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=3.320e^-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_3R_K	0.0004989

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	5.289	0.071
In_3R_K	16.5889	0.0002

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2096 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
3R	11885217	3R_11885217_SNP [dm3] 3R_16059495_SNP [dm6]	C	T	7.598e^-7	0.581	SYNONYMOUS_CODING msps
3L	5706169	3L_5706169_SNP [dm3] 3L_5713069_SNP [dm6]	C	A	1.028e^-6	0.581	UPSTREAM CG44521 INTRON sif
2L	12592688	2L_12592688_SNP [dm3] 2L_12592688_SNP [dm6]	C	G	1.252e^-6	0.581	INTRON nub
3L	1590943	3L_1590943_SNP [dm3] 3L_1590943_SNP [dm6]	T	C	2.410e^-6	0.581	INTRON CG13917
2L	11197137	2L_11197137_SNP [dm3] 2L_11197137_SNP [dm6]	T	C	2.413e^-6	0.581	INTRON Ca-beta
3R	7139117	3R_7139117_SNP [dm3] 3R_11313395_SNP [dm6]	T	C	2.528e^-6	0.581	INTERGENIC
X	6137389	X_6137389_SNP [dm3] X_6243356_SNP [dm6]	G	A	2.604e^-6	0.581	SYNONYMOUS_CODING Rbcn-3A	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	8138043	3R_8138043_SNP [dm3] 3R_12312321_SNP [dm6]	C	T	3.602e^-6	0.581	SYNONYMOUS_CODING CG4066	TF binding site mE1_TFBS_sens
3R	7026916	3R_7026916_SNP [dm3] 3R_11201194_SNP [dm6]	G	C	3.720e^-6	0.581	INTRON cu
3L	7568737	3L_7568737_SNP [dm3] 3L_7575637_SNP [dm6]	A	G	3.903e^-6	0.581	INTERGENIC
X	6137319	X_6137319_SNP [dm3] X_6243286_SNP [dm6]	T	G	3.934e^-6	0.581	SYNONYMOUS_CODING Rbcn-3A	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
X	6136089	X_6136089_SNP [dm3] X_6242056_SNP [dm6]	G	A	4.087e^-6	0.581	INTRON Rbcn-3A	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv
2L	12592690	2L_12592690_SNP [dm3] 2L_12592690_SNP [dm6]	A	G	4.809e^-6	0.581	INTRON nub
3R	7126770	3R_7126770_SNP [dm3] 3R_11301048_SNP [dm6]	T	C	4.834e^-6	0.581	INTRON CR31386	TF binding site mE1_TFBS_chinmo
3R	25398623	3R_25398623_SNP [dm3] 3R_29572901_SNP [dm6]	G	A	5.418e^-6	0.581	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3R	8340375	3R_8340375_SNP [dm3] 3R_12514653_SNP [dm6]	T	A	5.428e^-6	0.581	INTRON Octbeta3R
3R	9678205	3R_9678205_SNP [dm3] 3R_13852483_SNP [dm6]	A	T	5.480e^-6	0.581	INTERGENIC
X	6137320	X_6137320_SNP [dm3] X_6243287_SNP [dm6]	T	G	5.789e^-6	0.581	SYNONYMOUS_CODING Rbcn-3A	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	11819272	2L_11819272_SNP [dm3] 2L_11819272_SNP [dm6]	A	T	6.514e^-6	0.581	INTRON Pde1c
2L	11819269	2L_11819269_SNP [dm3] 2L_11819269_SNP [dm6]	T	C	6.518e^-6	0.581	INTRON Pde1c
3R	10119687	3R_10119687_DEL [dm3] 3R_14293965_DEL [dm6]	TTT	T	6.988e^-6	0.581	INTRON CG12207
2L	11819255	2L_11819255_SNP [dm3] 2L_11819255_SNP [dm6]	A	G	7.018e^-6	0.581	INTRON Pde1c
3R	7138391	3R_7138391_SNP [dm3] 3R_11312669_SNP [dm6]	A	G	7.120e^-6	0.581	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
2L	14426096	2L_14426096_SNP [dm3] 2L_14426096_SNP [dm6]	G	A	7.495e^-6	0.586	UPSTREAM Cpr35B INTERGENIC
3R	24698056	3R_24698056_SNP [dm3] 3R_28872334_SNP [dm6]	G	A	7.998e^-6	0.6	UPSTREAM CG14529 INTRON CG33203	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	11885437	3R_11885437_SNP [dm3] 3R_16059715_SNP [dm6]	C	T	8.401e^-6	0.606	DOWNSTREAM CG10185 INTRON msps
X	5716933	X_5716933_SNP [dm3] X_5822900_SNP [dm6]	G	A	1.058e^-5	0.704	INTRON CG15765
2L	7210991	2L_7210991_SNP [dm3] 2L_7210991_SNP [dm6]	T	A	1.060e^-5	0.704	INTRON CG13784
3R	8346633	3R_8346633_SNP [dm3] 3R_12520911_SNP [dm6]	G	A	1.088e^-5	0.704	INTRON Octbeta3R
3R	11587690	3R_11587690_SNP [dm3] 3R_15761968_SNP [dm6]	T	C	1.133e^-5	0.708	INTERGENIC
X	6137091	X_6137091_SNP [dm3] X_6243058_SNP [dm6]	G	A	1.214e^-5	0.71	SYNONYMOUS_CODING Rbcn-3A	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	12592685	2L_12592685_SNP [dm3] 2L_12592685_SNP [dm6]	T	A	1.226e^-5	0.71	INTRON nub
2L	20934671	2L_20934671_SNP [dm3] 2L_20934671_SNP [dm6]	G	A	1.262e^-5	0.71	UPSTREAM CG9270 INTERGENIC
2R	15120398	2R_15120398_SNP [dm3] 2R_19232893_SNP [dm6]	A	T	1.286e^-5	0.71	INTRON cora	TF binding site mE1_TFBS_HSA
3L	8863761	3L_8863761_DEL [dm3] 3L_8870661_DEL [dm6]	CATTATTAT	C	1.433e^-5	0.747	INTRON dally
3L	17583389	3L_17583389_SNP [dm3] 3L_17590289_SNP [dm6]	C	A	1.436e^-5	0.747	INTRON Eip74EF	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3L	5610219	3L_5610219_SNP [dm3] 3L_5617119_SNP [dm6]	T	C	1.473e^-5	0.747	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	18837007	3L_18837007_SNP [dm3] 3L_18843907_SNP [dm6]	A	T	1.532e^-5	0.756	INTRON Indy
3L	1590923	3L_1590923_SNP [dm3] 3L_1590923_SNP [dm6]	C	G	1.647e^-5	0.783	INTRON CG13917
3R	13639450	3R_13639450_SNP [dm3] 3R_17813728_SNP [dm6]	A	G	1.670e^-5	0.783	INTRON tinc	TF binding site mE1_TFBS_HSA
2L	11819266	2L_11819266_SNP [dm3] 2L_11819266_SNP [dm6]	T	G	1.797e^-5	0.81	INTRON Pde1c
3L	18837004	3L_18837004_SNP [dm3] 3L_18843904_SNP [dm6]	G	C	1.845e^-5	0.81	INTRON Indy
3R	25395959	3R_25395959_SNP [dm3] 3R_29570237_SNP [dm6]	T	A	1.908e^-5	0.81	INTERGENIC	TF binding site mE1_TFBS_chinmo
3L	9985612	3L_9985612_SNP [dm3] 3L_9992512_SNP [dm6]	G	C	1.937e^-5	0.81	INTRON dpr6
3L	1590897	3L_1590897_SNP [dm3] 3L_1590897_SNP [dm6]	T	C	1.944e^-5	0.81	INTRON CG13917
3L	5561727	3L_5561727_SNP [dm3] 3L_5568627_SNP [dm6]	C	T	1.994e^-5	0.812	SYNONYMOUS_CODING Msr-110 UPSTREAM snmRNA:357	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	7696878	2L_7696878_SNP [dm3] 2L_7696878_SNP [dm6]	T	A	2.034e^-5	0.812	INTRON Tep2
X	13069335	X_13069335_SNP [dm3] X_13175302_SNP [dm6]	C	T	2.195e^-5	0.817	INTRON CG34411	TF binding site BDTNP1_TFBS_twi
3R	13747042	3R_13747042_SNP [dm3] 3R_17921320_SNP [dm6]	C	A	2.218e^-5	0.817	UTR_5_PRIME cpo
3L	17123463	3L_17123463_SNP [dm3] 3L_17130363_SNP [dm6]	G	C	2.307e^-5	0.817	INTRON Rbp6
2R	20195111	2R_20195111_SNP [dm3] 2R_24307588_SNP [dm6]	G	A	2.354e^-5	0.817	INTRON betaTub60D	regulatory region REDfly_CRMs
2R	19238645	2R_19238645_SNP [dm3] 2R_23351122_SNP [dm6]	C	G	2.362e^-5	0.817	UPSTREAM CG34210 INTERGENIC
2L	8131413	2L_8131413_SNP [dm3] 2L_8131413_SNP [dm6]	T	A	2.412e^-5	0.817	UTR_5_PRIME CG8668	TF binding site BDTNP1_TFBS_da
3R	8288562	3R_8288562_SNP [dm3] 3R_12462840_SNP [dm6]	C	T	2.436e^-5	0.817	DOWNSTREAM CG12267 INTRON CG5608	TF binding site mE1_TFBS_inv
3L	8211275	3L_8211275_SNP [dm3] 3L_8218175_SNP [dm6]	A	T	2.439e^-5	0.817	DOWNSTREAM CG13674 INTERGENIC
2L	11417675	2L_11417675_SNP [dm3] 2L_11417675_SNP [dm6]	T	G	2.466e^-5	0.817	INTERGENIC	TF binding site mE1_TFBS_cad
X	16803257	X_16803257_SNP [dm3] X_16909224_SNP [dm6]	G	T	2.484e^-5	0.817	INTRON CR44754
2L	20934672	2L_20934672_SNP [dm3] 2L_20934672_SNP [dm6]	A	T	2.644e^-5	0.848	UPSTREAM CG9270 INTERGENIC
3R	6461164	3R_6461164_SNP [dm3] 3R_10635442_SNP [dm6]	A	C	2.668e^-5	0.848	INTRON hth
3L	1590899	3L_1590899_SNP [dm3] 3L_1590899_SNP [dm6]	T	A	2.837e^-5	0.867	INTRON CG13917
2R	12909983	2R_12909983_SNP [dm3] 2R_17022478_SNP [dm6]	G	T	2.844e^-5	0.867	SYNONYMOUS_CODING Ark	TF binding site mE1_TFBS_sens
3L	15774763	3L_15774763_SNP [dm3] 3L_15781663_SNP [dm6]	T	C	2.866e^-5	0.867	INTERGENIC
3R	25394283	3R_25394283_SNP [dm3] 3R_29568561_SNP [dm6]	A	G	2.941e^-5	0.869	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	18257588	2R_18257588_INS [dm3] 2R_22370083_INS [dm6]	C	CCTC	2.994e^-5	0.869	INTRON Liprin-gamma
2L	11922449	2L_11922449_SNP [dm3] 2L_11922449_SNP [dm6]	T	A	3.106e^-5	0.869	INTRON Pde1c
3R	7138798	3R_7138798_SNP [dm3] 3R_11313076_SNP [dm6]	G	A	3.184e^-5	0.869	INTERGENIC	TF binding site BDTNP1_TFBS_dl
2L	11823067	2L_11823067_SNP [dm3] 2L_11823067_SNP [dm6]	G	T	3.221e^-5	0.869	INTRON Pde1c
2L	9663622	2L_9663622_SNP [dm3] 2L_9663622_SNP [dm6]	G	A	3.230e^-5	0.869	INTERGENIC
3R	7138756	3R_7138756_SNP [dm3] 3R_11313034_SNP [dm6]	T	C	3.243e^-5	0.869	INTERGENIC	TF binding site BDTNP1_TFBS_dl
2L	12592679	2L_12592679_SNP [dm3] 2L_12592679_SNP [dm6]	C	T	3.305e^-5	0.869	INTRON nub
3L	17145867	3L_17145867_SNP [dm3] 3L_17152767_SNP [dm6]	T	A	3.308e^-5	0.869	INTRON Rbp6
2L	19439641	2L_19439641_SNP [dm3] 2L_19439641_SNP [dm6]	G	T	3.335e^-5	0.869	UPSTREAM CG10237 INTRON CG10237	TF binding site mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2L	11197259	2L_11197259_SNP [dm3] 2L_11197259_SNP [dm6]	C	T	3.428e^-5	0.869	INTRON Ca-beta
X	17647393	X_17647393_INS [dm3] X_17753360_INS [dm6]	A	TTAACT	3.533e^-5	0.869	INTERGENIC
3L	9425183	3L_9425183_SNP [dm3] 3L_9432083_SNP [dm6]	A	G	3.560e^-5	0.869	INTRON MTF-1	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
2L	10869580	2L_10869580_SNP [dm3] 2L_10869580_SNP [dm6]	T	C	3.661e^-5	0.869	UPSTREAM CG12517 INTERGENIC
3R	24697851	3R_24697851_SNP [dm3] 3R_28872129_SNP [dm6]	T	C	3.691e^-5	0.869	UPSTREAM CG14529 INTRON CG33203	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	25394303	3R_25394303_DEL [dm3] 3R_29568581_DEL [dm6]	GGAAA	T	3.702e^-5	0.869	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	12553396	2L_12553396_SNP [dm3] 2L_12553396_SNP [dm6]	G	A	3.748e^-5	0.869	INTERGENIC
3L	15774762	3L_15774762_SNP [dm3] 3L_15781662_SNP [dm6]	G	T	3.791e^-5	0.869	INTERGENIC
2L	16045056	2L_16045056_SNP [dm3] 2L_16045056_SNP [dm6]	C	A	3.793e^-5	0.869	INTRON BicC & 1 other
2L	8131488	2L_8131488_SNP [dm3] 2L_8131488_SNP [dm6]	G	T	3.814e^-5	0.869	SYNONYMOUS_CODING CG8668	TF binding site BDTNP1_TFBS_da
2L	11417684	2L_11417684_SNP [dm3] 2L_11417684_SNP [dm6]	C	T	3.889e^-5	0.869	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
3L	1593572	3L_1593572_SNP [dm3] 3L_1593572_SNP [dm6]	G	A	3.979e^-5	0.869	UTR_5_PRIME CG13917	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_z mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3L	1595568	3L_1595568_SNP [dm3] 3L_1595568_SNP [dm6]	A	G	3.993e^-5	0.869	SYNONYMOUS_CODING CG13917	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	2799791	3R_2799791_SNP [dm3] 3R_6974069_SNP [dm6]	T	C	4.234e^-5	0.869	INTRON Antp	TF binding site mE1_TFBS_bab1
2L	11922428	2L_11922428_SNP [dm3] 2L_11922428_SNP [dm6]	G	A	4.264e^-5	0.869	INTRON Pde1c
2R	19249905	2R_19249905_SNP [dm3] 2R_23362382_SNP [dm6]	C	T	4.264e^-5	0.869	SYNONYMOUS_CODING vir	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	7130115	3R_7130115_SNP [dm3] 3R_11304393_SNP [dm6]	C	T	4.278e^-5	0.869	INTRON CR31386	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
2R	16972415	2R_16972415_SNP [dm3] 2R_21084910_SNP [dm6]	T	G	4.292e^-5	0.869	INTRON Treh	TF binding site mE1_TFBS_cad
2L	20934675	2L_20934675_SNP [dm3] 2L_20934675_SNP [dm6]	C	G	4.369e^-5	0.869	UPSTREAM CG9270 INTERGENIC
3R	8888316	3R_8888316_SNP [dm3] 3R_13062594_SNP [dm6]	A	G	4.383e^-5	0.869	UTR_5_PRIME sim INTRON sim
3L	9316342	3L_9316342_SNP [dm3] 3L_9323242_SNP [dm6]	T	C	4.399e^-5	0.869	INTERGENIC
2L	14865403	2L_14865403_SNP [dm3] 2L_14865403_SNP [dm6]	C	A	4.436e^-5	0.869	INTERGENIC
X	8814616	X_8814616_SNP [dm3] X_8920583_SNP [dm6]	T	C	4.505e^-5	0.869	UPSTREAM CR44111 INTRON rdgA
2L	11348104	2L_11348104_SNP [dm3] 2L_11348104_SNP [dm6]	T	C	4.515e^-5	0.869	INTERGENIC
2L	10869670	2L_10869670_SNP [dm3] 2L_10869670_SNP [dm6]	T	C	4.528e^-5	0.869	UPSTREAM CG12517 INTERGENIC	TF binding site mE1_TFBS_inv
3L	18269289	3L_18269289_SNP [dm3] 3L_18276189_SNP [dm6]	T	G	4.744e^-5	0.869	INTERGENIC
2L	15854133	2L_15854133_SNP [dm3] 2L_15854133_SNP [dm6]	A	G	4.774e^-5	0.869	START_GAINED Tektin-A UTR_5_PRIME Tektin-A UPSTREAM Tektin-A DOWNSTREAM CG13243
3L	7307650	3L_7307650_SNP [dm3] 3L_7314550_SNP [dm6]	A	T	4.784e^-5	0.869	INTERGENIC

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Missing results

By genomic position
Variant impact
Gene name

Cuticul_7_11_C26_2 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results