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=1.146e^-8)
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

Covariate	p-value	Significance
In_2L_t	0.05831

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2393 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	17896790	2L_17896790_SNP [dm3] 2L_17896790_SNP [dm6]	A	T	5.671e^-7	0.566	INTERGENIC
2L	1819310	2L_1819310_SNP [dm3] 2L_1819310_SNP [dm6]	G	A	7.234e^-7	0.566	INTERGENIC
3R	18526806	3R_18526806_SNP [dm3] 3R_22701084_SNP [dm6]	A	G	9.050e^-7	0.566	UPSTREAM CG6972 DOWNSTREAM Cyp6d4 INTRON CCAP
3R	23563740	3R_23563740_SNP [dm3] 3R_27738018_SNP [dm6]	G	A	1.869e^-6	0.591	INTRON Ets98B	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2L	3001803	2L_3001803_SNP [dm3] 2L_3001803_SNP [dm6]	A	C	1.916e^-6	0.591	INTRON CG17265	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_sna
2L	17884043	2L_17884043_SNP [dm3] 2L_17884043_SNP [dm6]	C	T	2.105e^-6	0.591	INTERGENIC
X	10440786	X_10440786_SNP [dm3] X_10546753_SNP [dm6]	G	A	2.924e^-6	0.591	UTR_5_PRIME spri INTRON spri	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
3L	10503033	3L_10503033_SNP [dm3] 3L_10509933_SNP [dm6]	G	A	3.365e^-6	0.591	INTRON A2bp1
3L	6708378	3L_6708378_SNP [dm3] 3L_6715278_SNP [dm6]	G	A	3.903e^-6	0.591	SYNONYMOUS_CODING ple	TF binding site mE1_TFBS_chinmo
3R	9890857	3R_9890857_SNP [dm3] 3R_14065135_SNP [dm6]	A	G	4.664e^-6	0.591	INTRON foxo	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	9396551	2L_9396551_SNP [dm3] 2L_9396551_SNP [dm6]	G	A	4.712e^-6	0.591	DOWNSTREAM CG4438 INTRON Shawl
2R	16716811	2R_16716811_SNP [dm3] 2R_20829306_SNP [dm6]	G	A	4.764e^-6	0.591	SYNONYMOUS_CODING sktl INTRON insc	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2R	20173697	2R_20173697_SNP [dm3] 2R_24286174_SNP [dm6]	C	T	4.989e^-6	0.591	INTRON nvy	TF binding site mE1_TFBS_chinmo
3L	5522754	3L_5522754_SNP [dm3] 3L_5529654_SNP [dm6]	C	T	5.562e^-6	0.591	UPSTREAM Lkr INTERGENIC
X	14217060	X_14217060_SNP [dm3] X_14323027_SNP [dm6]	C	G	5.604e^-6	0.591	INTRON dpr8	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	25520272	3R_25520272_SNP [dm3] 3R_29694550_SNP [dm6]	T	C	6.659e^-6	0.591	INTRON dmrt99B
2L	17883167	2L_17883167_DEL [dm3] 2L_17883167_DEL [dm6]	AGACA	A	6.733e^-6	0.591	INTERGENIC
3L	8974462	3L_8974462_SNP [dm3] 3L_8981362_SNP [dm6]	T	A	6.867e^-6	0.591	UPSTREAM CG13314 DOWNSTREAM Galk INTERGENIC
3L	11309025	3L_11309025_SNP [dm3] 3L_11315925_SNP [dm6]	T	C	7.020e^-6	0.591	EXON CR44361	TF binding site BDTNP1_TFBS_twi
3L	10503024	3L_10503024_INS [dm3] 3L_10509924_INS [dm6]	G	GCATTT	7.742e^-6	0.591	INTRON A2bp1
3L	17612801	3L_17612801_SNP [dm3] 3L_17619701_SNP [dm6]	C	T	8.017e^-6	0.591	UPSTREAM Eip74EF DOWNSTREAM CG6259 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sbb mE1_TFBS_Trl
3L	10503050	3L_10503050_SNP [dm3] 3L_10509950_SNP [dm6]	T	C	8.354e^-6	0.591	INTRON A2bp1
2L	6910100	2L_6910100_SNP [dm3] 2L_6910100_SNP [dm6]	T	C	8.840e^-6	0.591	SYNONYMOUS_CODING Rat1 DOWNSTREAM Wee1	TF binding site mE1_TFBS_sens
3R	14016269	3R_14016269_SNP [dm3] 3R_18190547_SNP [dm6]	C	T	8.877e^-6	0.591	SYNONYMOUS_CODING MED17 DOWNSTREAM CG14313	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2L	2936372	2L_2936372_SNP [dm3] 2L_2936372_SNP [dm6]	T	G	8.941e^-6	0.591	INTRON lilli
X	18065438	X_18065438_SNP [dm3] X_18171405_SNP [dm6]	C	T	9.662e^-6	0.591	UTR_3_PRIME Frq1
3L	10503022	3L_10503022_SNP [dm3] 3L_10509922_SNP [dm6]	A	T	1.006e^-5	0.591	INTRON A2bp1
2L	10721693	2L_10721693_SNP [dm3] 2L_10721693_SNP [dm6]	C	A	1.055e^-5	0.591	INTERGENIC
3L	4313227	3L_4313227_SNP [dm3] 3L_4313227_SNP [dm6]	A	C	1.065e^-5	0.591	UPSTREAM Claspin INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med
3R	26238174	3R_26238174_SNP [dm3] 3R_30412452_SNP [dm6]	G	A	1.071e^-5	0.591	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	25520265	3R_25520265_SNP [dm3] 3R_29694543_SNP [dm6]	G	A	1.093e^-5	0.591	INTRON dmrt99B
3R	26238173	3R_26238173_SNP [dm3] 3R_30412451_SNP [dm6]	T	C	1.100e^-5	0.591	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	8974423	3L_8974423_SNP [dm3] 3L_8981323_SNP [dm6]	T	G	1.161e^-5	0.591	UPSTREAM CG13314 DOWNSTREAM Galk INTERGENIC
2R	20173752	2R_20173752_SNP [dm3] 2R_24286229_SNP [dm6]	G	A	1.163e^-5	0.591	INTRON nvy	TF binding site mE1_TFBS_chinmo
3L	5606582	3L_5606582_SNP [dm3] 3L_5613482_SNP [dm6]	G	A	1.178e^-5	0.591	INTERGENIC
3R	10420289	3R_10420289_SNP [dm3] 3R_14594567_SNP [dm6]	A	T	1.186e^-5	0.591	INTRON stumps	regulatory region REDfly_CRMs
3R	9226136	3R_9226136_DEL [dm3] 3R_13400414_DEL [dm6]	TTAGTTAT	T	1.192e^-5	0.591	INTRON CG9796
X	14217582	X_14217582_SNP [dm3] X_14323549_SNP [dm6]	A	G	1.226e^-5	0.591	INTRON dpr8
3R	20608213	3R_20608213_SNP [dm3] 3R_24782491_SNP [dm6]	T	G	1.246e^-5	0.591	NON_SYNONYMOUS_CODING CG42331	TF binding site mE1_TFBS_cad
2L	9396702	2L_9396702_SNP [dm3] 2L_9396702_SNP [dm6]	C	T	1.277e^-5	0.591	DOWNSTREAM CG4438 INTRON Shawl
2R	10580084	2R_10580084_SNP [dm3] 2R_14692579_SNP [dm6]	C	T	1.312e^-5	0.591	INTRON mspo
X	7969009	X_7969009_SNP [dm3] X_8074976_SNP [dm6]	T	C	1.324e^-5	0.591	SYNONYMOUS_CODING Upf2 UPSTREAM CG1571	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2L	18275370	2L_18275370_SNP [dm3] 2L_18275370_SNP [dm6]	C	T	1.371e^-5	0.598	INTRON CG42750
X	14217587	X_14217587_SNP [dm3] X_14323554_SNP [dm6]	G	C	1.408e^-5	0.6	INTRON dpr8
2L	2708746	2L_2708746_SNP [dm3] 2L_2708746_SNP [dm6]	A	G	1.478e^-5	0.615	INTRON CG31690
3R	25520296	3R_25520296_SNP [dm3] 3R_29694574_SNP [dm6]	T	C	1.508e^-5	0.615	INTRON dmrt99B
X	11353524	X_11353524_SNP [dm3] X_11459491_SNP [dm6]	C	T	1.559e^-5	0.622	UPSTREAM CG43155 DOWNSTREAM HP5 INTERGENIC
2L	12093598	2L_12093598_SNP [dm3] 2L_12093598_SNP [dm6]	G	A	1.695e^-5	0.662	UPSTREAM Pex19 INTRON Pex19	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	18264634	2R_18264634_SNP [dm3] 2R_22377129_SNP [dm6]	G	A	1.811e^-5	0.684	SYNONYMOUS_CODING Rtf1	TF binding site mE1_TFBS_sens
3L	3591606	3L_3591606_SNP [dm3] 3L_3591606_SNP [dm6]	T	C	1.823e^-5	0.684	INTRON Eip63E
2L	3002173	2L_3002173_SNP [dm3] 2L_3002173_SNP [dm6]	A	T	1.940e^-5	0.7	INTRON CG17265
2R	17618532	2R_17618532_INS [dm3] 2R_21731027_INS [dm6]	T	TT	1.940e^-5	0.7	INTERGENIC
3L	4313226	3L_4313226_SNP [dm3] 3L_4313226_SNP [dm6]	A	T	2.032e^-5	0.711	UPSTREAM Claspin INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med
3L	10503036	3L_10503036_SNP [dm3] 3L_10509936_SNP [dm6]	T	A	2.075e^-5	0.711	INTRON A2bp1
3L	8974628	3L_8974628_SNP [dm3] 3L_8981528_SNP [dm6]	G	C	2.100e^-5	0.711	UPSTREAM CG13314 DOWNSTREAM Galk INTERGENIC
2R	20173695	2R_20173695_SNP [dm3] 2R_24286172_SNP [dm6]	C	G	2.123e^-5	0.711	INTRON nvy	TF binding site mE1_TFBS_chinmo
3R	19919361	3R_19919361_SNP [dm3] 3R_24093639_SNP [dm6]	C	G	2.219e^-5	0.73	INTRON 4EHP	TF binding site mE1_TFBS_HSA
3R	25603092	3R_25603092_SNP [dm3] 3R_29777370_SNP [dm6]	G	A	2.306e^-5	0.74	INTRON kay	TF binding site BDTNP1_TFBS_z
3R	19919356	3R_19919356_SNP [dm3] 3R_24093634_SNP [dm6]	A	G	2.326e^-5	0.74	INTRON 4EHP	TF binding site mE1_TFBS_HSA
3R	24508657	3R_24508657_SNP [dm3] 3R_28682935_SNP [dm6]	G	A	2.472e^-5	0.74	INTRON CG9990	TF binding site BDTNP1_TFBS_z
X	14223693	X_14223693_SNP [dm3] X_14329660_SNP [dm6]	A	G	2.534e^-5	0.74	INTRON dpr8
X	2214175	X_2214175_INS [dm3] X_2320142_INS [dm6]	G	GCTGAG	2.546e^-5	0.74	INTRON phl	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3L	4313231	3L_4313231_SNP [dm3] 3L_4313231_SNP [dm6]	T	A	2.561e^-5	0.74	UPSTREAM Claspin INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med
X	2936925	X_2936925_SNP [dm3] X_3042892_SNP [dm6]	T	G	2.661e^-5	0.74	INTRON kirre
2L	21793557	2L_21793557_SNP [dm3] 2L_21793557_SNP [dm6]	G	T	2.765e^-5	0.74	INTRON CG31612	TF binding site BDTNP1_TFBS_z
2R	16892064	2R_16892064_SNP [dm3] 2R_21004559_SNP [dm6]	C	T	2.784e^-5	0.74	SYNONYMOUS_CODING CG10543	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
X	18065437	X_18065437_SNP [dm3] X_18171404_SNP [dm6]	C	T	2.844e^-5	0.74	UTR_3_PRIME Frq1
2L	17890074	2L_17890074_SNP [dm3] 2L_17890074_SNP [dm6]	C	T	2.893e^-5	0.74	INTERGENIC
3L	4717977	3L_4717977_SNP [dm3] 3L_4717977_SNP [dm6]	C	G	2.963e^-5	0.74	INTRON RhoGEF64C
X	19610876	X_19610876_SNP [dm3] X_19716843_SNP [dm6]	A	T	3.015e^-5	0.74	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi
X	16613801	X_16613801_SNP [dm3] X_16719768_SNP [dm6]	G	A	3.038e^-5	0.74	INTRON CG34325
X	19610872	X_19610872_SNP [dm3] X_19716839_SNP [dm6]	T	C	3.105e^-5	0.74	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi
2L	7263994	2L_7263994_SNP [dm3] 2L_7263994_SNP [dm6]	C	T	3.166e^-5	0.74	INTRON Wnt4	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	9413152	2L_9413152_SNP [dm3] 2L_9413152_SNP [dm6]	G	A	3.194e^-5	0.74	INTRON Shawl
3L	10300434	3L_10300434_SNP [dm3] 3L_10307334_SNP [dm6]	C	A	3.255e^-5	0.74	INTERGENIC	TF binding site BDTNP1_TFBS_dl
2R	18710973	2R_18710973_SNP [dm3] 2R_22823450_SNP [dm6]	A	G	3.265e^-5	0.74	NON_SYNONYMOUS_CODING CG42284	TF binding site mE1_TFBS_chinmo
X	14219696	X_14219696_SNP [dm3] X_14325663_SNP [dm6]	A	G	3.322e^-5	0.74	INTRON dpr8
3R	9610066	3R_9610066_SNP [dm3] 3R_13784344_SNP [dm6]	T	G	3.404e^-5	0.74	NON_SYNONYMOUS_CODING Dip-B	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3L	4313230	3L_4313230_SNP [dm3] 3L_4313230_SNP [dm6]	T	A	3.435e^-5	0.74	UPSTREAM Claspin INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med
3R	9312331	3R_9312331_INS [dm3] 3R_13486609_INS [dm6]	T	TT	3.442e^-5	0.74	INTERGENIC
2R	21095619	2R_21095619_SNP [dm3] 2R_25208096_SNP [dm6]	T	C	3.459e^-5	0.74	INTRON CG9380
2L	17890082	2L_17890082_SNP [dm3] 2L_17890082_SNP [dm6]	A	G	3.483e^-5	0.74	INTERGENIC
X	3559606	X_3559606_SNP [dm3] X_3665573_SNP [dm6]	T	A	3.547e^-5	0.74	UTR_3_PRIME AstA-R1
2L	21815305	2L_21815305_SNP [dm3] 2L_21815305_SNP [dm6]	C	A	3.549e^-5	0.74	INTERGENIC
2L	10098800	2L_10098800_SNP [dm3] 2L_10098800_SNP [dm6]	A	G	3.604e^-5	0.74	INTRON CG34109 & 1 other
2R	17603473	2R_17603473_SNP [dm3] 2R_21715968_SNP [dm6]	C	T	3.669e^-5	0.74	UTR_3_PRIME HmgD DOWNSTREAM Tango11	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad
2R	10584402	2R_10584402_DEL [dm3] 2R_14696897_DEL [dm6]	ATGCAAGCATCATAA...	A	3.670e^-5	0.74	INTRON mspo
2L	12397204	2L_12397204_SNP [dm3] 2L_12397204_SNP [dm6]	A	T	3.684e^-5	0.74	UTR_3_PRIME bru-2
2R	18603310	2R_18603310_SNP [dm3] 2R_22715805_SNP [dm6]	T	C	3.685e^-5	0.74	SYNONYMOUS_CODING CG30268	TF binding site BDTNP1_TFBS_twi
X	2220271	X_2220271_SNP [dm3] X_2326238_SNP [dm6]	C	T	3.780e^-5	0.74	UPSTREAM CG14050 & 1 other INTRON phl	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
3R	20607158	3R_20607158_SNP [dm3] 3R_24781436_SNP [dm6]	G	A	3.892e^-5	0.74	INTRON CG42331	TF binding site mE1_TFBS_chinmo mE1_TFBS_inv
X	2944848	X_2944848_SNP [dm3] X_3050815_SNP [dm6]	G	A	3.922e^-5	0.74	INTRON kirre
X	2937656	X_2937656_SNP [dm3] X_3043623_SNP [dm6]	T	C	3.962e^-5	0.74	INTRON kirre
2L	10722478	2L_10722478_SNP [dm3] 2L_10722478_SNP [dm6]	A	T	4.018e^-5	0.74	INTERGENIC
X	3559607	X_3559607_SNP [dm3] X_3665574_SNP [dm6]	C	A	4.058e^-5	0.74	UTR_3_PRIME AstA-R1
X	2944197	X_2944197_SNP [dm3] X_3050164_SNP [dm6]	A	T	4.082e^-5	0.74	INTRON kirre
2L	21746983	2L_21746983_SNP [dm3] 2L_21746983_SNP [dm6]	A	T	4.109e^-5	0.74	SYNONYMOUS_CODING step INTRON step	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	3179249	2L_3179249_SNP [dm3] 2L_3179249_SNP [dm6]	G	T	4.226e^-5	0.74	INTRON CG34393
X	2944225	X_2944225_SNP [dm3] X_3050192_SNP [dm6]	T	A	4.238e^-5	0.74	INTRON kirre
2L	17882573	2L_17882573_SNP [dm3] 2L_17882573_SNP [dm6]	T	C	4.264e^-5	0.74	INTERGENIC

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Missing results

By genomic position
Variant impact
Gene name

TotalVariants_X phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results