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=4.936e^-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_2R_NS	0.02627

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	13.2694	0.0013
In_2R_NS	16.5718	0.0003

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2228 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	16035506	X_16035506_SNP [dm3] X_16141473_SNP [dm6]	A	G	6.738e^-7	0.64	INTRON disco-r
2R	18455476	2R_18455476_SNP [dm3] 2R_22567971_SNP [dm6]	G	A	6.828e^-7	0.64	INTRON dnr1
X	6704289	X_6704289_SNP [dm3] X_6810256_SNP [dm6]	G	T	1.026e^-6	0.642	NON_SYNONYMOUS_CODING pod1	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2R	19789418	2R_19789418_SNP [dm3] 2R_23901895_SNP [dm6]	C	G	1.931e^-6	0.658	NON_SYNONYMOUS_CODING Lpt	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	12788320	2R_12788320_SNP [dm3] 2R_16900815_SNP [dm6]	A	C	1.980e^-6	0.658	INTRON inaC
2R	12383797	2R_12383797_INS [dm3] 2R_16496292_INS [dm6]	A	CT	2.828e^-6	0.658	DOWNSTREAM CG7813 INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2R	18427191	2R_18427191_SNP [dm3] 2R_22539686_SNP [dm6]	T	C	3.832e^-6	0.658	INTRON px
2L	11865268	2L_11865268_INS [dm3] 2L_11865268_INS [dm6]	A	AAAA	4.210e^-6	0.658	INTRON Pde1c
X	11821675	X_11821675_SNP [dm3] X_11927642_SNP [dm6]	G	A	5.592e^-6	0.658	SYNONYMOUS_CODING CG10362
2L	10665030	2L_10665030_SNP [dm3] 2L_10665030_SNP [dm6]	T	A	5.733e^-6	0.658	INTRON CG31871
2L	5787358	2L_5787358_SNP [dm3] 2L_5787358_SNP [dm6]	C	T	5.747e^-6	0.658	INTRON CG9171
2R	19570894	2R_19570894_SNP [dm3] 2R_23683371_SNP [dm6]	C	T	6.392e^-6	0.658	UPSTREAM St3 DOWNSTREAM St1 INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
X	8971396	X_8971396_SNP [dm3] X_9077363_SNP [dm6]	T	C	6.951e^-6	0.658	INTRON CG44325	TF binding site mE1_TFBS_inv
3R	18622502	3R_18622502_SNP [dm3] 3R_22796780_SNP [dm6]	T	C	7.485e^-6	0.658	INTERGENIC
2L	9194548	2L_9194548_SNP [dm3] 2L_9194548_SNP [dm6]	G	T	7.860e^-6	0.658	INTRON tai
3L	11980965	3L_11980965_SNP [dm3] 3L_11987865_SNP [dm6]	C	T	7.902e^-6	0.658	SYNONYMOUS_CODING CG6938	TF binding site mE1_TFBS_cad
2L	11865278	2L_11865278_SNP [dm3] 2L_11865278_SNP [dm6]	G	A	9.014e^-6	0.658	INTRON Pde1c
2R	12383782	2R_12383782_SNP [dm3] 2R_16496277_SNP [dm6]	C	T	9.324e^-6	0.658	DOWNSTREAM CG7813 INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
X	16592979	X_16592979_SNP [dm3] X_16698946_SNP [dm6]	C	A	9.755e^-6	0.658	DOWNSTREAM CG9676 INTRON CG4678
2R	16706777	2R_16706777_SNP [dm3] 2R_20819272_SNP [dm6]	G	A	1.006e^-5	0.658	INTERGENIC
2L	1041146	2L_1041146_SNP [dm3] 2L_1041146_SNP [dm6]	C	G	1.092e^-5	0.658	INTRON IA-2
2R	19593567	2R_19593567_SNP [dm3] 2R_23706044_SNP [dm6]	G	C	1.101e^-5	0.658	NON_SYNONYMOUS_CODING l_2_not UPSTREAM l_2_tid DOWNSTREAM l_2_dtl	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3R	18704267	3R_18704267_SNP [dm3] 3R_22878545_SNP [dm6]	C	T	1.180e^-5	0.658	INTERGENIC	TF binding site BDTNP1_TFBS_Med BDTNP1_TFBS_twi
X	12263837	X_12263837_SNP [dm3] X_12369804_SNP [dm6]	A	C	1.210e^-5	0.658	INTERGENIC
3R	24996775	3R_24996775_SNP [dm3] 3R_29171053_SNP [dm6]	C	T	1.210e^-5	0.658	SYNONYMOUS_CODING CG11898 DOWNSTREAM CG14509	TF binding site mE1_TFBS_kn
2R	16247137	2R_16247137_SNP [dm3] 2R_20359632_SNP [dm6]	T	C	1.230e^-5	0.658	INTERGENIC
2R	16247151	2R_16247151_SNP [dm3] 2R_20359646_SNP [dm6]	C	T	1.247e^-5	0.658	INTERGENIC
2L	7576820	2L_7576820_SNP [dm3] 2L_7576820_SNP [dm6]	T	A	1.287e^-5	0.658	UPSTREAM RapGAP1 INTRON RapGAP1	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_Trl
X	8427950	X_8427950_INS [dm3] X_8533917_INS [dm6]	C	CGGAC	1.308e^-5	0.658	INTRON Nrg	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	7577021	2L_7577021_SNP [dm3] 2L_7577021_SNP [dm6]	C	T	1.367e^-5	0.658	UPSTREAM RapGAP1 INTRON RapGAP1	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_sens mE1_TFBS_Trl
X	11821678	X_11821678_SNP [dm3] X_11927645_SNP [dm6]	T	G	1.422e^-5	0.658	SYNONYMOUS_CODING CG10362
3R	18622654	3R_18622654_SNP [dm3] 3R_22796932_SNP [dm6]	C	T	1.435e^-5	0.658	INTERGENIC
X	16035639	X_16035639_SNP [dm3] X_16141606_SNP [dm6]	A	G	1.457e^-5	0.658	INTRON disco-r
X	15501795	X_15501795_SNP [dm3] X_15607762_SNP [dm6]	C	T	1.462e^-5	0.658	NON_SYNONYMOUS_CODING sog	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	11534766	3L_11534766_SNP [dm3] 3L_11541666_SNP [dm6]	G	A	1.465e^-5	0.658	INTRON Mob2
2R	15262336	2R_15262336_SNP [dm3] 2R_19374831_SNP [dm6]	G	A	1.504e^-5	0.658	UPSTREAM CG10062 INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2R	19570970	2R_19570970_SNP [dm3] 2R_23683447_SNP [dm6]	T	C	1.509e^-5	0.658	SYNONYMOUS_CODING St3 DOWNSTREAM St1	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
2R	18343882	2R_18343882_SNP [dm3] 2R_22456377_SNP [dm6]	C	G	1.556e^-5	0.658	INTRON CG10384
2R	17024847	2R_17024847_SNP [dm3] 2R_21137342_SNP [dm6]	G	T	1.607e^-5	0.658	INTRON Magi
X	9342909	X_9342909_SNP [dm3] X_9448876_SNP [dm6]	T	C	1.685e^-5	0.658	INTRON mgl	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_prd mE1_TFBS_HSA
X	7255572	X_7255572_SNP [dm3] X_7361539_SNP [dm6]	C	A	1.738e^-5	0.658	INTRON CG1677 & 1 other	TF binding site mE1_TFBS_Kr
2L	2607542	2L_2607542_SNP [dm3] 2L_2607542_SNP [dm6]	G	A	1.789e^-5	0.658	INTERGENIC
2L	1041148	2L_1041148_SNP [dm3] 2L_1041148_SNP [dm6]	G	A	1.790e^-5	0.658	INTRON IA-2
2R	15262230	2R_15262230_DEL [dm3] 2R_19374725_DEL [dm6]	GCG	G	1.797e^-5	0.658	UPSTREAM CG10062 INTERGENIC	TF binding site mE1_TFBS_inv
X	14763147	X_14763147_SNP [dm3] X_14869114_SNP [dm6]	T	C	1.798e^-5	0.658	INTRON Flo2 & 1 other
X	5680229	X_5680229_SNP [dm3] X_5786196_SNP [dm6]	T	A	1.814e^-5	0.658	INTRON CG42699	TF binding site mE1_TFBS_chinmo
2R	18316084	2R_18316084_SNP [dm3] 2R_22428579_SNP [dm6]	T	C	1.826e^-5	0.658	INTRON ppk12
2R	19591967	2R_19591967_SNP [dm3] 2R_23704444_SNP [dm6]	C	T	1.889e^-5	0.658	SYNONYMOUS_CODING l_2_dtl DOWNSTREAM l_2_not	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
X	14763121	X_14763121_SNP [dm3] X_14869088_SNP [dm6]	C	T	1.903e^-5	0.658	INTRON Flo2 & 1 other
2R	16247135	2R_16247135_SNP [dm3] 2R_20359630_SNP [dm6]	G	A	1.975e^-5	0.658	INTERGENIC
3L	5309749	3L_5309749_SNP [dm3] 3L_5316649_SNP [dm6]	T	C	2.033e^-5	0.658	UPSTREAM CR45741 INTERGENIC
2R	19602165	2R_19602165_SNP [dm3] 2R_23714642_SNP [dm6]	C	T	2.057e^-5	0.658	INTRON Sesn
3L	12862127	3L_12862127_DEL [dm3] 3L_12869027_DEL [dm6]	TC	T	2.088e^-5	0.658	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	18084905	2R_18084905_SNP [dm3] 2R_22197400_SNP [dm6]	C	T	2.149e^-5	0.658	UPSTREAM snoRNA:Or-CD1 INTRON Swim	TF binding site BDTNP1_TFBS_dl
X	16594650	X_16594650_SNP [dm3] X_16700617_SNP [dm6]	A	G	2.159e^-5	0.658	UTR_3_PRIME spheroide UPSTREAM CG9676 INTRON CG4678
X	6704060	X_6704060_SNP [dm3] X_6810027_SNP [dm6]	C	A	2.243e^-5	0.658	SYNONYMOUS_CODING pod1	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3R	11392357	3R_11392357_SNP [dm3] 3R_15566635_SNP [dm6]	A	T	2.262e^-5	0.658	INTERGENIC
2R	16937757	2R_16937757_SNP [dm3] 2R_21050252_SNP [dm6]	A	T	2.290e^-5	0.658	UTR_3_PRIME shg	TF binding site BDTNP1_TFBS_dl
3L	5890694	3L_5890694_SNP [dm3] 3L_5897594_SNP [dm6]	G	T	2.294e^-5	0.658	UPSTREAM CG5592 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
3R	12363439	3R_12363439_SNP [dm3] 3R_16537717_SNP [dm6]	A	G	2.300e^-5	0.658	INTRON CG42342
2L	21906643	2L_21906643_SNP [dm3] 2L_21906643_SNP [dm6]	C	T	2.309e^-5	0.658	SYNONYMOUS_CODING CG1428	TF binding site mE1_TFBS_cad
X	5694093	X_5694093_SNP [dm3] X_5800060_SNP [dm6]	A	G	2.352e^-5	0.658	INTERGENIC
2R	19612129	2R_19612129_SNP [dm3] 2R_23724606_SNP [dm6]	T	A	2.436e^-5	0.658	INTRON Sesn
2L	11865260	2L_11865260_SNP [dm3] 2L_11865260_SNP [dm6]	C	T	2.452e^-5	0.658	INTRON Pde1c
2L	20508888	2L_20508888_SNP [dm3] 2L_20508888_SNP [dm6]	A	G	2.454e^-5	0.658	INTERGENIC
2R	18084911	2R_18084911_SNP [dm3] 2R_22197406_SNP [dm6]	G	A	2.499e^-5	0.658	UPSTREAM snoRNA:Or-CD1 INTRON Swim	TF binding site BDTNP1_TFBS_dl
2R	11213150	2R_11213150_SNP [dm3] 2R_15325645_SNP [dm6]	G	A	2.570e^-5	0.658	UTR_3_PRIME CG8157 DOWNSTREAM Arf51F & 1 other	TF binding site BDTNP1_TFBS_dl
3R	27145838	3R_27145838_SNP [dm3] 3R_31320116_SNP [dm6]	G	A	2.606e^-5	0.658	INTRON CG34347
X	14763129	X_14763129_DEL [dm3] X_14869096_DEL [dm6]	AA	A	2.607e^-5	0.658	INTRON Flo2 & 1 other
3R	11392269	3R_11392269_SNP [dm3] 3R_15566547_SNP [dm6]	A	T	2.689e^-5	0.658	INTERGENIC
3R	11392300	3R_11392300_SNP [dm3] 3R_15566578_SNP [dm6]	C	A	2.689e^-5	0.658	INTERGENIC
3R	11392363	3R_11392363_SNP [dm3] 3R_15566641_SNP [dm6]	T	C	2.689e^-5	0.658	INTERGENIC
2R	11715975	2R_11715975_SNP [dm3] 2R_15828470_SNP [dm6]	C	T	2.706e^-5	0.658	INTRON tun & 1 other
2L	12298969	2L_12298969_SNP [dm3] 2L_12298969_SNP [dm6]	G	A	2.726e^-5	0.658	SYNONYMOUS_CODING aret	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv
3L	418716	3L_418716_SNP [dm3] 3L_418716_SNP [dm6]	C	G	2.740e^-5	0.658	INTERGENIC
2R	18316068	2R_18316068_SNP [dm3] 2R_22428563_SNP [dm6]	A	T	2.748e^-5	0.658	INTRON ppk12
2R	19588037	2R_19588037_SNP [dm3] 2R_23700514_SNP [dm6]	T	G	2.775e^-5	0.658	SYNONYMOUS_CODING CG4091
X	5694101	X_5694101_SNP [dm3] X_5800068_SNP [dm6]	A	C	2.788e^-5	0.658	INTERGENIC
2R	17457026	2R_17457026_SNP [dm3] 2R_21569521_SNP [dm6]	T	A	2.829e^-5	0.658	INTRON CG10440	TF binding site mE1_TFBS_HSA
3R	11392264	3R_11392264_SNP [dm3] 3R_15566542_SNP [dm6]	G	A	2.834e^-5	0.658	INTERGENIC
3R	18622387	3R_18622387_SNP [dm3] 3R_22796665_SNP [dm6]	A	T	2.848e^-5	0.658	INTERGENIC
3R	12352727	3R_12352727_SNP [dm3] 3R_16527005_SNP [dm6]	C	T	2.924e^-5	0.658	INTRON CG42342	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_eve mE1_TFBS_HSA
3R	22211439	3R_22211439_SNP [dm3] 3R_26385717_SNP [dm6]	T	C	2.949e^-5	0.658	INTERGENIC
3R	22211453	3R_22211453_SNP [dm3] 3R_26385731_SNP [dm6]	C	G	2.949e^-5	0.658	INTERGENIC
X	13062814	X_13062814_SNP [dm3] X_13168781_SNP [dm6]	G	A	3.014e^-5	0.663	INTRON CG34411
X	16592973	X_16592973_SNP [dm3] X_16698940_SNP [dm6]	G	A	3.072e^-5	0.663	DOWNSTREAM CG9676 INTRON CG4678
2R	15262223	2R_15262223_SNP [dm3] 2R_19374718_SNP [dm6]	A	G	3.106e^-5	0.663	UPSTREAM CG10062 INTERGENIC	TF binding site mE1_TFBS_inv
3R	9283153	3R_9283153_SNP [dm3] 3R_13457431_SNP [dm6]	G	A	3.147e^-5	0.663	INTRON CR17025 & 1 other
2L	9522681	2L_9522681_SNP [dm3] 2L_9522681_SNP [dm6]	C	T	3.147e^-5	0.663	INTRON Oatp30B	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
3R	24796524	3R_24796524_SNP [dm3] 3R_28970802_SNP [dm6]	T	G	3.199e^-5	0.664	UPSTREAM CG14521 EXON CR45669
3R	18926949	3R_18926949_SNP [dm3] 3R_23101227_SNP [dm6]	A	G	3.220e^-5	0.664	DOWNSTREAM CG6738 INTRON CG13830
2R	9477824	2R_9477824_SNP [dm3] 2R_13590319_SNP [dm6]	A	G	3.257e^-5	0.664	INTRON CG6191 & 1 other
2R	10912555	2R_10912555_SNP [dm3] 2R_15025050_SNP [dm6]	T	C	3.312e^-5	0.666	UPSTREAM CR45256 & 1 other INTRON hbs	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
2R	17853143	2R_17853143_SNP [dm3] 2R_21965638_SNP [dm6]	G	A	3.362e^-5	0.666	INTRON ppk9
2L	20508890	2L_20508890_SNP [dm3] 2L_20508890_SNP [dm6]	A	G	3.372e^-5	0.666	INTERGENIC
3R	11392277	3R_11392277_SNP [dm3] 3R_15566555_SNP [dm6]	T	A	3.477e^-5	0.672	INTERGENIC
3R	11546840	3R_11546840_SNP [dm3] 3R_15721118_SNP [dm6]	T	C	3.501e^-5	0.672	INTERGENIC
3L	5890698	3L_5890698_SNP [dm3] 3L_5897598_SNP [dm6]	T	C	3.511e^-5	0.672	UPSTREAM CG5592 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
3R	18926946	3R_18926946_SNP [dm3] 3R_23101224_SNP [dm6]	C	A	3.740e^-5	0.703	DOWNSTREAM CG6738 INTRON CG13830
2L	4294293	2L_4294293_SNP [dm3] 2L_4294293_SNP [dm6]	A	T	3.750e^-5	0.703	INTRON tutl

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Missing results

By genomic position
Variant impact
Gene name

mn_Viability phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results