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=1.997e^-7)
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	0.0058308
In_3R_K	0.0002936

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	15.6946	0.0004
In_3R_K	8.4621	0.0145

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2466 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	12151214	X_12151214_SNP [dm3] X_12257181_SNP [dm6]	A	G	4.001e^-7	0.27	INTRON Ten-a
X	12151320	X_12151320_SNP [dm3] X_12257287_SNP [dm6]	A	T	5.884e^-7	0.27	INTRON Ten-a
X	12151446	X_12151446_SNP [dm3] X_12257413_SNP [dm6]	A	T	6.226e^-7	0.27	INTRON Ten-a
2L	20074668	2L_20074668_SNP [dm3] 2L_20074668_SNP [dm6]	T	C	9.870e^-7	0.27	DOWNSTREAM bwa INTRON pr	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med
2L	14012555	2L_14012555_SNP [dm3] 2L_14012555_SNP [dm6]	T	C	1.048e^-6	0.27	UPSTREAM bgm INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
X	5815192	X_5815192_SNP [dm3] X_5921159_SNP [dm6]	T	C	1.120e^-6	0.27	INTRON CG3726
X	5404350	X_5404350_SNP [dm3] X_5510317_SNP [dm6]	C	T	1.221e^-6	0.27	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	2919910	2L_2919910_SNP [dm3] 2L_2919910_SNP [dm6]	C	T	1.246e^-6	0.27	INTRON lilli
X	12151397	X_12151397_SNP [dm3] X_12257364_SNP [dm6]	C	T	1.295e^-6	0.27	INTRON Ten-a
2L	14426268	2L_14426268_SNP [dm3] 2L_14426268_SNP [dm6]	A	G	1.659e^-6	0.287	INTERGENIC
X	12151545	X_12151545_SNP [dm3] X_12257512_SNP [dm6]	T	C	1.682e^-6	0.287	INTRON Ten-a
2R	13119498	2R_13119498_SNP [dm3] 2R_17231993_SNP [dm6]	C	T	2.095e^-6	0.305	INTRON mbl
2R	14883286	2R_14883286_DEL [dm3] 2R_18995781_DEL [dm6]	ATAGGCTTGA	A	2.116e^-6	0.305	DOWNSTREAM snoRNA:abba-a INTRON tn
2L	1639637	2L_1639637_SNP [dm3] 2L_1639637_SNP [dm6]	A	G	2.313e^-6	0.31	INTERGENIC
X	5404373	X_5404373_SNP [dm3] X_5510340_SNP [dm6]	A	T	2.929e^-6	0.34	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	20704871	3R_20704871_INS [dm3] 3R_24879149_INS [dm6]	T	TGC	3.131e^-6	0.34	DOWNSTREAM CG31381 INTRON CG11089	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	11191327	2L_11191327_SNP [dm3] 2L_11191327_SNP [dm6]	A	T	3.312e^-6	0.34	INTRON Ca-beta	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_prd mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	12924149	2L_12924149_SNP [dm3] 2L_12924149_SNP [dm6]	A	G	3.358e^-6	0.34	INTRON ACXA	TF binding site mE1_TFBS_hkb mE1_TFBS_HSA
2R	17405949	2R_17405949_SNP [dm3] 2R_21518444_SNP [dm6]	C	T	3.449e^-6	0.34	DOWNSTREAM CG30288 INTRON CG10494	TF binding site mE1_TFBS_sens
2L	14426085	2L_14426085_SNP [dm3] 2L_14426085_SNP [dm6]	T	A	4.122e^-6	0.34	UPSTREAM Cpr35B INTERGENIC
2L	10901648	2L_10901648_SNP [dm3] 2L_10901648_SNP [dm6]	T	G	4.353e^-6	0.34	SYNONYMOUS_CODING CG14070
2L	15200116	2L_15200116_SNP [dm3] 2L_15200116_SNP [dm6]	T	G	4.367e^-6	0.34	UTR_5_PRIME CG4168
2L	20038457	2L_20038457_SNP [dm3] 2L_20038457_SNP [dm6]	C	T	4.492e^-6	0.34	INTRON sNPF
3R	8221792	3R_8221792_SNP [dm3] 3R_12396070_SNP [dm6]	T	G	4.501e^-6	0.34	UPSTREAM CG10096 & 1 other INTRON CG34402 EXON Cyp9f3Psi
2L	20042586	2L_20042586_SNP [dm3] 2L_20042586_SNP [dm6]	A	T	4.861e^-6	0.34	INTRON sNPF
X	12151337	X_12151337_SNP [dm3] X_12257304_SNP [dm6]	A	G	5.273e^-6	0.34	INTRON Ten-a
2L	6698981	2L_6698981_SNP [dm3] 2L_6698981_SNP [dm6]	A	T	5.615e^-6	0.34	INTRON Tsp
2R	13119500	2R_13119500_SNP [dm3] 2R_17231995_SNP [dm6]	G	C	6.007e^-6	0.34	INTRON mbl
2L	14419968	2L_14419968_SNP [dm3] 2L_14419968_SNP [dm6]	C	A	6.048e^-6	0.34	INTERGENIC
X	12079754	X_12079754_SNP [dm3] X_12185721_SNP [dm6]	G	A	6.070e^-6	0.34	INTRON Ten-a
2L	451889	2L_451889_SNP [dm3] 2L_451889_SNP [dm6]	G	A	6.168e^-6	0.34	UPSTREAM crq INTRON crq	TF binding site mE1_TFBS_inv
2L	8372130	2L_8372130_SNP [dm3] 2L_8372130_SNP [dm6]	C	T	6.430e^-6	0.34	UPSTREAM CG17292 INTRON CG17292
3R	14845685	3R_14845685_SNP [dm3] 3R_19019963_SNP [dm6]	C	T	6.565e^-6	0.34	DOWNSTREAM gukh INTRON gukh
X	19545957	X_19545957_SNP [dm3] X_19651924_SNP [dm6]	C	T	6.572e^-6	0.34	UTR_5_PRIME Ranbp21 UPSTREAM CG14215 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_D mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Ubx
3L	5073331	3L_5073331_SNP [dm3] 3L_5073331_SNP [dm6]	G	A	6.765e^-6	0.34	INTRON Con
2R	10942238	2R_10942238_SNP [dm3] 2R_15054733_SNP [dm6]	T	G	7.141e^-6	0.34	DOWNSTREAM CG33467 INTERGENIC
2R	17405940	2R_17405940_SNP [dm3] 2R_21518435_SNP [dm6]	A	T	7.194e^-6	0.34	DOWNSTREAM CG30288 INTRON CG10494	TF binding site mE1_TFBS_sens
2L	13822668	2L_13822668_SNP [dm3] 2L_13822668_SNP [dm6]	T	C	7.243e^-6	0.34	INTRON b	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
X	19545968	X_19545968_SNP [dm3] X_19651935_SNP [dm6]	T	C	7.247e^-6	0.34	UTR_5_PRIME Ranbp21 UPSTREAM CG14215 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_D mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Ubx
2L	20038844	2L_20038844_SNP [dm3] 2L_20038844_SNP [dm6]	C	A	7.362e^-6	0.34	INTRON sNPF
2L	14426106	2L_14426106_SNP [dm3] 2L_14426106_SNP [dm6]	A	G	7.425e^-6	0.34	UPSTREAM Cpr35B INTERGENIC
3R	14996833	3R_14996833_SNP [dm3] 3R_19171111_SNP [dm6]	C	G	7.946e^-6	0.355	DOWNSTREAM sqz INTERGENIC
2L	7750613	2L_7750613_SNP [dm3] 2L_7750613_SNP [dm6]	C	T	8.141e^-6	0.355	INTERGENIC
3L	3260995	3L_3260995_SNP [dm3] 3L_3260995_SNP [dm6]	C	T	8.403e^-6	0.358	INTRON ckd
2R	14883273	2R_14883273_SNP [dm3] 2R_18995768_SNP [dm6]	G	A	9.000e^-6	0.37	DOWNSTREAM snoRNA:abba-a INTRON tn
X	12151363	X_12151363_SNP [dm3] X_12257330_SNP [dm6]	T	A	9.228e^-6	0.37	INTRON Ten-a
X	12151241	X_12151241_SNP [dm3] X_12257208_SNP [dm6]	G	A	9.275e^-6	0.37	INTRON Ten-a
2R	19508734	2R_19508734_DEL [dm3] 2R_23621211_DEL [dm6]	TG	T	9.942e^-6	0.386	INTERGENIC	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
2R	12810421	2R_12810421_SNP [dm3] 2R_16922916_SNP [dm6]	T	A	1.033e^-5	0.386	INTERGENIC
3R	24904551	3R_24904551_SNP [dm3] 3R_29078829_SNP [dm6]	T	C	1.035e^-5	0.386	INTRON CG11873
2L	15940976	2L_15940976_SNP [dm3] 2L_15940976_SNP [dm6]	G	A	1.050e^-5	0.386	UPSTREAM CG12448 INTRON beat-Ib
2R	12810415	2R_12810415_SNP [dm3] 2R_16922910_SNP [dm6]	T	C	1.103e^-5	0.393	INTERGENIC
3L	14441441	3L_14441441_SNP [dm3] 3L_14448341_SNP [dm6]	A	T	1.142e^-5	0.393	UTR_5_PRIME bbg INTRON bbg	TF binding site BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sbb mE1_TFBS_Trl
2L	12313752	2L_12313752_SNP [dm3] 2L_12313752_SNP [dm6]	T	C	1.189e^-5	0.393	DOWNSTREAM aret INTERGENIC
2L	13822658	2L_13822658_SNP [dm3] 2L_13822658_SNP [dm6]	G	A	1.192e^-5	0.393	INTRON b	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	14001452	2L_14001452_SNP [dm3] 2L_14001452_SNP [dm6]	T	A	1.209e^-5	0.393	UPSTREAM rk INTERGENIC	TF binding site mE1_TFBS_GATAe mE1_TFBS_HSA
X	12145819	X_12145819_INS [dm3] X_12251786_INS [dm6]	T	TGGGATT	1.232e^-5	0.393	INTRON Ten-a	TF binding site mE1_TFBS_inv
2L	13822626	2L_13822626_SNP [dm3] 2L_13822626_SNP [dm6]	A	G	1.297e^-5	0.393	INTRON b	TF binding site mE1_TFBS_cad
2L	13822642	2L_13822642_INS [dm3] 2L_13822642_INS [dm6]	A	AG	1.297e^-5	0.393	INTRON b	TF binding site mE1_TFBS_cad
X	12151380	X_12151380_SNP [dm3] X_12257347_SNP [dm6]	G	A	1.325e^-5	0.393	INTRON Ten-a
2L	20044880	2L_20044880_SNP [dm3] 2L_20044880_SNP [dm6]	T	C	1.350e^-5	0.393	INTRON sNPF
2R	17405935	2R_17405935_SNP [dm3] 2R_21518430_SNP [dm6]	A	C	1.370e^-5	0.393	DOWNSTREAM CG30288 INTRON CG10494	TF binding site mE1_TFBS_sens
2L	15641089	2L_15641089_SNP [dm3] 2L_15641089_SNP [dm6]	A	C	1.382e^-5	0.393	INTERGENIC
2L	6932879	2L_6932879_SNP [dm3] 2L_6932879_SNP [dm6]	A	G	1.412e^-5	0.393	SYNONYMOUS_CODING CG18304 DOWNSTREAM Hrb27C & 1 other	TF binding site mE1_TFBS_cad
3L	3261003	3L_3261003_SNP [dm3] 3L_3261003_SNP [dm6]	T	C	1.413e^-5	0.393	INTRON ckd
2L	13822648	2L_13822648_SNP [dm3] 2L_13822648_SNP [dm6]	A	T	1.417e^-5	0.393	INTRON b	TF binding site mE1_TFBS_cad
3R	20610616	3R_20610616_SNP [dm3] 3R_24784894_SNP [dm6]	G	A	1.418e^-5	0.393	UTR_3_PRIME CG5805 DOWNSTREAM CG42331
2R	12810422	2R_12810422_SNP [dm3] 2R_16922917_SNP [dm6]	A	G	1.425e^-5	0.393	INTERGENIC
2L	13822639	2L_13822639_SNP [dm3] 2L_13822639_SNP [dm6]	C	A	1.444e^-5	0.393	INTRON b	TF binding site mE1_TFBS_cad
2L	16389889	2L_16389889_SNP [dm3] 2L_16389889_SNP [dm6]	A	T	1.477e^-5	0.395	INTERGENIC
3R	8532736	3R_8532736_SNP [dm3] 3R_12707014_SNP [dm6]	A	T	1.514e^-5	0.395	SPLICE_SITE_REGION mus308 INTRON mus308	TF binding site mE1_TFBS_cad
2R	8410549	2R_8410549_SNP [dm3] 2R_12523044_SNP [dm6]	T	C	1.561e^-5	0.395	DOWNSTREAM CG33632 INTERGENIC	transposable element FlyBase
2R	12809928	2R_12809928_SNP [dm3] 2R_16922423_SNP [dm6]	C	A	1.567e^-5	0.395	INTERGENIC
2L	451707	2L_451707_SNP [dm3] 2L_451707_SNP [dm6]	G	T	1.582e^-5	0.395	UPSTREAM crq INTRON crq	TF binding site mE1_TFBS_inv
3R	14144811	3R_14144811_SNP [dm3] 3R_18319089_SNP [dm6]	A	C	1.608e^-5	0.395	INTRON CG31235
3R	21584080	3R_21584080_SNP [dm3] 3R_25758358_SNP [dm6]	G	T	1.622e^-5	0.395	INTRON LpR1
2R	12539528	2R_12539528_SNP [dm3] 2R_16652023_SNP [dm6]	A	G	1.637e^-5	0.395	DOWNSTREAM gprs INTRON Amyrel	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	13822634	2L_13822634_SNP [dm3] 2L_13822634_SNP [dm6]	T	G	1.644e^-5	0.395	INTRON b	TF binding site mE1_TFBS_cad
3L	18093340	3L_18093340_SNP [dm3] 3L_18100240_SNP [dm6]	C	A	1.695e^-5	0.402	INTRON CG13698
2L	798775	2L_798775_SNP [dm3] 2L_798775_SNP [dm6]	C	T	1.742e^-5	0.408	INTERGENIC
2L	20017099	2L_20017099_SNP [dm3] 2L_20017099_SNP [dm6]	T	G	1.765e^-5	0.409	UTR_5_PRIME CG43861
2L	1628272	2L_1628272_SNP [dm3] 2L_1628272_SNP [dm6]	A	T	1.823e^-5	0.417	INTERGENIC
X	14545703	X_14545703_INS [dm3] X_14651670_INS [dm6]	T	TT	1.917e^-5	0.419	INTRON NetA	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi
3L	10707071	3L_10707071_SNP [dm3] 3L_10713971_SNP [dm6]	T	A	1.931e^-5	0.419	INTERGENIC
3L	3261013	3L_3261013_DEL [dm3] 3L_3261013_DEL [dm6]	ATT	G	1.938e^-5	0.419	INTRON ckd
3L	9865111	3L_9865111_SNP [dm3] 3L_9872011_SNP [dm6]	A	T	1.982e^-5	0.419	INTERGENIC	TF binding site mE1_TFBS_D
2R	12883841	2R_12883841_SNP [dm3] 2R_16996336_SNP [dm6]	A	G	1.997e^-5	0.419	DOWNSTREAM ste24c & 1 other INTRON ste24c & 1 other
3L	18090802	3L_18090802_SNP [dm3] 3L_18097702_SNP [dm6]	G	A	2.058e^-5	0.419	INTRON CG13698
2L	8371979	2L_8371979_SNP [dm3] 2L_8371979_SNP [dm6]	A	G	2.077e^-5	0.419	UPSTREAM CG17292 INTRON CG17292
2L	435921	2L_435921_SNP [dm3] 2L_435921_SNP [dm6]	G	A	2.087e^-5	0.419	INTRON ex	TF binding site mE1_TFBS_chinmo
3R	7760866	3R_7760866_SNP [dm3] 3R_11935144_SNP [dm6]	G	A	2.121e^-5	0.419	INTRON Cad87A
2R	13119399	2R_13119399_SNP [dm3] 2R_17231894_SNP [dm6]	T	C	2.125e^-5	0.419	INTRON mbl
3R	8363127	3R_8363127_SNP [dm3] 3R_12537405_SNP [dm6]	A	G	2.143e^-5	0.419	INTRON Octbeta3R
2R	14283427	2R_14283427_SNP [dm3] 2R_18395922_SNP [dm6]	T	G	2.147e^-5	0.419	DOWNSTREAM Idgf5 & 1 other INTERGENIC
2L	2287292	2L_2287292_SNP [dm3] 2L_2287292_SNP [dm6]	G	C	2.171e^-5	0.419	UTR_3_PRIME CG42658 UPSTREAM CG31681
2L	16389803	2L_16389803_SNP [dm3] 2L_16389803_SNP [dm6]	G	A	2.180e^-5	0.419	INTERGENIC
2L	1180652	2L_1180652_SNP [dm3] 2L_1180652_SNP [dm6]	G	T	2.188e^-5	0.419	SYNONYMOUS_CODING CG4896 UTR_3_PRIME CG4896
3L	18099093	3L_18099093_SNP [dm3] 3L_18105993_SNP [dm6]	A	T	2.203e^-5	0.419	UTR_5_PRIME CG13698 UPSTREAM mRpS26	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_eve mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3R	11310575	3R_11310575_SNP [dm3] 3R_15484853_SNP [dm6]	A	C	2.211e^-5	0.419	UTR_3_PRIME Trissin DOWNSTREAM Trissin & 1 other
2R	19415959	2R_19415959_SNP [dm3] 2R_23528436_SNP [dm6]	G	A	2.300e^-5	0.429	NON_SYNONYMOUS_CODING bw DOWNSTREAM mi

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Missing results

By genomic position
Variant impact
Gene name

Cuticul_5_9_C25_1_2 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results