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=4.692e^-2)
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
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2184 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	3798326	X_3798326_SNP [dm3] X_3904293_SNP [dm6]	T	C	4.525e^-7	0.776	SYNONYMOUS_CODING CG42541
3L	13057520	3L_13057520_SNP [dm3] 3L_13064420_SNP [dm6]	G	A	1.833e^-6	0.776	DOWNSTREAM CG34429 INTERGENIC
2R	10616651	2R_10616651_SNP [dm3] 2R_14729146_SNP [dm6]	T	A	2.620e^-6	0.776	INTERGENIC
2L	19824495	2L_19824495_SNP [dm3] 2L_19824495_SNP [dm6]	C	A	3.930e^-6	0.776	INTRON sick
3R	23652339	3R_23652339_SNP [dm3] 3R_27826617_SNP [dm6]	A	G	4.534e^-6	0.776	INTRON CG34353	TF binding site BDTNP1_TFBS_da
3R	24273489	3R_24273489_SNP [dm3] 3R_28447767_SNP [dm6]	G	A	5.899e^-6	0.776	INTRON beat-VI
3L	2530988	3L_2530988_SNP [dm3] 3L_2530988_SNP [dm6]	A	T	5.924e^-6	0.776	INTRON Spn	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_HSA
2L	16996208	2L_16996208_SNP [dm3] 2L_16996208_SNP [dm6]	T	C	6.251e^-6	0.776	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3R	8354045	3R_8354045_SNP [dm3] 3R_12528323_SNP [dm6]	C	T	6.828e^-6	0.776	INTRON Octbeta3R & 1 other
X	5085856	X_5085856_INS [dm3] X_5191823_INS [dm6]	T	TC	9.399e^-6	0.776	INTRON rg & 1 other
2L	16874529	2L_16874529_SNP [dm3] 2L_16874529_SNP [dm6]	T	C	1.021e^-5	0.776	INTRON CR31781
2L	16874546	2L_16874546_SNP [dm3] 2L_16874546_SNP [dm6]	T	A	1.021e^-5	0.776	INTRON CR31781
3R	22463417	3R_22463417_DEL [dm3] 3R_26637695_DEL [dm6]	TTAGAAGC	T	1.045e^-5	0.776	DOWNSTREAM TwdlS INTERGENIC
3L	10478152	3L_10478152_SNP [dm3] 3L_10485052_SNP [dm6]	C	G	1.076e^-5	0.776	INTRON A2bp1
3L	3973912	3L_3973912_SNP [dm3] 3L_3973912_SNP [dm6]	G	A	1.076e^-5	0.776	DOWNSTREAM CG43915 INTERGENIC	regulatory region REDfly_CRMs TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	23517865	3R_23517865_INS [dm3] 3R_27692143_INS [dm6]	G	GG	1.176e^-5	0.776	UTR_3_PRIME CG12880	TF binding site mE1_TFBS_chinmo
3R	22463502	3R_22463502_SNP [dm3] 3R_26637780_SNP [dm6]	T	A	1.213e^-5	0.776	DOWNSTREAM TwdlS INTERGENIC
3R	25070245	3R_25070245_SNP [dm3] 3R_29244523_SNP [dm6]	A	G	1.320e^-5	0.776	UPSTREAM CG31445 DOWNSTREAM SP1029 INTRON CG31445
3R	23531183	3R_23531183_SNP [dm3] 3R_27705461_SNP [dm6]	C	T	1.323e^-5	0.776	SPLICE_SITE_REGION CG12428 INTRON CG12428	TF binding site mE1_TFBS_chinmo
3L	5410078	3L_5410078_SNP [dm3] 3L_5416978_SNP [dm6]	G	A	1.324e^-5	0.776	INTERGENIC
2L	16996126	2L_16996126_SNP [dm3] 2L_16996126_SNP [dm6]	T	G	1.376e^-5	0.776	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2L	11620215	2L_11620215_SNP [dm3] 2L_11620215_SNP [dm6]	C	T	1.385e^-5	0.776	INTRON kek2	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
3L	2530907	3L_2530907_SNP [dm3] 3L_2530907_SNP [dm6]	A	T	1.477e^-5	0.776	INTRON Spn	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1
2L	16874502	2L_16874502_SNP [dm3] 2L_16874502_SNP [dm6]	A	T	1.498e^-5	0.776	INTRON CR31781
2L	16874540	2L_16874540_SNP [dm3] 2L_16874540_SNP [dm6]	C	T	1.498e^-5	0.776	INTRON CR31781
3R	2782332	3R_2782332_SNP [dm3] 3R_6956610_SNP [dm6]	G	T	1.505e^-5	0.776	INTRON Antp	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	3520579	3L_3520579_SNP [dm3] 3L_3520579_SNP [dm6]	T	G	1.597e^-5	0.776	INTRON Eip63E
3R	22463426	3R_22463426_SNP [dm3] 3R_26637704_SNP [dm6]	G	T	1.651e^-5	0.776	DOWNSTREAM TwdlS INTERGENIC
3R	22463427	3R_22463427_SNP [dm3] 3R_26637705_SNP [dm6]	A	C	1.651e^-5	0.776	DOWNSTREAM TwdlS INTERGENIC
3R	22463449	3R_22463449_SNP [dm3] 3R_26637727_SNP [dm6]	G	T	1.651e^-5	0.776	DOWNSTREAM TwdlS INTERGENIC
2R	19505830	2R_19505830_SNP [dm3] 2R_23618307_SNP [dm6]	G	T	1.909e^-5	0.776	INTERGENIC
3L	1395772	3L_1395772_SNP [dm3] 3L_1395772_SNP [dm6]	T	A	1.925e^-5	0.776	INTRON Ptp61F	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	6458194	3R_6458194_SNP [dm3] 3R_10632472_SNP [dm6]	T	C	1.951e^-5	0.776	INTRON hth	TF binding site mE1_TFBS_cad
2L	16874536	2L_16874536_SNP [dm3] 2L_16874536_SNP [dm6]	G	T	1.991e^-5	0.776	INTRON CR31781
3R	22463461	3R_22463461_SNP [dm3] 3R_26637739_SNP [dm6]	C	A	2.064e^-5	0.776	DOWNSTREAM TwdlS INTERGENIC
2L	11784311	2L_11784311_SNP [dm3] 2L_11784311_SNP [dm6]	G	A	2.181e^-5	0.776	INTERGENIC
3R	22463478	3R_22463478_INS [dm3] 3R_26637756_INS [dm6]	T	TTTCA	2.268e^-5	0.776	DOWNSTREAM TwdlS INTERGENIC
3L	3520566	3L_3520566_SNP [dm3] 3L_3520566_SNP [dm6]	T	A	2.633e^-5	0.776	INTRON Eip63E
3R	25609102	3R_25609102_SNP [dm3] 3R_29783380_SNP [dm6]	T	C	2.736e^-5	0.776	INTRON kay	TF binding site BDTNP1_TFBS_z mE1_TFBS_HSA
2L	15930371	2L_15930371_SNP [dm3] 2L_15930371_SNP [dm6]	C	A	2.866e^-5	0.776	INTRON beat-Ib
2L	15930381	2L_15930381_SNP [dm3] 2L_15930381_SNP [dm6]	C	G	2.866e^-5	0.776	INTRON beat-Ib
X	3741039	X_3741039_SNP [dm3] X_3847006_SNP [dm6]	A	C	2.899e^-5	0.776	INTRON ec	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
2R	17438999	2R_17438999_SNP [dm3] 2R_21551494_SNP [dm6]	G	A	2.953e^-5	0.776	INTRON Egfr	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi
2L	16935782	2L_16935782_SNP [dm3] 2L_16935782_SNP [dm6]	C	T	2.964e^-5	0.776	INTERGENIC
2L	11896894	2L_11896894_SNP [dm3] 2L_11896894_SNP [dm6]	A	C	2.967e^-5	0.776	UPSTREAM Pde1c INTRON Pde1c
3L	10478014	3L_10478014_SNP [dm3] 3L_10484914_SNP [dm6]	C	T	2.967e^-5	0.776	INTRON A2bp1
2L	20879854	2L_20879854_SNP [dm3] 2L_20879854_SNP [dm6]	A	G	3.001e^-5	0.776	INTRON sky & 1 other
2L	20419019	2L_20419019_SNP [dm3] 2L_20419019_SNP [dm6]	G	A	3.076e^-5	0.776	UPSTREAM snoRNA:Psi18S-525d & 5 others DOWNSTREAM snoRNA:Psi18S-525a & 3 others INTRON Arpc2 EXON snoRNA:Psi18S-640b	TF binding site mE1_TFBS_zfh1
2L	16996242	2L_16996242_SNP [dm3] 2L_16996242_SNP [dm6]	T	C	3.137e^-5	0.776	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3L	10478277	3L_10478277_SNP [dm3] 3L_10485177_SNP [dm6]	G	A	3.235e^-5	0.776	INTRON A2bp1
2L	17006672	2L_17006672_SNP [dm3] 2L_17006672_SNP [dm6]	A	G	3.250e^-5	0.776	INTERGENIC
3L	5053262	3L_5053262_SNP [dm3] 3L_5053262_SNP [dm6]	G	A	3.390e^-5	0.776	INTRON Con
3R	23526478	3R_23526478_SNP [dm3] 3R_27700756_SNP [dm6]	A	G	3.497e^-5	0.776	NON_SYNONYMOUS_CODING btz UPSTREAM ALiX	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_chinmo
2L	17338174	2L_17338174_SNP [dm3] 2L_17338174_SNP [dm6]	G	A	3.615e^-5	0.776	INTERGENIC
2L	17338212	2L_17338212_SNP [dm3] 2L_17338212_SNP [dm6]	T	C	3.615e^-5	0.776	INTERGENIC
2L	19816702	2L_19816702_SNP [dm3] 2L_19816702_SNP [dm6]	G	A	3.671e^-5	0.776	UPSTREAM snRNA:U2:38ABa DOWNSTREAM snRNA:U5:38ABb INTRON sick	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_HSA
3R	17009847	3R_17009847_SNP [dm3] 3R_21184125_SNP [dm6]	A	T	3.835e^-5	0.776	INTRON SNF4Agamma	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2L	12643551	2L_12643551_SNP [dm3] 2L_12643551_SNP [dm6]	T	C	3.893e^-5	0.776	INTRON Ref2
X	3800268	X_3800268_SNP [dm3] X_3906235_SNP [dm6]	G	A	3.907e^-5	0.776	SYNONYMOUS_CODING CG42541	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sbb
2L	16934432	2L_16934432_SNP [dm3] 2L_16934432_SNP [dm6]	C	T	4.061e^-5	0.776	INTERGENIC
2L	16934446	2L_16934446_SNP [dm3] 2L_16934446_SNP [dm6]	A	G	4.061e^-5	0.776	INTERGENIC
3L	3520578	3L_3520578_SNP [dm3] 3L_3520578_SNP [dm6]	T	C	4.112e^-5	0.776	INTRON Eip63E
2L	16879587	2L_16879587_SNP [dm3] 2L_16879587_SNP [dm6]	C	A	4.147e^-5	0.776	SYNONYMOUS_CODING CG34313 UTR_5_PRIME CG31743 UPSTREAM CG32832	TF binding site BDTNP1_TFBS_Med mE1_TFBS_disco mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_Ubx
2R	8512019	2R_8512019_SNP [dm3] 2R_12624514_SNP [dm6]	G	C	4.169e^-5	0.776	INTRON CG30054
3R	8353814	3R_8353814_SNP [dm3] 3R_12528092_SNP [dm6]	C	T	4.205e^-5	0.776	INTRON Octbeta3R & 1 other
3L	15457936	3L_15457936_SNP [dm3] 3L_15464836_SNP [dm6]	G	T	4.584e^-5	0.776	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	1177759	3L_1177759_SNP [dm3] 3L_1177759_SNP [dm6]	C	T	4.623e^-5	0.776	UPSTREAM bab2 INTERGENIC	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_Trl
3R	6480607	3R_6480607_SNP [dm3] 3R_10654885_SNP [dm6]	T	C	4.637e^-5	0.776	INTERGENIC
3L	2783449	3L_2783449_SNP [dm3] 3L_2783449_SNP [dm6]	G	A	4.646e^-5	0.776	SYNONYMOUS_CODING pgant6	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
2R	5606995	2R_5606995_SNP [dm3] 2R_9719490_SNP [dm6]	A	C	4.679e^-5	0.776	NON_SYNONYMOUS_CODING sqa
2L	4340696	2L_4340696_SNP [dm3] 2L_4340696_SNP [dm6]	T	C	4.844e^-5	0.776	INTRON Atet
2R	11630397	2R_11630397_SNP [dm3] 2R_15742892_SNP [dm6]	C	G	4.895e^-5	0.776	INTRON CG30089	TF binding site mE1_TFBS_HSA
3L	2202884	3L_2202884_SNP [dm3] 3L_2202884_SNP [dm6]	C	T	5.004e^-5	0.776	INTERGENIC
X	5005222	X_5005222_SNP [dm3] X_5111189_SNP [dm6]	C	A	5.020e^-5	0.776	INTRON rg & 1 other
2L	9200049	2L_9200049_SNP [dm3] 2L_9200049_SNP [dm6]	G	A	5.035e^-5	0.776	INTRON tai
3L	2413105	3L_2413105_DEL [dm3] 3L_2413105_DEL [dm6]	CTATATATTAC...	C	5.039e^-5	0.776	UPSTREAM CG45186 INTRON CG45186
3L	2877587	3L_2877587_SNP [dm3] 3L_2877587_SNP [dm6]	C	T	5.131e^-5	0.776	INTRON CG43444
3L	1438738	3L_1438738_SNP [dm3] 3L_1438738_SNP [dm6]	T	A	5.137e^-5	0.776	UPSTREAM SA-2 INTRON Ptp61F	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cnc mE1_TFBS_HSA mE1_TFBS_sens
2L	16905005	2L_16905005_SNP [dm3] 2L_16905005_SNP [dm6]	T	G	5.169e^-5	0.776	INTRON tweek
3R	23652337	3R_23652337_SNP [dm3] 3R_27826615_SNP [dm6]	G	C	5.217e^-5	0.776	INTRON CG34353	TF binding site BDTNP1_TFBS_da
3R	6970086	3R_6970086_SNP [dm3] 3R_11144364_SNP [dm6]	A	T	5.239e^-5	0.776	UTR_3_PRIME CheA86a
2L	12724307	2L_12724307_SNP [dm3] 2L_12724307_SNP [dm6]	G	A	5.242e^-5	0.776	SYNONYMOUS_CODING MRP	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	12724310	2L_12724310_SNP [dm3] 2L_12724310_SNP [dm6]	C	A	5.242e^-5	0.776	SYNONYMOUS_CODING MRP	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	4635521	2L_4635521_SNP [dm3] 2L_4635521_SNP [dm6]	A	C	5.264e^-5	0.776	INTERGENIC
2L	16917319	2L_16917319_SNP [dm3] 2L_16917319_SNP [dm6]	A	T	5.266e^-5	0.776	DOWNSTREAM tweek INTERGENIC
3R	18658047	3R_18658047_SNP [dm3] 3R_22832325_SNP [dm6]	G	A	5.344e^-5	0.776	INTERGENIC
3R	24446690	3R_24446690_SNP [dm3] 3R_28620968_SNP [dm6]	G	C	5.442e^-5	0.776	INTRON CG10011	TF binding site BDTNP1_TFBS_twi
2R	12479789	2R_12479789_SNP [dm3] 2R_16592284_SNP [dm6]	T	A	5.461e^-5	0.776	INTRON CG8306
2L	7586792	2L_7586792_SNP [dm3] 2L_7586792_SNP [dm6]	T	A	5.555e^-5	0.776	INTERGENIC
2L	11324625	2L_11324625_SNP [dm3] 2L_11324625_SNP [dm6]	T	A	5.636e^-5	0.776	INTERGENIC
3R	13959624	3R_13959624_SNP [dm3] 3R_18133902_SNP [dm6]	G	A	5.866e^-5	0.776	UTR_3_PRIME sr DOWNSTREAM sr
3R	25994436	3R_25994436_SNP [dm3] 3R_30168714_SNP [dm6]	G	A	5.929e^-5	0.776	SYNONYMOUS_CODING CG31028
3L	3002952	3L_3002952_SNP [dm3] 3L_3002952_SNP [dm6]	G	T	5.986e^-5	0.776	UPSTREAM FMRFaR INTRON FMRFaR
2L	20881288	2L_20881288_SNP [dm3] 2L_20881288_SNP [dm6]	A	G	6.019e^-5	0.776	INTRON sky & 1 other
2L	9714247	2L_9714247_SNP [dm3] 2L_9714247_SNP [dm6]	C	T	6.024e^-5	0.776	UTR_3_PRIME Nckx30C
2R	17413079	2R_17413079_SNP [dm3] 2R_21525574_SNP [dm6]	T	C	6.171e^-5	0.776	INTRON Egfr	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens
2L	16917322	2L_16917322_SNP [dm3] 2L_16917322_SNP [dm6]	C	T	6.314e^-5	0.776	DOWNSTREAM tweek INTERGENIC
3R	26039909	3R_26039909_SNP [dm3] 3R_30214187_SNP [dm6]	G	C	6.357e^-5	0.776	UPSTREAM CecB INTERGENIC
2L	5800417	2L_5800417_SNP [dm3] 2L_5800417_SNP [dm6]	T	G	6.365e^-5	0.776	UPSTREAM CG9171 DOWNSTREAM CG14005 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_Trl
2R	11141515	2R_11141515_SNP [dm3] 2R_15254010_SNP [dm6]	A	G	6.562e^-5	0.776	INTRON scb	TF binding site mE1_TFBS_cad

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Missing results

By genomic position
Variant impact
Gene name

pc_FL_Hobo_HC phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results