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=5.008e^-16)
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	<2e-16
In_2R_NS	0.0837

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	60.9409	5.8458e-14
In_2R_NS	15.7921	0.0004

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

4705 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	14336797	2L_14336797_SNP [dm3] 2L_14336797_SNP [dm6]	T	A	5.709e^-7	0.253	INTRON CG33090	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2R	5505861	2R_5505861_SNP [dm3] 2R_9618356_SNP [dm6]	A	G	8.822e^-7	0.253	INTRON Mmp2
3L	12638578	3L_12638578_SNP [dm3] 3L_12645478_SNP [dm6]	A	T	1.020e^-6	0.253	EXON CR32111
2L	4831737	2L_4831737_SNP [dm3] 2L_4831737_SNP [dm6]	C	T	1.290e^-6	0.253	SYNONYMOUS_CODING Ir25a	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	4831728	2L_4831728_SNP [dm3] 2L_4831728_SNP [dm6]	C	T	1.503e^-6	0.253	SYNONYMOUS_CODING Ir25a	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	4831707	2L_4831707_SNP [dm3] 2L_4831707_SNP [dm6]	G	C	1.567e^-6	0.253	SYNONYMOUS_CODING Ir25a	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	5505915	2R_5505915_SNP [dm3] 2R_9618410_SNP [dm6]	T	A	1.647e^-6	0.253	INTRON Mmp2
2L	6339739	2L_6339739_INS [dm3] 2L_6339739_INS [dm6]	C	TCGA	1.749e^-6	0.253	UPSTREAM Cpr INTRON Cpr	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_hkb mE1_TFBS_HSA mE1_TFBS_Trl
2L	11637759	2L_11637759_SNP [dm3] 2L_11637759_SNP [dm6]	A	T	1.757e^-6	0.253	INTERGENIC
3L	8033392	3L_8033392_SNP [dm3] 3L_8040292_SNP [dm6]	T	C	1.813e^-6	0.253	INTRON nmo
X	8183193	X_8183193_SNP [dm3] X_8289160_SNP [dm6]	G	C	1.814e^-6	0.253	INTRON nAChRalpha3
3L	12323377	3L_12323377_SNP [dm3] 3L_12330277_SNP [dm6]	C	A	2.163e^-6	0.253	INTRON CG32105	TF binding site mE1_TFBS_cad
3R	13653464	3R_13653464_DEL [dm3] 3R_17827742_DEL [dm6]	TT	T	2.394e^-6	0.253	INTRON tinc	TF binding site mE1_TFBS_cad
2L	9396702	2L_9396702_SNP [dm3] 2L_9396702_SNP [dm6]	C	T	2.491e^-6	0.253	DOWNSTREAM CG4438 INTRON Shawl
3R	20620849	3R_20620849_SNP [dm3] 3R_24795127_SNP [dm6]	C	A	2.554e^-6	0.253	INTRON Ets96B
X	18065438	X_18065438_SNP [dm3] X_18171405_SNP [dm6]	C	T	2.690e^-6	0.253	UTR_3_PRIME Frq1
2L	19783571	2L_19783571_SNP [dm3] 2L_19783571_SNP [dm6]	T	C	2.707e^-6	0.253	INTRON CdGAPr
3L	12638598	3L_12638598_SNP [dm3] 3L_12645498_SNP [dm6]	T	G	2.873e^-6	0.253	EXON CR32111
2L	9396551	2L_9396551_SNP [dm3] 2L_9396551_SNP [dm6]	G	A	2.915e^-6	0.253	DOWNSTREAM CG4438 INTRON Shawl
2L	8702777	2L_8702777_SNP [dm3] 2L_8702777_SNP [dm6]	A	T	3.182e^-6	0.253	UPSTREAM CR44992 INTRON Hnf4	TF binding site BDTNP1_TFBS_twi
2R	18603310	2R_18603310_SNP [dm3] 2R_22715805_SNP [dm6]	T	C	3.184e^-6	0.253	SYNONYMOUS_CODING CG30268	TF binding site BDTNP1_TFBS_twi
2L	21747097	2L_21747097_SNP [dm3] 2L_21747097_SNP [dm6]	C	A	3.495e^-6	0.253	SYNONYMOUS_CODING step INTRON step	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	3887450	2L_3887450_SNP [dm3] 2L_3887450_SNP [dm6]	C	T	3.780e^-6	0.253	SYNONYMOUS_CODING capu UTR_5_PRIME capu INTRON capu
3R	19565130	3R_19565130_SNP [dm3] 3R_23739408_SNP [dm6]	C	G	3.813e^-6	0.253	INTRON Hmgcr
2L	4833570	2L_4833570_SNP [dm3] 2L_4833570_SNP [dm6]	G	A	3.892e^-6	0.253	SYNONYMOUS_CODING Ir25a
2L	4209784	2L_4209784_DEL [dm3] 2L_4209784_DEL [dm6]	CC	C	4.019e^-6	0.253	INTRON ft	TF binding site mE1_TFBS_inv
3L	12638597	3L_12638597_SNP [dm3] 3L_12645497_SNP [dm6]	C	A	4.178e^-6	0.253	EXON CR32111
2L	1010550	2L_1010550_DEL [dm3] 2L_1010550_DEL [dm6]	TT	T	4.320e^-6	0.253	UTR_3_PRIME IA-2 DOWNSTREAM IA-2
2L	21746983	2L_21746983_SNP [dm3] 2L_21746983_SNP [dm6]	A	T	4.323e^-6	0.253	SYNONYMOUS_CODING step INTRON step	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	3141826	2R_3141826_DEL [dm3] 2R_7254321_DEL [dm6]	AA	A	4.579e^-6	0.253	UPSTREAM CR45280 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
X	2936925	X_2936925_SNP [dm3] X_3042892_SNP [dm6]	T	G	5.076e^-6	0.253	INTRON kirre
2L	4341047	2L_4341047_SNP [dm3] 2L_4341047_SNP [dm6]	G	A	5.150e^-6	0.253	INTRON Atet
X	5849952	X_5849952_SNP [dm3] X_5955919_SNP [dm6]	T	A	5.245e^-6	0.253	INTRON CG6067
3R	22233658	3R_22233658_SNP [dm3] 3R_26407936_SNP [dm6]	C	T	5.304e^-6	0.253	INTERGENIC
3L	2401408	3L_2401408_SNP [dm3] 3L_2401408_SNP [dm6]	C	G	5.440e^-6	0.253	INTRON CG45186
2L	7617877	2L_7617877_SNP [dm3] 2L_7617877_SNP [dm6]	A	T	5.725e^-6	0.253	INTERGENIC
2L	3492177	2L_3492177_INS [dm3] 2L_3492177_INS [dm6]	G	GAAAGAAAA	5.759e^-6	0.253	INTERGENIC	TF binding site mE1_TFBS_inv
2R	18855621	2R_18855621_SNP [dm3] 2R_22968098_SNP [dm6]	T	C	5.874e^-6	0.253	INTERGENIC
3L	12638570	3L_12638570_SNP [dm3] 3L_12645470_SNP [dm6]	G	A	6.273e^-6	0.253	EXON CR32111
X	18065437	X_18065437_SNP [dm3] X_18171404_SNP [dm6]	C	T	6.298e^-6	0.253	UTR_3_PRIME Frq1
3R	18581582	3R_18581582_SNP [dm3] 3R_22755860_SNP [dm6]	C	T	6.312e^-6	0.253	INTRON Usp12-46 & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
2L	9011470	2L_9011470_SNP [dm3] 2L_9011470_SNP [dm6]	T	C	6.380e^-6	0.253	UPSTREAM CG13102 DOWNSTREAM CG9568 INTERGENIC
X	16559137	X_16559137_DEL [dm3] X_16665104_DEL [dm6]	ATAT	G	6.427e^-6	0.253	UPSTREAM CG15865 INTRON r
2R	6896980	2R_6896980_SNP [dm3] 2R_11009475_SNP [dm6]	A	G	6.613e^-6	0.253	INTRON luna	TF binding site mE1_TFBS_inv
3L	12638634	3L_12638634_SNP [dm3] 3L_12645534_SNP [dm6]	C	A	6.827e^-6	0.253	EXON CR32111
2L	2225658	2L_2225658_SNP [dm3] 2L_2225658_SNP [dm6]	G	A	6.851e^-6	0.253	UTR_3_PRIME CG15387 UPSTREAM rti DOWNSTREAM papi	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med
3R	23563740	3R_23563740_SNP [dm3] 3R_27738018_SNP [dm6]	G	A	6.992e^-6	0.253	INTRON Ets98B	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3L	1300670	3L_1300670_DEL [dm3] 3L_1300670_DEL [dm6]	GTAAG	G	7.130e^-6	0.253	DOWNSTREAM Rac1 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_twi
3R	10849978	3R_10849978_SNP [dm3] 3R_15024256_SNP [dm6]	T	G	7.381e^-6	0.253	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3L	12638612	3L_12638612_SNP [dm3] 3L_12645512_SNP [dm6]	G	A	7.437e^-6	0.253	EXON CR32111
3R	18581576	3R_18581576_SNP [dm3] 3R_22755854_SNP [dm6]	T	C	7.505e^-6	0.253	INTRON Usp12-46 & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
2L	11391599	2L_11391599_SNP [dm3] 2L_11391599_SNP [dm6]	C	T	7.600e^-6	0.253	INTRON CR43681	regulatory region REDfly_CRMs
3L	12638608	3L_12638608_SNP [dm3] 3L_12645508_SNP [dm6]	A	T	7.673e^-6	0.253	EXON CR32111
2L	1876828	2L_1876828_SNP [dm3] 2L_1876828_SNP [dm6]	T	C	7.784e^-6	0.253	INTRON CG31663
2L	9839544	2L_9839544_SNP [dm3] 2L_9839544_SNP [dm6]	T	G	7.820e^-6	0.253	INTRON nAChRalpha6	TF binding site mE1_TFBS_chinmo
3L	20571364	3L_20571364_SNP [dm3] 3L_20578264_SNP [dm6]	C	T	7.875e^-6	0.253	INTERGENIC
2L	2225660	2L_2225660_SNP [dm3] 2L_2225660_SNP [dm6]	T	A	7.881e^-6	0.253	UTR_3_PRIME CG15387 UPSTREAM rti DOWNSTREAM papi	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med
2L	2225661	2L_2225661_SNP [dm3] 2L_2225661_SNP [dm6]	G	A	7.931e^-6	0.253	UTR_3_PRIME CG15387 UPSTREAM rti DOWNSTREAM papi	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med
X	7438968	X_7438968_SNP [dm3] X_7544935_SNP [dm6]	A	G	8.255e^-6	0.253	INTRON CG32719	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
2L	22062746	2L_22062746_SNP [dm3] 2L_22062746_SNP [dm6]	C	T	8.526e^-6	0.253	INTERGENIC	transposable element FlyBase
3L	12638607	3L_12638607_SNP [dm3] 3L_12645507_SNP [dm6]	G	T	8.722e^-6	0.253	EXON CR32111
3L	12638615	3L_12638615_SNP [dm3] 3L_12645515_SNP [dm6]	T	G	8.751e^-6	0.253	EXON CR32111
2L	10824249	2L_10824249_DEL [dm3] 2L_10824249_DEL [dm6]	CGAAAC	A	8.924e^-6	0.253	INTRON Nos
2L	2822837	2L_2822837_DEL [dm3] 2L_2822837_DEL [dm6]	TGAGT	T	8.951e^-6	0.253	DOWNSTREAM CG3123 INTRON Duox
2L	11901722	2L_11901722_SNP [dm3] 2L_11901722_SNP [dm6]	T	A	9.231e^-6	0.253	INTRON Pde1c
X	8183996	X_8183996_DEL [dm3] X_8289963_DEL [dm6]	TTAGTTTAAAGCTGGTGGCT...	T	9.241e^-6	0.253	INTRON nAChRalpha3
3R	25659763	3R_25659763_SNP [dm3] 3R_29834041_SNP [dm6]	A	C	9.454e^-6	0.253	SYNONYMOUS_CODING Atg16 UPSTREAM Atg16	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad
3L	12638611	3L_12638611_SNP [dm3] 3L_12645511_SNP [dm6]	C	G	9.525e^-6	0.253	EXON CR32111
2L	16128208	2L_16128208_SNP [dm3] 2L_16128208_SNP [dm6]	T	C	9.533e^-6	0.253	INTERGENIC
2R	3812727	2R_3812727_SNP [dm3] 2R_7925222_SNP [dm6]	A	G	9.543e^-6	0.253	UPSTREAM Kdm4A INTERGENIC	TF binding site BDTNP1_TFBS_prd
X	21447726	X_21447726_SNP [dm3] X_21576699_SNP [dm6]	T	A	9.624e^-6	0.253	INTERGENIC
2L	1620263	2L_1620263_SNP [dm3] 2L_1620263_SNP [dm6]	G	A	9.707e^-6	0.253	EXON CR44603
2L	12296927	2L_12296927_SNP [dm3] 2L_12296927_SNP [dm6]	A	G	9.856e^-6	0.253	INTRON aret
2R	11873761	2R_11873761_SNP [dm3] 2R_15986256_SNP [dm6]	G	A	1.022e^-5	0.256	INTRON Strn-Mlck
2L	20086170	2L_20086170_SNP [dm3] 2L_20086170_SNP [dm6]	G	A	1.030e^-5	0.256	INTRON neb	TF binding site BDTNP1_TFBS_dl mE1_TFBS_GATAe mE1_TFBS_HSA
2L	851138	2L_851138_SNP [dm3] 2L_851138_SNP [dm6]	C	T	1.037e^-5	0.256	UPSTREAM drongo DOWNSTREAM CG4291 EXON CR44060	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_h
2L	3565146	2L_3565146_SNP [dm3] 2L_3565146_SNP [dm6]	T	C	1.110e^-5	0.265	INTERGENIC
2L	3565165	2L_3565165_SNP [dm3] 2L_3565165_SNP [dm6]	G	A	1.110e^-5	0.265	INTERGENIC	TF binding site mE1_TFBS_HSA
X	2937656	X_2937656_SNP [dm3] X_3043623_SNP [dm6]	T	C	1.116e^-5	0.265	INTRON kirre
2L	3967200	2L_3967200_SNP [dm3] 2L_3967200_SNP [dm6]	A	G	1.136e^-5	0.265	INTRON fred
2L	9358594	2L_9358594_SNP [dm3] 2L_9358594_SNP [dm6]	A	C	1.339e^-5	0.265	INTERGENIC
3L	12638617	3L_12638617_SNP [dm3] 3L_12645517_SNP [dm6]	T	G	1.343e^-5	0.265	EXON CR32111
2L	161394	2L_161394_DEL [dm3] 2L_161394_DEL [dm6]	GGTCCCTATAGTAGAGG...	G	1.367e^-5	0.265	UTR_5_PRIME spen INTRON spen	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_Kr mE1_TFBS_sens mE1_TFBS_Trl mE1_TFBS_zfh1
3R	12764484	3R_12764484_SNP [dm3] 3R_16938762_SNP [dm6]	A	G	1.391e^-5	0.265	INTRON Abd-B	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
2L	1819310	2L_1819310_SNP [dm3] 2L_1819310_SNP [dm6]	G	A	1.392e^-5	0.265	INTERGENIC
2L	4355118	2L_4355118_SNP [dm3] 2L_4355118_SNP [dm6]	T	C	1.411e^-5	0.265	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_sens
3R	21017532	3R_21017532_SNP [dm3] 3R_25191810_SNP [dm6]	C	A	1.424e^-5	0.265	SYNONYMOUS_CODING dan INTRON lobo	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	21747859	2L_21747859_SNP [dm3] 2L_21747859_SNP [dm6]	C	G	1.434e^-5	0.265	INTRON step	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
3L	20564574	3L_20564574_SNP [dm3] 3L_20571474_SNP [dm6]	G	A	1.441e^-5	0.265	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	3812654	2R_3812654_SNP [dm3] 2R_7925149_SNP [dm6]	A	T	1.446e^-5	0.265	UPSTREAM Kdm4A INTERGENIC	TF binding site BDTNP1_TFBS_prd
X	2944197	X_2944197_SNP [dm3] X_3050164_SNP [dm6]	A	T	1.449e^-5	0.265	INTRON kirre
3R	19585112	3R_19585112_SNP [dm3] 3R_23759390_SNP [dm6]	C	A	1.465e^-5	0.265	NON_SYNONYMOUS_CODING Plip UPSTREAM Hrd3 DOWNSTREAM CG10219	TF binding site mE1_TFBS_sens
2L	3534347	2L_3534347_SNP [dm3] 2L_3534347_SNP [dm6]	C	G	1.477e^-5	0.265	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
2L	9011468	2L_9011468_SNP [dm3] 2L_9011468_SNP [dm6]	A	T	1.505e^-5	0.265	UPSTREAM CG13102 DOWNSTREAM CG9568 INTERGENIC
X	2944225	X_2944225_SNP [dm3] X_3050192_SNP [dm6]	T	A	1.527e^-5	0.265	INTRON kirre
3L	12319994	3L_12319994_SNP [dm3] 3L_12326894_SNP [dm6]	T	C	1.531e^-5	0.265	INTERGENIC
2R	19543550	2R_19543550_SNP [dm3] 2R_23656027_SNP [dm6]	T	G	1.543e^-5	0.265	INTERGENIC	TF binding site BDTNP1_TFBS_dl
2L	20091564	2L_20091564_SNP [dm3] 2L_20091564_SNP [dm6]	T	C	1.543e^-5	0.265	UPSTREAM CG10721 & 1 other INTRON CG10721	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd mE1_TFBS_HSA mE1_TFBS_Ubx
2L	2634891	2L_2634891_SNP [dm3] 2L_2634891_SNP [dm6]	A	T	1.544e^-5	0.265	INTERGENIC
3R	20634435	3R_20634435_SNP [dm3] 3R_24808713_SNP [dm6]	T	C	1.558e^-5	0.265	DOWNSTREAM CG6980 INTRON CG5807

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Missing results

By genomic position
Variant impact
Gene name

TotalVariants_2L phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results