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=1.777e^-9)
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

2077 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	6292356	X_6292356_INS [dm3] X_6398323_INS [dm6]	T	TAATTACATTACA...	3.551e^-7	0.448	INTERGENIC
3L	13778968	3L_13778968_SNP [dm3] 3L_13785868_SNP [dm6]	A	G	4.777e^-7	0.448	INTRON bru-3
3L	13779081	3L_13779081_SNP [dm3] 3L_13785981_SNP [dm6]	A	T	1.080e^-6	0.675	INTRON bru-3
3L	15274336	3L_15274336_SNP [dm3] 3L_15281236_SNP [dm6]	T	C	2.196e^-6	0.735	INTERGENIC
3L	13778679	3L_13778679_SNP [dm3] 3L_13785579_SNP [dm6]	C	G	2.258e^-6	0.735	INTRON bru-3
3L	13778680	3L_13778680_SNP [dm3] 3L_13785580_SNP [dm6]	C	A	2.392e^-6	0.735	INTRON bru-3
2R	2919411	2R_2919411_SNP [dm3] 2R_7031906_SNP [dm6]	T	C	3.077e^-6	0.735	SYNONYMOUS_CODING Tsp42Eg
3L	15273575	3L_15273575_SNP [dm3] 3L_15280475_SNP [dm6]	G	A	4.637e^-6	0.735	INTERGENIC
3R	8154162	3R_8154162_SNP [dm3] 3R_12328440_SNP [dm6]	A	T	4.850e^-6	0.735	UPSTREAM CR45583 DOWNSTREAM CR45584 INTERGENIC
3L	9132740	3L_9132740_SNP [dm3] 3L_9139640_SNP [dm6]	G	A	5.348e^-6	0.735	INTRON nwk
3L	13778676	3L_13778676_SNP [dm3] 3L_13785576_SNP [dm6]	A	T	5.470e^-6	0.735	INTRON bru-3
3L	6365631	3L_6365631_SNP [dm3] 3L_6372531_SNP [dm6]	C	A	6.778e^-6	0.735	INTERGENIC
3L	19688262	3L_19688262_SNP [dm3] 3L_19695162_SNP [dm6]	G	A	7.831e^-6	0.735	INTRON verm
3L	18785293	3L_18785293_SNP [dm3] 3L_18792193_SNP [dm6]	G	A	1.008e^-5	0.735	INTRON ftz-f1	TF binding site BDTNP1_TFBS_dl mE1_TFBS_zfh1
3R	8154272	3R_8154272_SNP [dm3] 3R_12328550_SNP [dm6]	T	A	1.054e^-5	0.735	UPSTREAM CR45583 DOWNSTREAM CR45584 INTERGENIC
2L	12415955	2L_12415955_SNP [dm3] 2L_12415955_SNP [dm6]	C	T	1.176e^-5	0.735	INTRON vir-1
X	6292354	X_6292354_SNP [dm3] X_6398321_SNP [dm6]	C	T	1.196e^-5	0.735	INTERGENIC
3R	14175014	3R_14175014_SNP [dm3] 3R_18349292_SNP [dm6]	C	A	1.197e^-5	0.735	INTRON CG15803
3L	13779041	3L_13779041_DEL [dm3] 3L_13785941_DEL [dm6]	GCAG	G	1.219e^-5	0.735	INTRON bru-3
3R	11290385	3R_11290385_SNP [dm3] 3R_15464663_SNP [dm6]	C	T	1.232e^-5	0.735	INTRON AdamTS-A
2L	2516579	2L_2516579_SNP [dm3] 2L_2516579_SNP [dm6]	T	C	1.273e^-5	0.735	DOWNSTREAM CG3528 INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3R	14175017	3R_14175017_SNP [dm3] 3R_18349295_SNP [dm6]	A	T	1.300e^-5	0.735	INTRON CG15803
3L	13778987	3L_13778987_SNP [dm3] 3L_13785887_SNP [dm6]	C	T	1.336e^-5	0.735	INTRON bru-3
3R	14112763	3R_14112763_SNP [dm3] 3R_18287041_SNP [dm6]	T	A	1.371e^-5	0.735	DOWNSTREAM CG8064 INTRON CG7131	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	10401472	3R_10401472_SNP [dm3] 3R_14575750_SNP [dm6]	A	G	1.423e^-5	0.735	DOWNSTREAM CG44094 INTRON CG7987	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_Trl
X	6292355	X_6292355_SNP [dm3] X_6398322_SNP [dm6]	T	G	1.548e^-5	0.735	INTERGENIC
3L	13634112	3L_13634112_SNP [dm3] 3L_13641012_SNP [dm6]	T	C	1.584e^-5	0.735	INTRON bru-3	TF binding site mE1_TFBS_chinmo
3L	14509408	3L_14509408_SNP [dm3] 3L_14516308_SNP [dm6]	A	T	1.606e^-5	0.735	INTRON bbg
3R	14093494	3R_14093494_SNP [dm3] 3R_18267772_SNP [dm6]	C	T	1.671e^-5	0.735	UPSTREAM CG18599 INTERGENIC	TF binding site mE1_TFBS_run
3R	15332848	3R_15332848_DEL [dm3] 3R_19507126_DEL [dm6]	GCTG	G	1.684e^-5	0.735	INTRON Dys
3R	16083338	3R_16083338_SNP [dm3] 3R_20257616_SNP [dm6]	C	T	1.690e^-5	0.735	INTRON cic	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_zfh1
X	6109389	X_6109389_SNP [dm3] X_6215356_SNP [dm6]	G	T	1.835e^-5	0.735	INTERGENIC
3L	9614673	3L_9614673_SNP [dm3] 3L_9621573_SNP [dm6]	G	A	1.840e^-5	0.735	SYNONYMOUS_CODING LanB2	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
X	9085759	X_9085759_SNP [dm3] X_9191726_SNP [dm6]	T	G	1.841e^-5	0.735	SYNONYMOUS_CODING CG12057 UPSTREAM CG12056	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	9999978	3L_9999978_SNP [dm3] 3L_10006878_SNP [dm6]	G	C	1.857e^-5	0.735	INTRON dpr6
2R	2683863	2R_2683863_SNP [dm3] 2R_6796358_SNP [dm6]	C	T	1.879e^-5	0.735	INTRON Epac
3R	26152017	3R_26152017_SNP [dm3] 3R_30326295_SNP [dm6]	T	C	1.953e^-5	0.735	INTRON hdc	insulator Insulator_Class_II.mE01 TF binding site mE1_TFBS_chinmo
2L	16574149	2L_16574149_SNP [dm3] 2L_16574149_SNP [dm6]	A	G	1.991e^-5	0.735	INTRON CG42389
2R	10175330	2R_10175330_SNP [dm3] 2R_14287825_SNP [dm6]	A	T	1.995e^-5	0.735	UPSTREAM Ih INTRON Ih
2R	6981939	2R_6981939_SNP [dm3] 2R_11094434_SNP [dm6]	C	T	2.013e^-5	0.735	INTRON luna	TF binding site mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_sens
3R	10404979	3R_10404979_SNP [dm3] 3R_14579257_SNP [dm6]	A	C	2.015e^-5	0.735	INTRON stumps
3L	13592733	3L_13592733_SNP [dm3] 3L_13599633_SNP [dm6]	T	C	2.032e^-5	0.735	INTRON bru-3 EXON CR45120
2L	5407332	2L_5407332_SNP [dm3] 2L_5407332_SNP [dm6]	G	C	2.082e^-5	0.735	SYNONYMOUS_CODING H15	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
2R	2683849	2R_2683849_SNP [dm3] 2R_6796344_SNP [dm6]	T	A	2.151e^-5	0.735	INTRON Epac
3L	13778773	3L_13778773_SNP [dm3] 3L_13785673_SNP [dm6]	T	G	2.200e^-5	0.735	INTRON bru-3
3R	14112789	3R_14112789_SNP [dm3] 3R_18287067_SNP [dm6]	C	G	2.295e^-5	0.735	DOWNSTREAM CG8064 INTRON CG7131	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	20513527	2L_20513527_SNP [dm3] 2L_20513527_SNP [dm6]	G	C	2.340e^-5	0.735	UPSTREAM CR45702 INTERGENIC
3L	18216713	3L_18216713_SNP [dm3] 3L_18223613_SNP [dm6]	A	G	2.408e^-5	0.735	INTERGENIC	TF binding site mE1_TFBS_inv
3L	5491304	3L_5491304_SNP [dm3] 3L_5498204_SNP [dm6]	T	A	2.425e^-5	0.735	NON_SYNONYMOUS_CODING blanks	TF binding site mE1_TFBS_cnc
2R	12261227	2R_12261227_DEL [dm3] 2R_16373722_DEL [dm6]	CAGCTAAC	C	2.463e^-5	0.735	INTERGENIC
3L	18216755	3L_18216755_SNP [dm3] 3L_18223655_SNP [dm6]	T	C	2.497e^-5	0.735	INTERGENIC	TF binding site mE1_TFBS_inv
3L	12434651	3L_12434651_SNP [dm3] 3L_12441551_SNP [dm6]	G	T	2.498e^-5	0.735	INTERGENIC	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
3L	12210136	3L_12210136_SNP [dm3] 3L_12217036_SNP [dm6]	G	C	2.572e^-5	0.735	INTRON app
2R	14837253	2R_14837253_SNP [dm3] 2R_18949748_SNP [dm6]	G	A	2.588e^-5	0.735	INTRON sano	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	18216746	3L_18216746_SNP [dm3] 3L_18223646_SNP [dm6]	G	T	2.640e^-5	0.735	INTERGENIC	TF binding site mE1_TFBS_inv
3R	8154288	3R_8154288_SNP [dm3] 3R_12328566_SNP [dm6]	T	A	2.645e^-5	0.735	UPSTREAM CR45583 DOWNSTREAM CR45584 INTERGENIC
3L	14509420	3L_14509420_SNP [dm3] 3L_14516320_SNP [dm6]	C	G	2.661e^-5	0.735	INTRON bbg
3L	19457405	3L_19457405_SNP [dm3] 3L_19464305_SNP [dm6]	C	A	2.699e^-5	0.735	NON_SYNONYMOUS_CODING CG14095
2R	15479116	2R_15479116_SNP [dm3] 2R_19591611_SNP [dm6]	G	A	2.708e^-5	0.735	INTRON sm
3R	16082917	3R_16082917_SNP [dm3] 3R_20257195_SNP [dm6]	A	G	2.795e^-5	0.735	INTRON cic	TF binding site BDTNP1_TFBS_dl
3R	9842015	3R_9842015_SNP [dm3] 3R_14016293_SNP [dm6]	T	G	2.838e^-5	0.735	INTRON rdx
3L	15280763	3L_15280763_SNP [dm3] 3L_15287663_SNP [dm6]	T	C	2.851e^-5	0.735	INTERGENIC
2L	15775741	2L_15775741_SNP [dm3] 2L_15775741_SNP [dm6]	G	A	2.898e^-5	0.735	DOWNSTREAM CG43760 INTERGENIC
3L	14313095	3L_14313095_SNP [dm3] 3L_14319995_SNP [dm6]	T	G	2.906e^-5	0.735	INTRON fz
3R	6265489	3R_6265489_SNP [dm3] 3R_10439767_SNP [dm6]	A	T	2.908e^-5	0.735	INTERGENIC
3L	7474330	3L_7474330_SNP [dm3] 3L_7481230_SNP [dm6]	G	C	2.945e^-5	0.735	INTERGENIC
2L	1732430	2L_1732430_SNP [dm3] 2L_1732430_SNP [dm6]	T	C	2.968e^-5	0.735	UPSTREAM CG17646 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
2L	12287942	2L_12287942_DEL [dm3] 2L_12287942_DEL [dm6]	TT	T	3.012e^-5	0.735	INTRON aret
3L	18216753	3L_18216753_SNP [dm3] 3L_18223653_SNP [dm6]	C	A	3.042e^-5	0.735	INTERGENIC	TF binding site mE1_TFBS_inv
3L	18216750	3L_18216750_SNP [dm3] 3L_18223650_SNP [dm6]	A	T	3.162e^-5	0.735	INTERGENIC	TF binding site mE1_TFBS_inv
3L	14509424	3L_14509424_SNP [dm3] 3L_14516324_SNP [dm6]	T	C	3.167e^-5	0.735	INTRON bbg
3L	18216758	3L_18216758_SNP [dm3] 3L_18223658_SNP [dm6]	T	G	3.273e^-5	0.735	INTERGENIC	TF binding site mE1_TFBS_inv
2R	2683796	2R_2683796_SNP [dm3] 2R_6796291_SNP [dm6]	T	C	3.414e^-5	0.735	INTRON Epac
3L	12434657	3L_12434657_SNP [dm3] 3L_12441557_SNP [dm6]	G	T	3.427e^-5	0.735	INTERGENIC	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
3R	11464738	3R_11464738_INS [dm3] 3R_15639016_INS [dm6]	T	TTAGTTAATATTTTCAA...	3.450e^-5	0.735	DOWNSTREAM CG43336 INTERGENIC	TF binding site BDTNP1_TFBS_da
3R	11464743	3R_11464743_INS [dm3] 3R_15639021_INS [dm6]	A	AAACACAACTATAGTGAATT...	3.450e^-5	0.735	DOWNSTREAM CG43336 INTERGENIC	TF binding site BDTNP1_TFBS_da
3L	8814770	3L_8814770_INS [dm3] 3L_8821670_INS [dm6]	C	CGGC	3.460e^-5	0.735	INTERGENIC
2R	3288988	2R_3288988_SNP [dm3] 2R_7401483_SNP [dm6]	A	G	3.466e^-5	0.735	UPSTREAM CG11113 DOWNSTREAM CG11112 INTRON Eaf
3R	14032944	3R_14032944_SNP [dm3] 3R_18207222_SNP [dm6]	T	C	3.468e^-5	0.735	INTRON CG7985
3L	18216735	3L_18216735_SNP [dm3] 3L_18223635_SNP [dm6]	C	G	3.548e^-5	0.735	INTERGENIC	TF binding site mE1_TFBS_inv
X	15156950	X_15156950_INS [dm3] X_15262917_INS [dm6]	A	ATT	3.579e^-5	0.735	INTERGENIC
3R	14112756	3R_14112756_SNP [dm3] 3R_18287034_SNP [dm6]	T	C	3.584e^-5	0.735	DOWNSTREAM CG8064 INTRON CG7131	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	14112758	3R_14112758_SNP [dm3] 3R_18287036_SNP [dm6]	C	A	3.584e^-5	0.735	DOWNSTREAM CG8064 INTRON CG7131	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	6737400	2L_6737400_SNP [dm3] 2L_6737400_SNP [dm6]	C	T	3.587e^-5	0.735	SYNONYMOUS_CODING TTLL3A	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3R	11464735	3R_11464735_SNP [dm3] 3R_15639013_SNP [dm6]	T	A	3.588e^-5	0.735	DOWNSTREAM CG43336 INTERGENIC	TF binding site BDTNP1_TFBS_da
2R	9268130	2R_9268130_SNP [dm3] 2R_13380625_SNP [dm6]	T	A	3.618e^-5	0.735	INTERGENIC	TF binding site mE1_TFBS_chinmo
2R	10993522	2R_10993522_SNP [dm3] 2R_15106017_SNP [dm6]	T	A	3.731e^-5	0.735	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	10175299	2R_10175299_SNP [dm3] 2R_14287794_SNP [dm6]	A	G	3.764e^-5	0.735	UPSTREAM Ih INTRON Ih
3R	10401529	3R_10401529_SNP [dm3] 3R_14575807_SNP [dm6]	C	T	3.824e^-5	0.735	UTR_5_PRIME CG7987 DOWNSTREAM CG44094	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_Trl
3L	14509523	3L_14509523_SNP [dm3] 3L_14516423_SNP [dm6]	C	A	3.828e^-5	0.735	INTRON bbg
2L	10352691	2L_10352691_DEL [dm3] 2L_10352691_DEL [dm6]	CA	T	3.835e^-5	0.735	UPSTREAM CG34367 INTRON CG34367
X	19667099	X_19667099_SNP [dm3] X_19773066_SNP [dm6]	T	C	3.863e^-5	0.735	INTRON vfl	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	13241544	3L_13241544_SNP [dm3] 3L_13248444_SNP [dm6]	A	G	3.894e^-5	0.735	SYNONYMOUS_CODING CG32119 INTRON caps
3L	8377747	3L_8377747_SNP [dm3] 3L_8384647_SNP [dm6]	T	C	3.952e^-5	0.735	INTRON ImpE1	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3L	10818484	3L_10818484_SNP [dm3] 3L_10825384_SNP [dm6]	A	G	3.970e^-5	0.735	EXON CR45246
2R	6854868	2R_6854868_SNP [dm3] 2R_10967363_SNP [dm6]	A	C	4.018e^-5	0.735	INTERGENIC	TF binding site mE1_TFBS_HSA
3R	14112769	3R_14112769_DEL [dm3] 3R_18287047_DEL [dm6]	AT	G	4.027e^-5	0.735	DOWNSTREAM CG8064 INTRON CG7131	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
X	15156910	X_15156910_DEL [dm3] X_15262877_DEL [dm6]	AAAATCA	A	4.036e^-5	0.735	INTERGENIC
3L	18216702	3L_18216702_DEL [dm3] 3L_18223602_DEL [dm6]	AT	A	4.156e^-5	0.735	INTERGENIC	TF binding site mE1_TFBS_inv
3L	18216709	3L_18216709_SNP [dm3] 3L_18223609_SNP [dm6]	G	A	4.156e^-5	0.735	INTERGENIC	TF binding site mE1_TFBS_inv

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Phenotype distribution and association to known covariates

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GWAS results