3409 & 1 other	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	16808233	3L_16808233_SNP [dm3] 3L_16815133_SNP [dm6]	C	A	2.145e^-5	1	INTRON nudC & 1 other
3R	20400897	3R_20400897_SNP [dm3] 3R_24575175_SNP [dm6]	C	T	2.160e^-5	1	INTRON CG13624
2R	4462304	2R_4462304_SNP [dm3] 2R_8574799_SNP [dm6]	A	T	2.209e^-5	1	SPLICE_SITE_REGION CG42326 INTRON CG42326	TF binding site mE1_TFBS_cad
3L	2156209	3L_2156209_SNP [dm3] 3L_2156209_SNP [dm6]	T	A	2.303e^-5	1	INTRON CG15822
3R	25675409	3R_25675409_SNP [dm3] 3R_29849687_SNP [dm6]	T	C	2.393e^-5	1	SYNONYMOUS_CODING Cad99C	TF binding site mE1_TFBS_cad
3R	22953238	3R_22953238_SNP [dm3] 3R_27127516_SNP [dm6]	G	C	2.700e^-5	1	NON_SYNONYMOUS_CODING CG6051	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	22734958	3R_22734958_DEL [dm3] 3R_26909236_DEL [dm6]	ATAACCAGACTCT...	A	2.712e^-5	1	INTRON T48	TF binding site mE1_TFBS_cad
3L	2728757	3L_2728757_SNP [dm3] 3L_2728757_SNP [dm6]	G	A	2.805e^-5	1	SYNONYMOUS_CODING Mrtf UTR_5_PRIME Mrtf	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2R	10880999	2R_10880999_SNP [dm3] 2R_14993494_SNP [dm6]	G	A	3.182e^-5	1	INTRON CG10265	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_sens
2R	6484631	2R_6484631_SNP [dm3] 2R_10597126_SNP [dm6]	C	T	3.303e^-5	1	INTRON psq	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	10881056	2R_10881056_SNP [dm3] 2R_14993551_SNP [dm6]	A	T	3.324e^-5	1	NON_SYNONYMOUS_CODING CG10265	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_sens
3R	9967112	3R_9967112_SNP [dm3] 3R_14141390_SNP [dm6]	G	T	3.364e^-5	1	INTERGENIC
3L	15849402	3L_15849402_SNP [dm3] 3L_15856302_SNP [dm6]	T	G	3.579e^-5	1	NON_SYNONYMOUS_CODING pHCl INTRON pHCl
3R	7121924	3R_7121924_SNP [dm3] 3R_11296202_SNP [dm6]	A	G	3.679e^-5	1	INTRON CR31386	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
3R	6960554	3R_6960554_SNP [dm3] 3R_11134832_SNP [dm6]	C	T	3.785e^-5	1	INTERGENIC
2L	3702529	2L_3702529_SNP [dm3] 2L_3702529_SNP [dm6]	G	A	3.877e^-5	1	UPSTREAM CR44311 DOWNSTREAM CG42467 & 1 other INTERGENIC
2L	16937466	2L_16937466_SNP [dm3] 2L_16937466_SNP [dm6]	C	A	3.937e^-5	1	INTERGENIC
3R	10106325	3R_10106325_SNP [dm3] 3R_14280603_SNP [dm6]	A	G	3.940e^-5	1	INTRON trx
3L	10462005	3L_10462005_SNP [dm3] 3L_10468905_SNP [dm6]	T	C	3.985e^-5	1	UTR_3_PRIME S-Lap3 DOWNSTREAM S-Lap3
X	17035908	X_17035908_SNP [dm3] X_17141875_SNP [dm6]	C	A	4.001e^-5	1	UTR_5_PRIME mei-218 UPSTREAM mei-218 INTRON mei-218 & 1 other
3R	7122348	3R_7122348_SNP [dm3] 3R_11296626_SNP [dm6]	C	T	4.151e^-5	1	INTRON CR31386	TF binding site mE1_TFBS_chinmo
3L	3584461	3L_3584461_SNP [dm3] 3L_3584461_SNP [dm6]	C	T	4.255e^-5	1	INTRON Eip63E
3L	8358530	3L_8358530_SNP [dm3] 3L_8365430_SNP [dm6]	C	T	4.313e^-5	1	INTERGENIC
3R	24675727	3R_24675727_SNP [dm3] 3R_28850005_SNP [dm6]	C	T	4.326e^-5	1	INTRON spg
3R	26819823	3R_26819823_INS [dm3] 3R_30994101_INS [dm6]	G	GAGCTTCG	4.342e^-5	1	INTRON 5-HT7
2R	5934471	2R_5934471_SNP [dm3] 2R_10046966_SNP [dm6]	A	T	4.454e^-5	1	INTRON oys	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_prd BDTNP1_TFBS_twi
3R	6960557	3R_6960557_SNP [dm3] 3R_11134835_SNP [dm6]	T	A	4.514e^-5	1	INTERGENIC
3R	23250529	3R_23250529_SNP [dm3] 3R_27424807_SNP [dm6]	A	C	4.729e^-5	1	INTRON side
2R	20629833	2R_20629833_SNP [dm3] 2R_24742310_SNP [dm6]	T	C	4.750e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	14967560	2R_14967560_SNP [dm3] 2R_19080055_SNP [dm6]	T	C	4.848e^-5	1	INTRON 5-HT1A
X	7086324	X_7086324_SNP [dm3] X_7192291_SNP [dm6]	T	A	4.904e^-5	1	INTRON CG9650 & 1 other	TF binding site mE1_TFBS_HSA mE1_TFBS_jumu mE1_TFBS_sbb
2L	1577244	2L_1577244_DEL [dm3] 2L_1577244_DEL [dm6]	AGATTTAGAAGTCTTGTTA...	A	4.905e^-5	1	INTRON haf
3R	22953916	3R_22953916_SNP [dm3] 3R_27128194_SNP [dm6]	C	T	4.914e^-5	1	SYNONYMOUS_CODING CG6051	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
X	3044462	X_3044462_SNP [dm3] X_3150429_SNP [dm6]	A	C	4.934e^-5	1	INTRON N	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	7033337	3L_7033337_SNP [dm3] 3L_7040237_SNP [dm6]	A	G	5.042e^-5	1	INTRON Mp
3R	6918060	3R_6918060_SNP [dm3] 3R_11092338_SNP [dm6]	A	T	5.258e^-5	1	INTERGENIC
2L	2588672	2L_2588672_SNP [dm3] 2L_2588672_SNP [dm6]	A	G	5.348e^-5	1	INTERGENIC
3R	11207134	3R_11207134_SNP [dm3] 3R_15381412_SNP [dm6]	T	C	5.412e^-5	1	UTR_3_PRIME h-cup INTRON Rbp
3R	21622593	3R_21622593_SNP [dm3] 3R_25796871_SNP [dm6]	C	T	5.479e^-5	1	EXON CR43847	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3L	1012173	3L_1012173_INS [dm3] 3L_1012173_INS [dm6]	G	GG	5.490e^-5	1	INTRON trio
2L	5631179	2L_5631179_SNP [dm3] 2L_5631179_SNP [dm6]	A	C	5.610e^-5	1	DOWNSTREAM CR44822 INTRON CG31646	TF binding site BDTNP1_TFBS_twi
X	1629663	X_1629663_SNP [dm3] X_1735630_SNP [dm6]	T	C	5.692e^-5	1	DOWNSTREAM Scgdelta INTERGENIC
3R	22301238	3R_22301238_SNP [dm3] 3R_26475516_SNP [dm6]	G	A	5.807e^-5	1	SYNONYMOUS_CODING plum
3L	2729551	3L_2729551_SNP [dm3] 3L_2729551_SNP [dm6]	T	G	5.840e^-5	1	INTRON Mrtf
3L	12012229	3L_12012229_SNP [dm3] 3L_12019129_SNP [dm6]	C	T	5.867e^-5	1	INTRON rols
3L	10638473	3L_10638473_SNP [dm3] 3L_10645373_SNP [dm6]	A	G	5.890e^-5	1	DOWNSTREAM CG14153 INTRON CG32066
3R	11040094	3R_11040094_SNP [dm3] 3R_15214372_SNP [dm6]	G	A	5.935e^-5	1	SPLICE_SITE_REGION CG4210 UPSTREAM CG6654 DOWNSTREAM SIDL INTRON CG4210
2L	2316374	2L_2316374_SNP [dm3] 2L_2316374_SNP [dm6]	G	A	6.029e^-5	1	INTRON CG9967 & 1 other
2R	17576027	2R_17576027_SNP [dm3] 2R_21688522_SNP [dm6]	C	G	6.029e^-5	1	UTR_5_PRIME CG30285 UPSTREAM Tbp & 1 other	TF binding site BDTNP1_TFBS_dl
2L	4916546	2L_4916546_SNP [dm3] 2L_4916546_SNP [dm6]	A	C	6.114e^-5	1	INTRON hoe1
3L	12866309	3L_12866309_SNP [dm3] 3L_12873209_SNP [dm6]	T	A	6.181e^-5	1	INTERGENIC
3L	669197	3L_669197_SNP [dm3] 3L_669197_SNP [dm6]	T	G	6.409e^-5	1	INTERGENIC	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3L	9141307	3L_9141307_SNP [dm3] 3L_9148207_SNP [dm6]	G	A	6.420e^-5	1	UTR_3_PRIME Rdl
3L	11369111	3L_11369111_SNP [dm3] 3L_11376011_SNP [dm6]	T	A	6.525e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad
2R	18499015	2R_18499015_SNP [dm3] 2R_22611510_SNP [dm6]	A	G	6.593e^-5	1	SYNONYMOUS_CODING CG4329	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2L	4172552	2L_4172552_SNP [dm3] 2L_4172552_SNP [dm6]	T	G	6.680e^-5	1	INTERGENIC
2L	4181118	2L_4181118_SNP [dm3] 2L_4181118_SNP [dm6]	T	C	6.714e^-5	1	INTERGENIC
2R	8188140	2R_8188140_SNP [dm3] 2R_12300635_SNP [dm6]	C	T	6.769e^-5	1	UTR_3_PRIME CG42700 INTRON CG8850	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
X	7086317	X_7086317_SNP [dm3] X_7192284_SNP [dm6]	C	A	6.859e^-5	1	INTRON CG9650 & 1 other	TF binding site mE1_TFBS_HSA mE1_TFBS_jumu mE1_TFBS_sbb
3R	25956440	3R_25956440_SNP [dm3] 3R_30130718_SNP [dm6]	A	C	6.943e^-5	1	SYNONYMOUS_CODING CG31029	TF binding site BDTNP1_TFBS_twi mE1_TFBS_chinmo mE1_TFBS_HSA
2L	5037634	2L_5037634_DEL [dm3] 2L_5037634_DEL [dm6]	TT	T	6.973e^-5	1	UPSTREAM SP555 & 1 other DOWNSTREAM Cg25C INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_Trl
3L	2156615	3L_2156615_SNP [dm3] 3L_2156615_SNP [dm6]	T	G	6.988e^-5	1	INTRON CG15822	TF binding site mE1_TFBS_cad
2R	5903609	2R_5903609_INS [dm3] 2R_10016104_INS [dm6]	T	TAT	7.012e^-5	1	INTRON Pka-R2
2L	3110364	2L_3110364_SNP [dm3] 2L_3110364_SNP [dm6]	T	A	7.086e^-5	1	SYNONYMOUS_CODING PpD6 INTRON toc	TF binding site mE1_TFBS_HSA
2R	5942318	2R_5942318_DEL [dm3] 2R_10054813_DEL [dm6]	TTTCAT	T	7.158e^-5	1	UPSTREAM Def INTRON magu	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad
3L	9461956	3L_9461956_SNP [dm3] 3L_9468856_SNP [dm6]	G	C	7.234e^-5	1	INTRON CG44838	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med
2L	3850726	2L_3850726_SNP [dm3] 2L_3850726_SNP [dm6]	C	T	7.327e^-5	1	INTERGENIC
3L	11266348	3L_11266348_SNP [dm3] 3L_11273248_SNP [dm6]	A	T	7.352e^-5	1	DOWNSTREAM CR44720 INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	12852441	3L_12852441_SNP [dm3] 3L_12859341_SNP [dm6]	C	T	7.509e^-5	1	NON_SYNONYMOUS_CODING CG32107
2R	17691549	2R_17691549_SNP [dm3] 2R_21804044_SNP [dm6]	C	T	7.566e^-5	1	EXON CR9284
3R	13589972	3R_13589972_SNP [dm3] 3R_17764250_SNP [dm6]	C	T	7.609e^-5	1	INTERGENIC
3R	6488766	3R_6488766_SNP [dm3] 3R_10663044_SNP [dm6]	C	T	7.773e^-5	1	INTERGENIC
X	8931352	X_8931352_SNP [dm3] X_9037319_SNP [dm6]	T	C	7.827e^-5	1	INTRON CR43836 & 1 other
3R	22734991	3R_22734991_SNP [dm3] 3R_26909269_SNP [dm6]	A	T	8.055e^-5	1	INTRON T48	TF binding site mE1_TFBS_cad
2L	9409742	2L_9409742_SNP [dm3] 2L_9409742_SNP [dm6]	G	C	8.127e^-5	1	INTRON Shawl
X	7086276	X_7086276_SNP [dm3] X_7192243_SNP [dm6]	A	G	8.161e^-5	1	INTRON CG9650 & 1 other	TF binding site mE1_TFBS_HSA mE1_TFBS_jumu mE1_TFBS_sbb
3R	24675717	3R_24675717_SNP [dm3] 3R_28849995_SNP [dm6]	G	A	8.179e^-5	1	INTRON spg
3R	7130733	3R_7130733_DEL [dm3] 3R_11305011_DEL [dm6]	CGCACACAC	C	8.321e^-5	1	INTRON CR31386	TF binding site BDTNP1_TFBS_twi
3R	12021305	3R_12021305_SNP [dm3] 3R_16195583_SNP [dm6]	T	G	8.417e^-5	1	INTRON sra
X	7086295	X_7086295_SNP [dm3] X_7192262_SNP [dm6]	A	T	8.521e^-5	1	INTRON CG9650 & 1 other	TF binding site mE1_TFBS_HSA mE1_TFBS_jumu mE1_TFBS_sbb
3L	10940355	3L_10940355_SNP [dm3] 3L_10947255_SNP [dm6]	C	T	8.557e^-5	1	INTERGENIC	TF binding site mE1_TFBS_inv
3L	10458731	3L_10458731_SNP [dm3] 3L_10465631_SNP [dm6]	T	A	8.647e^-5	1	UPSTREAM S-Lap3 DOWNSTREAM CG32061 INTRON S-Lap3
3R	10043797	3R_10043797_SNP [dm3] 3R_14218075_SNP [dm6]	A	G	8.972e^-5	1	UPSTREAM CG9649 DOWNSTREAM CG31326 INTERGENIC

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By genomic position
Variant impact
Gene name

PC1_Nutri_Score_Low phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results