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=7.712e^-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_Mo	0.0467

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
wolba	2.7478	0.0974
In_3R_Mo	6.1098	0.0471

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2332 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
2L	13641000	2L_13641000_INS [dm3] 2L_13641000_INS [dm6]	T	TT	6.021e^-7	0.51	INTRON ics	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	25795787	3R_25795787_SNP [dm3] 3R_29970065_SNP [dm6]	C	T	7.436e^-7	0.51	UPSTREAM TkR99D INTERGENIC
3L	2644168	3L_2644168_SNP [dm3] 3L_2644168_SNP [dm6]	A	T	9.740e^-7	0.51	UPSTREAM CG14949 INTERGENIC
3L	20595178	3L_20595178_SNP [dm3] 3L_20602078_SNP [dm6]	G	A	1.317e^-6	0.51	INTRON knrl
3R	25772771	3R_25772771_SNP [dm3] 3R_29947049_SNP [dm6]	G	C	1.531e^-6	0.51	SYNONYMOUS_CODING CG15523	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
X	19016562	X_19016562_SNP [dm3] X_19122529_SNP [dm6]	A	C	2.264e^-6	0.51	INTERGENIC
3L	20595131	3L_20595131_SNP [dm3] 3L_20602031_SNP [dm6]	T	C	2.864e^-6	0.51	INTRON knrl
3R	13891519	3R_13891519_SNP [dm3] 3R_18065797_SNP [dm6]	A	C	2.954e^-6	0.51	INTERGENIC
2R	16931871	2R_16931871_SNP [dm3] 2R_21044366_SNP [dm6]	T	C	3.173e^-6	0.51	INTERGENIC
3L	5273681	3L_5273681_SNP [dm3] 3L_5280581_SNP [dm6]	G	C	3.406e^-6	0.51	INTERGENIC
2R	13076808	2R_13076808_SNP [dm3] 2R_17189303_SNP [dm6]	C	A	4.246e^-6	0.51	UPSTREAM CR45323 & 1 other INTERGENIC
3R	25075753	3R_25075753_SNP [dm3] 3R_29250031_SNP [dm6]	G	C	4.429e^-6	0.51	INTRON SP1029
2R	13076733	2R_13076733_SNP [dm3] 2R_17189228_SNP [dm6]	G	A	4.490e^-6	0.51	UPSTREAM CR45323 & 1 other INTERGENIC
3R	26896010	3R_26896010_SNP [dm3] 3R_31070288_SNP [dm6]	C	A	4.937e^-6	0.51	INTRON Sox100B	TF binding site BDTNP1_TFBS_twi
2R	13076873	2R_13076873_SNP [dm3] 2R_17189368_SNP [dm6]	T	A	5.689e^-6	0.51	UPSTREAM CR44389 EXON CR45323
2R	546420	2R_546420_SNP [dm3] 2R_4658915_SNP [dm6]	G	C	5.701e^-6	0.51	INTERGENIC	TF binding site mE1_TFBS_cad
3R	14697761	3R_14697761_INS [dm3] 3R_18872039_INS [dm6]	A	ATTT	6.438e^-6	0.51	INTERGENIC
2R	13076805	2R_13076805_SNP [dm3] 2R_17189300_SNP [dm6]	T	C	6.453e^-6	0.51	UPSTREAM CR45323 & 1 other INTERGENIC
3L	5419757	3L_5419757_SNP [dm3] 3L_5426657_SNP [dm6]	G	C	6.484e^-6	0.51	INTRON CG34391	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	10244988	3L_10244988_SNP [dm3] 3L_10251888_SNP [dm6]	G	T	6.501e^-6	0.51	INTERGENIC
3R	25075808	3R_25075808_SNP [dm3] 3R_29250086_SNP [dm6]	C	A	6.603e^-6	0.51	INTRON SP1029
3L	16420906	3L_16420906_SNP [dm3] 3L_16427806_SNP [dm6]	T	G	6.889e^-6	0.51	INTRON CG33158 & 1 other
3R	25076129	3R_25076129_DEL [dm3] 3R_29250407_DEL [dm6]	CAC	C	6.976e^-6	0.51	UTR_5_PRIME SP1029	TF binding site BDTNP1_TFBS_twi
2L	5126457	2L_5126457_SNP [dm3] 2L_5126457_SNP [dm6]	G	A	7.184e^-6	0.51	SYNONYMOUS_CODING Msp300	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	5126487	2L_5126487_SNP [dm3] 2L_5126487_SNP [dm6]	G	A	7.184e^-6	0.51	SYNONYMOUS_CODING Msp300	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	5128209	2L_5128209_SNP [dm3] 2L_5128209_SNP [dm6]	G	A	7.184e^-6	0.51	SYNONYMOUS_CODING Msp300 INTRON Msp300
3L	6372625	3L_6372625_SNP [dm3] 3L_6379525_SNP [dm6]	A	G	7.727e^-6	0.51	INTERGENIC	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	25772483	3R_25772483_SNP [dm3] 3R_29946761_SNP [dm6]	G	A	7.943e^-6	0.51	SYNONYMOUS_CODING CG15523	TF binding site mE1_TFBS_cad
3L	3949365	3L_3949365_SNP [dm3] 3L_3949365_SNP [dm6]	T	C	8.086e^-6	0.51	UPSTREAM CG14983 DOWNSTREAM CG10853 INTERGENIC
2R	16113704	2R_16113704_SNP [dm3] 2R_20226199_SNP [dm6]	A	T	8.159e^-6	0.51	INTERGENIC
2R	12665744	2R_12665744_INS [dm3] 2R_16778239_INS [dm6]	T	TT	8.474e^-6	0.512	UPSTREAM Vkor INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	12665572	2R_12665572_SNP [dm3] 2R_16778067_SNP [dm6]	G	A	8.849e^-6	0.518	UPSTREAM Vkor INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	2618297	2R_2618297_DEL [dm3] 2R_6730792_DEL [dm6]	TCCTTGTCGT	T	9.197e^-6	0.522	CODON_DELETION l_2_01289 INTRON l_2_01289
3L	3951520	3L_3951520_SNP [dm3] 3L_3951520_SNP [dm6]	G	A	1.025e^-5	0.565	INTRON CG14984
3L	10473404	3L_10473404_SNP [dm3] 3L_10480304_SNP [dm6]	C	G	1.132e^-5	0.594	INTERGENIC
3R	25075810	3R_25075810_SNP [dm3] 3R_29250088_SNP [dm6]	A	T	1.141e^-5	0.594	INTRON SP1029
3R	9614053	3R_9614053_SNP [dm3] 3R_13788331_SNP [dm6]	A	G	1.289e^-5	0.64	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	13076850	2R_13076850_SNP [dm3] 2R_17189345_SNP [dm6]	G	A	1.298e^-5	0.64	UPSTREAM CR44389 EXON CR45323
3R	21787943	3R_21787943_SNP [dm3] 3R_25962221_SNP [dm6]	C	G	1.368e^-5	0.656	DOWNSTREAM CG14540 INTRON boss
2R	16363069	2R_16363069_SNP [dm3] 2R_20475564_SNP [dm6]	G	C	1.399e^-5	0.656	INTRON CG12484
3L	3686501	3L_3686501_SNP [dm3] 3L_3686501_SNP [dm6]	C	T	1.538e^-5	0.679	INTERGENIC
3R	9401582	3R_9401582_SNP [dm3] 3R_13575860_SNP [dm6]	G	C	1.582e^-5	0.679	DOWNSTREAM CR43848 INTERGENIC
X	10406496	X_10406496_SNP [dm3] X_10512463_SNP [dm6]	A	G	1.666e^-5	0.679	INTRON spri
X	19173631	X_19173631_SNP [dm3] X_19279598_SNP [dm6]	T	C	1.696e^-5	0.679	SYNONYMOUS_CODING CG8028	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3R	27471265	3R_27471265_SNP [dm3] 3R_31645543_SNP [dm6]	G	A	1.753e^-5	0.679	INTRON kek6
3R	27471266	3R_27471266_SNP [dm3] 3R_31645544_SNP [dm6]	G	A	1.753e^-5	0.679	INTRON kek6
X	13905845	X_13905845_SNP [dm3] X_14011812_SNP [dm6]	T	C	1.764e^-5	0.679	INTERGENIC
3L	1137713	3L_1137713_SNP [dm3] 3L_1137713_SNP [dm6]	C	T	1.880e^-5	0.679	INTERGENIC
3L	17498401	3L_17498401_SNP [dm3] 3L_17505301_SNP [dm6]	T	A	1.901e^-5	0.679	INTRON Oatp74D	TF binding site BDTNP1_TFBS_Med BDTNP1_TFBS_twi
2R	16363105	2R_16363105_DEL [dm3] 2R_20475600_DEL [dm6]	AGTACTATGCAATCAAATT...	A	1.961e^-5	0.679	INTRON CG12484
2R	12665578	2R_12665578_SNP [dm3] 2R_16778073_SNP [dm6]	C	T	1.982e^-5	0.679	UPSTREAM Vkor INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	19506109	2R_19506109_SNP [dm3] 2R_23618586_SNP [dm6]	T	C	2.005e^-5	0.679	INTERGENIC
2L	8168762	2L_8168762_SNP [dm3] 2L_8168762_SNP [dm6]	G	A	2.045e^-5	0.679	INTRON Piezo
2R	13076696	2R_13076696_INS [dm3] 2R_17189191_INS [dm6]	T	TGGTTTTTGAGTTAT...	2.093e^-5	0.679	UPSTREAM CR45323 & 1 other INTERGENIC
2L	13487337	2L_13487337_SNP [dm3] 2L_13487337_SNP [dm6]	C	A	2.098e^-5	0.679	INTRON CG42784
3L	21601049	3L_21601049_SNP [dm3] 3L_21607949_SNP [dm6]	C	T	2.128e^-5	0.679	UPSTREAM TfAP-2 INTRON TfAP-2	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	13776786	3R_13776786_INS [dm3] 3R_17951064_INS [dm6]	A	ACATA	2.165e^-5	0.679	INTRON cpo	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	25773348	3R_25773348_SNP [dm3] 3R_29947626_SNP [dm6]	T	C	2.224e^-5	0.679	SYNONYMOUS_CODING CG15523	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	16363033	2R_16363033_SNP [dm3] 2R_20475528_SNP [dm6]	C	G	2.243e^-5	0.679	INTRON CG12484
3L	3797201	3L_3797201_SNP [dm3] 3L_3797201_SNP [dm6]	A	C	2.280e^-5	0.679	INTRON CG32264
3L	3794031	3L_3794031_SNP [dm3] 3L_3794031_SNP [dm6]	C	T	2.287e^-5	0.679	INTRON CG32264
3R	9614049	3R_9614049_SNP [dm3] 3R_13788327_SNP [dm6]	A	T	2.316e^-5	0.679	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	19450560	3L_19450560_INS [dm3] 3L_19457460_INS [dm6]	T	TA	2.332e^-5	0.679	INTERGENIC	transposable element FlyBase
3R	15277948	3R_15277948_SNP [dm3] 3R_19452226_SNP [dm6]	C	A	2.338e^-5	0.679	INTRON CG31221	TF binding site mE1_TFBS_Kr
3R	10118006	3R_10118006_SNP [dm3] 3R_14292284_SNP [dm6]	G	A	2.361e^-5	0.679	INTRON CG12207
3R	25795346	3R_25795346_SNP [dm3] 3R_29969624_SNP [dm6]	T	C	2.447e^-5	0.679	UPSTREAM TkR99D INTERGENIC
3R	25758548	3R_25758548_SNP [dm3] 3R_29932826_SNP [dm6]	C	T	2.483e^-5	0.679	UPSTREAM CG42557 & 1 other INTRON Cog7	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3L	4860909	3L_4860909_SNP [dm3] 3L_4860909_SNP [dm6]	C	G	2.499e^-5	0.679	UPSTREAM CG17150 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_sna
2L	5050624	2L_5050624_SNP [dm3] 2L_5050624_SNP [dm6]	G	T	2.537e^-5	0.679	UPSTREAM CG9121 DOWNSTREAM eIF-3p40 INTRON CG9121
2R	12665763	2R_12665763_SNP [dm3] 2R_16778258_SNP [dm6]	C	T	2.567e^-5	0.679	UPSTREAM Vkor INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
X	8753777	X_8753777_SNP [dm3] X_8859744_SNP [dm6]	A	G	2.605e^-5	0.679	INTRON CG12075
3R	9401573	3R_9401573_SNP [dm3] 3R_13575851_SNP [dm6]	A	G	2.610e^-5	0.679	DOWNSTREAM CR43848 INTERGENIC
2L	20795215	2L_20795215_SNP [dm3] 2L_20795215_SNP [dm6]	A	G	2.645e^-5	0.679	INTRON vari EXON CR44146
3R	9774844	3R_9774844_SNP [dm3] 3R_13949122_SNP [dm6]	G	A	2.692e^-5	0.68	UTR_3_PRIME CG31517	TF binding site BDTNP1_TFBS_twi
3L	1235258	3L_1235258_DEL [dm3] 3L_1235258_DEL [dm6]	TAAATTGCTTAAAATA...	T	2.722e^-5	0.68	UTR_3_PRIME CG33966 UPSTREAM CR45747 & 1 other
3R	13312753	3R_13312753_SNP [dm3] 3R_17487031_SNP [dm6]	C	T	2.829e^-5	0.682	INTRON Dscam3
2L	11621318	2L_11621318_SNP [dm3] 2L_11621318_SNP [dm6]	G	T	2.835e^-5	0.682	UTR_5_PRIME kek2
3R	20727509	3R_20727509_SNP [dm3] 3R_24901787_SNP [dm6]	T	C	2.916e^-5	0.682	NON_SYNONYMOUS_CODING CG10845 INTRON CG13643	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3L	5693504	3L_5693504_SNP [dm3] 3L_5700404_SNP [dm6]	A	G	2.917e^-5	0.682	INTRON sif
2R	546070	2R_546070_SNP [dm3] 2R_4658565_SNP [dm6]	A	C	3.044e^-5	0.682	INTERGENIC	TF binding site mE1_TFBS_cad
3L	17448452	3L_17448452_SNP [dm3] 3L_17455352_SNP [dm6]	G	T	3.049e^-5	0.682	UTR_3_PRIME CG18265 DOWNSTREAM CG18265
2R	16363028	2R_16363028_DEL [dm3] 2R_20475523_DEL [dm6]	GGC	G	3.054e^-5	0.682	INTRON CG12484
3R	15277868	3R_15277868_SNP [dm3] 3R_19452146_SNP [dm6]	C	A	3.137e^-5	0.682	INTRON CG31221
3L	2158587	3L_2158587_SNP [dm3] 3L_2158587_SNP [dm6]	C	T	3.173e^-5	0.682	SYNONYMOUS_CODING CG15822	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2R	12570080	2R_12570080_SNP [dm3] 2R_16682575_SNP [dm6]	A	G	3.198e^-5	0.682	INTRON CG30463
3R	25795369	3R_25795369_SNP [dm3] 3R_29969647_SNP [dm6]	T	A	3.203e^-5	0.682	UPSTREAM TkR99D INTERGENIC
2R	12667091	2R_12667091_SNP [dm3] 2R_16779586_SNP [dm6]	C	T	3.205e^-5	0.682	UPSTREAM resilin DOWNSTREAM Vkor INTERGENIC	TF binding site mE1_TFBS_cad
3R	25075366	3R_25075366_SNP [dm3] 3R_29249644_SNP [dm6]	A	G	3.264e^-5	0.682	UPSTREAM SP1029 INTRON SP1029
2R	13076703	2R_13076703_SNP [dm3] 2R_17189198_SNP [dm6]	T	C	3.269e^-5	0.682	UPSTREAM CR45323 & 1 other INTERGENIC
X	16612574	X_16612574_DEL [dm3] X_16718541_DEL [dm6]	ATATA	A	3.283e^-5	0.682	INTRON CG34325
3L	1815466	3L_1815466_SNP [dm3] 3L_1815466_SNP [dm6]	A	G	3.312e^-5	0.682	INTRON GV1
3L	6741800	3L_6741800_SNP [dm3] 3L_6748700_SNP [dm6]	C	T	3.351e^-5	0.683	SYNONYMOUS_CODING velo	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	6914028	3L_6914028_SNP [dm3] 3L_6920928_SNP [dm6]	G	C	3.426e^-5	0.685	INTERGENIC
2R	16363037	2R_16363037_INS [dm3] 2R_20475532_INS [dm6]	C	CCTGTAC	3.446e^-5	0.685	INTRON CG12484
3R	13615950	3R_13615950_SNP [dm3] 3R_17790228_SNP [dm6]	C	A	3.515e^-5	0.685	INTRON CG43102
3L	3719765	3L_3719765_SNP [dm3] 3L_3719765_SNP [dm6]	G	A	3.516e^-5	0.685	INTRON CG32264
X	9503226	X_9503226_SNP [dm3] X_9609193_SNP [dm6]	T	G	3.733e^-5	0.685	UTR_5_PRIME CG42797 UPSTREAM Aats-lys	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	19171658	3R_19171658_DEL [dm3] 3R_23345936_DEL [dm6]	GT	G	3.737e^-5	0.685	UTR_5_PRIME pnt	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_GATAe mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2R	15202883	2R_15202883_SNP [dm3] 2R_19315378_SNP [dm6]	A	G	3.765e^-5	0.685	INTRON Rgk1
2L	4333914	2L_4333914_SNP [dm3] 2L_4333914_SNP [dm6]	C	T	3.798e^-5	0.685	UTR_5_PRIME Atet	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Trl mE1_TFBS_zfh1

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By genomic position
Variant impact
Gene name

PC2_Nutri_Score_High phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results