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=1.664e^-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

Covariate	p-value	Significance
In_2L_t	0.01368
In_3R_P	0.07176

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	11.3613	0.0034

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2067 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	14001452	2L_14001452_SNP [dm3] 2L_14001452_SNP [dm6]	T	A	1.016e^-6	0.74	UPSTREAM rk INTERGENIC	TF binding site mE1_TFBS_GATAe mE1_TFBS_HSA
2L	13842345	2L_13842345_SNP [dm3] 2L_13842345_SNP [dm6]	G	A	2.901e^-6	0.74	UPSTREAM CG33307 DOWNSTREAM CG33306 INTRON CenG1A	TF binding site mE1_TFBS_bab1
X	10798033	X_10798033_SNP [dm3] X_10904000_SNP [dm6]	A	G	3.684e^-6	0.74	INTERGENIC
2L	14012555	2L_14012555_SNP [dm3] 2L_14012555_SNP [dm6]	T	C	3.936e^-6	0.74	UPSTREAM bgm INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2R	3305394	2R_3305394_SNP [dm3] 2R_7417889_SNP [dm6]	T	C	4.305e^-6	0.74	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad
2L	15461665	2L_15461665_SNP [dm3] 2L_15461665_SNP [dm6]	A	G	4.713e^-6	0.74	INTERGENIC
X	9490774	X_9490774_SNP [dm3] X_9596741_SNP [dm6]	T	G	4.765e^-6	0.74	INTERGENIC
X	10798115	X_10798115_SNP [dm3] X_10904082_SNP [dm6]	T	C	5.149e^-6	0.74	INTERGENIC
2R	14883286	2R_14883286_DEL [dm3] 2R_18995781_DEL [dm6]	ATAGGCTTGA	A	5.205e^-6	0.74	DOWNSTREAM snoRNA:abba-a INTRON tn
X	10798126	X_10798126_SNP [dm3] X_10904093_SNP [dm6]	G	A	5.915e^-6	0.74	INTERGENIC
2L	13842350	2L_13842350_DEL [dm3] 2L_13842350_DEL [dm6]	CAAAT	C	6.429e^-6	0.74	UPSTREAM CG33307 DOWNSTREAM CG33306 INTRON CenG1A	TF binding site mE1_TFBS_bab1
2R	12474615	2R_12474615_SNP [dm3] 2R_16587110_SNP [dm6]	T	A	6.701e^-6	0.74	UTR_3_PRIME CG8311 DOWNSTREAM RpLP2	TF binding site BDTNP1_TFBS_dl
3R	19894978	3R_19894978_SNP [dm3] 3R_24069256_SNP [dm6]	T	A	6.907e^-6	0.74	INTRON 4EHP
2L	11930160	2L_11930160_SNP [dm3] 2L_11930160_SNP [dm6]	G	A	7.099e^-6	0.74	INTERGENIC
3L	19217913	3L_19217913_SNP [dm3] 3L_19224813_SNP [dm6]	A	G	7.142e^-6	0.74	INTRON fz2
2L	12924149	2L_12924149_SNP [dm3] 2L_12924149_SNP [dm6]	A	G	7.912e^-6	0.74	INTRON ACXA	TF binding site mE1_TFBS_hkb mE1_TFBS_HSA
2R	9974029	2R_9974029_SNP [dm3] 2R_14086524_SNP [dm6]	G	T	8.156e^-6	0.74	INTRON Prosap
2R	18200328	2R_18200328_DEL [dm3] 2R_22312823_DEL [dm6]	TCGCACTCGCCTTGTTTGTT...	T	8.901e^-6	0.74	UPSTREAM CR44758 & 1 other INTERGENIC
2L	1628335	2L_1628335_SNP [dm3] 2L_1628335_SNP [dm6]	C	G	9.391e^-6	0.74	INTERGENIC
2R	9974020	2R_9974020_DEL [dm3] 2R_14086515_DEL [dm6]	TA	C	1.088e^-5	0.74	INTRON Prosap
2L	2877581	2L_2877581_SNP [dm3] 2L_2877581_SNP [dm6]	A	G	1.102e^-5	0.74	UPSTREAM CG31950 DOWNSTREAM CG8814 INTRON Prx6005	TF binding site BDTNP1_TFBS_dl
2L	617998	2L_617998_SNP [dm3] 2L_617998_SNP [dm6]	C	T	1.181e^-5	0.74	INTERGENIC
3R	13607731	3R_13607731_SNP [dm3] 3R_17782009_SNP [dm6]	A	T	1.274e^-5	0.74	INTRON CG43102
3L	19217897	3L_19217897_SNP [dm3] 3L_19224797_SNP [dm6]	G	A	1.274e^-5	0.74	INTRON fz2
2L	10019067	2L_10019067_SNP [dm3] 2L_10019067_SNP [dm6]	T	G	1.298e^-5	0.74	INTERGENIC
2R	12474609	2R_12474609_SNP [dm3] 2R_16587104_SNP [dm6]	T	C	1.299e^-5	0.74	UTR_3_PRIME CG8311 DOWNSTREAM RpLP2	TF binding site BDTNP1_TFBS_dl
2R	3305395	2R_3305395_SNP [dm3] 2R_7417890_SNP [dm6]	C	T	1.394e^-5	0.74	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad
2L	8405804	2L_8405804_SNP [dm3] 2L_8405804_SNP [dm6]	C	A	1.420e^-5	0.74	INTRON emb	TF binding site mE1_TFBS_sens
2L	8405848	2L_8405848_SNP [dm3] 2L_8405848_SNP [dm6]	G	T	1.420e^-5	0.74	INTRON emb	TF binding site mE1_TFBS_sens
2L	8405852	2L_8405852_SNP [dm3] 2L_8405852_SNP [dm6]	A	G	1.420e^-5	0.74	INTRON emb	TF binding site mE1_TFBS_sens
2L	8405862	2L_8405862_SNP [dm3] 2L_8405862_SNP [dm6]	A	T	1.420e^-5	0.74	INTRON emb	TF binding site mE1_TFBS_sens
2L	8405874	2L_8405874_SNP [dm3] 2L_8405874_SNP [dm6]	G	T	1.420e^-5	0.74	INTRON emb	TF binding site mE1_TFBS_sens
2L	8405911	2L_8405911_SNP [dm3] 2L_8405911_SNP [dm6]	T	G	1.420e^-5	0.74	SPLICE_SITE_REGION emb INTRON emb	TF binding site mE1_TFBS_sens
2L	8405913	2L_8405913_SNP [dm3] 2L_8405913_SNP [dm6]	C	T	1.420e^-5	0.74	SPLICE_SITE_REGION emb INTRON emb	TF binding site mE1_TFBS_sens
2L	8405971	2L_8405971_SNP [dm3] 2L_8405971_SNP [dm6]	A	G	1.420e^-5	0.74	SYNONYMOUS_CODING emb
2R	3264528	2R_3264528_SNP [dm3] 2R_7377023_SNP [dm6]	C	T	1.439e^-5	0.74	INTRON Dscam1	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
2L	8405463	2L_8405463_SNP [dm3] 2L_8405463_SNP [dm6]	A	G	1.488e^-5	0.74	SYNONYMOUS_CODING emb	TF binding site mE1_TFBS_sens
2L	12982292	2L_12982292_SNP [dm3] 2L_12982292_SNP [dm6]	G	A	1.511e^-5	0.74	DOWNSTREAM Vha68-3 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	18197000	2R_18197000_DEL [dm3] 2R_22309495_DEL [dm6]	CC	C	1.542e^-5	0.74	INTRON wdp	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
X	9490721	X_9490721_DEL [dm3] X_9596688_DEL [dm6]	GTAGTAAG	G	1.577e^-5	0.74	INTERGENIC
2L	8371525	2L_8371525_INS [dm3] 2L_8371525_INS [dm6]	A	ATGGGCCTCAAAAA...	1.733e^-5	0.78	UPSTREAM CR45341 & 1 other INTRON CG17292
X	4438542	X_4438542_SNP [dm3] X_4544509_SNP [dm6]	A	T	1.835e^-5	0.78	DOWNSTREAM Usf & 1 other INTRON CR32773	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	11190970	2L_11190970_SNP [dm3] 2L_11190970_SNP [dm6]	T	C	1.871e^-5	0.78	INTRON Ca-beta	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_prd mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_HSA
2L	13842371	2L_13842371_SNP [dm3] 2L_13842371_SNP [dm6]	A	T	1.917e^-5	0.78	UPSTREAM CG33307 DOWNSTREAM CG33306 INTRON CenG1A	TF binding site mE1_TFBS_bab1
2L	12313752	2L_12313752_SNP [dm3] 2L_12313752_SNP [dm6]	T	C	1.942e^-5	0.78	DOWNSTREAM aret INTERGENIC
X	4438547	X_4438547_SNP [dm3] X_4544514_SNP [dm6]	A	G	1.990e^-5	0.78	DOWNSTREAM Usf & 1 other INTRON CR32773	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	1639637	2L_1639637_SNP [dm3] 2L_1639637_SNP [dm6]	A	G	2.020e^-5	0.78	INTERGENIC
2R	17768964	2R_17768964_SNP [dm3] 2R_21881459_SNP [dm6]	C	T	2.073e^-5	0.78	UTR_3_PRIME PpN58A INTRON Fili
X	4438551	X_4438551_SNP [dm3] X_4544518_SNP [dm6]	T	C	2.148e^-5	0.78	DOWNSTREAM Usf & 1 other INTRON CR32773	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	14883324	2R_14883324_INS [dm3] 2R_18995819_INS [dm6]	T	TAAT	2.158e^-5	0.78	DOWNSTREAM snoRNA:abba-a INTRON tn
2R	3307134	2R_3307134_SNP [dm3] 2R_7419629_SNP [dm6]	G	T	2.180e^-5	0.78	START_GAINED so UTR_5_PRIME so	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2R	14883273	2R_14883273_SNP [dm3] 2R_18995768_SNP [dm6]	G	A	2.188e^-5	0.78	DOWNSTREAM snoRNA:abba-a INTRON tn
3R	11719656	3R_11719656_INS [dm3] 3R_15893934_INS [dm6]	C	CC	2.205e^-5	0.78	INTRON CG14877
X	2237585	X_2237585_SNP [dm3] X_2343552_SNP [dm6]	T	C	2.304e^-5	0.78	UTR_3_PRIME phl DOWNSTREAM mRpL14	TF binding site mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_jumu mE1_TFBS_Trl
X	9093714	X_9093714_SNP [dm3] X_9199681_SNP [dm6]	G	A	2.314e^-5	0.78	SYNONYMOUS_CODING su_r_	TF binding site BDTNP1_TFBS_sna mE1_TFBS_chinmo mE1_TFBS_HSA
3R	8511738	3R_8511738_SNP [dm3] 3R_12686016_SNP [dm6]	C	T	2.328e^-5	0.78	INTRON kar	TF binding site mE1_TFBS_cad
X	8408285	X_8408285_SNP [dm3] X_8514252_SNP [dm6]	G	T	2.376e^-5	0.782	INTRON CG33181
2L	11773290	2L_11773290_SNP [dm3] 2L_11773290_SNP [dm6]	G	A	2.440e^-5	0.789	INTERGENIC
2R	3305403	2R_3305403_SNP [dm3] 2R_7417898_SNP [dm6]	T	G	2.632e^-5	0.807	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad
2R	3305407	2R_3305407_SNP [dm3] 2R_7417902_SNP [dm6]	T	A	2.713e^-5	0.807	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad
2L	15985891	2L_15985891_SNP [dm3] 2L_15985891_SNP [dm6]	T	G	2.807e^-5	0.807	INTERGENIC
2L	1628224	2L_1628224_SNP [dm3] 2L_1628224_SNP [dm6]	C	T	2.877e^-5	0.807	INTERGENIC
2L	10884677	2L_10884677_SNP [dm3] 2L_10884677_SNP [dm6]	A	T	2.906e^-5	0.807	INTERGENIC
2L	15641089	2L_15641089_SNP [dm3] 2L_15641089_SNP [dm6]	A	C	3.013e^-5	0.807	INTERGENIC
2L	13087494	2L_13087494_SNP [dm3] 2L_13087494_SNP [dm6]	C	A	3.046e^-5	0.807	INTERGENIC
2L	14422258	2L_14422258_SNP [dm3] 2L_14422258_SNP [dm6]	G	A	3.066e^-5	0.807	INTERGENIC	TF binding site mE1_TFBS_cad
2L	14001442	2L_14001442_SNP [dm3] 2L_14001442_SNP [dm6]	C	T	3.077e^-5	0.807	UPSTREAM rk INTERGENIC	TF binding site mE1_TFBS_GATAe mE1_TFBS_HSA
2L	8372130	2L_8372130_SNP [dm3] 2L_8372130_SNP [dm6]	C	T	3.131e^-5	0.807	UPSTREAM CG17292 INTRON CG17292
2R	12164879	2R_12164879_SNP [dm3] 2R_16277374_SNP [dm6]	T	C	3.212e^-5	0.807	UTR_3_PRIME CG33017 DOWNSTREAM cato & 1 other
2L	12982234	2L_12982234_SNP [dm3] 2L_12982234_SNP [dm6]	C	A	3.217e^-5	0.807	DOWNSTREAM Vha68-3 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	15139082	2L_15139082_SNP [dm3] 2L_15139082_SNP [dm6]	C	A	3.236e^-5	0.807	INTERGENIC
3L	6449187	3L_6449187_SNP [dm3] 3L_6456087_SNP [dm6]	T	C	3.244e^-5	0.807	INTRON CG42747
2L	14001438	2L_14001438_SNP [dm3] 2L_14001438_SNP [dm6]	C	A	3.280e^-5	0.807	UPSTREAM rk INTERGENIC	TF binding site mE1_TFBS_GATAe mE1_TFBS_HSA
2R	12636335	2R_12636335_SNP [dm3] 2R_16748830_SNP [dm6]	A	T	3.342e^-5	0.807	UTR_3_PRIME Acp53C14b UPSTREAM Acp53C14a DOWNSTREAM Acp53C14b & 1 other
2L	11449080	2L_11449080_SNP [dm3] 2L_11449080_SNP [dm6]	C	T	3.419e^-5	0.807	INTERGENIC	regulatory region FlyBase REDfly_CRMs TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_gt mE1_TFBS_cad mE1_TFBS_HSA
3L	11177866	3L_11177866_SNP [dm3] 3L_11184766_SNP [dm6]	G	T	3.503e^-5	0.807	INTRON GlcAT-P
2R	6594685	2R_6594685_SNP [dm3] 2R_10707180_SNP [dm6]	G	A	3.525e^-5	0.807	SYNONYMOUS_CODING stan	TF binding site mE1_TFBS_cad
3L	6449202	3L_6449202_SNP [dm3] 3L_6456102_SNP [dm6]	T	C	3.604e^-5	0.807	INTRON CG42747
X	14545703	X_14545703_INS [dm3] X_14651670_INS [dm6]	T	TT	3.608e^-5	0.807	INTRON NetA	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi
3R	18983725	3R_18983725_SNP [dm3] 3R_23158003_SNP [dm6]	T	A	3.627e^-5	0.807	UPSTREAM unk DOWNSTREAM VhaAC39-2 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_bab1 mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_sens
3L	8032185	3L_8032185_SNP [dm3] 3L_8039085_SNP [dm6]	G	A	3.638e^-5	0.807	INTRON nmo	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2R	8274201	2R_8274201_SNP [dm3] 2R_12386696_SNP [dm6]	G	T	3.800e^-5	0.807	UTR_5_PRIME Cpr49Ac UPSTREAM Cpr49Ac
2L	15139064	2L_15139064_DEL [dm3] 2L_15139064_DEL [dm6]	TTACGAAAA	C	3.922e^-5	0.807	INTERGENIC
2R	18199358	2R_18199358_SNP [dm3] 2R_22311853_SNP [dm6]	C	G	3.977e^-5	0.807	UTR_5_PRIME wdp UPSTREAM wdp	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
X	4437897	X_4437897_SNP [dm3] X_4543864_SNP [dm6]	C	G	3.986e^-5	0.807	SYNONYMOUS_CODING CG3568 DOWNSTREAM Usf INTRON CR32773	TF binding site mE1_TFBS_sens
2L	15139061	2L_15139061_SNP [dm3] 2L_15139061_SNP [dm6]	T	A	4.001e^-5	0.807	INTERGENIC
X	2237930	X_2237930_SNP [dm3] X_2343897_SNP [dm6]	G	C	4.043e^-5	0.807	DOWNSTREAM mRpL14 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
2L	13842391	2L_13842391_SNP [dm3] 2L_13842391_SNP [dm6]	G	T	4.068e^-5	0.807	UPSTREAM CG33307 DOWNSTREAM CG33306 INTRON CenG1A	TF binding site mE1_TFBS_bab1
3L	18887336	3L_18887336_SNP [dm3] 3L_18894236_SNP [dm6]	A	C	4.073e^-5	0.807	DOWNSTREAM NijB INTRON CG3902
2L	1965998	2L_1965998_SNP [dm3] 2L_1965998_SNP [dm6]	T	C	4.085e^-5	0.807	DOWNSTREAM tRNA:CR31942 INTRON erm	TF binding site mE1_TFBS_chinmo
2L	10035637	2L_10035637_SNP [dm3] 2L_10035637_SNP [dm6]	C	T	4.138e^-5	0.807	INTRON obst-B
3L	11180021	3L_11180021_SNP [dm3] 3L_11186921_SNP [dm6]	G	C	4.165e^-5	0.807	INTRON GlcAT-P
2R	12389671	2R_12389671_SNP [dm3] 2R_16502166_SNP [dm6]	C	A	4.169e^-5	0.807	INTRON Sema-2a	TF binding site BDTNP1_TFBS_twi
2L	12982221	2L_12982221_SNP [dm3] 2L_12982221_SNP [dm6]	G	T	4.188e^-5	0.807	DOWNSTREAM Vha68-3 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	7226594	2L_7226594_DEL [dm3] 2L_7226594_DEL [dm6]	GG	G	4.219e^-5	0.807	UTR_3_PRIME Ndae1 INTRON Ndae1	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_run
2L	15139105	2L_15139105_MNP [dm3] 2L_15139105_MNP [dm6]	GTA	TCC	4.223e^-5	0.807	INTERGENIC
2L	22360950	2L_22360950_SNP [dm3] 2L_22360950_SNP [dm6]	T	G	4.252e^-5	0.807	INTRON CG17018	transposable element FlyBase
3L	18072017	3L_18072017_SNP [dm3] 3L_18078917_SNP [dm6]	T	G	4.282e^-5	0.807	DOWNSTREAM CR45392 INTERGENIC
2L	12982269	2L_12982269_SNP [dm3] 2L_12982269_SNP [dm6]	G	A	4.388e^-5	0.807	DOWNSTREAM Vha68-3 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	12810421	2R_12810421_SNP [dm3] 2R_16922916_SNP [dm6]	T	A	4.390e^-5	0.807	INTERGENIC

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Missing results

By genomic position
Variant impact
Gene name

Cuticul_3_Me_C23_C24 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results