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=8.658e^-2)
Null hypothesis is not rejected (p>0.05).
Interpretation: 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	0.01361
In_3R_Mo	0.05263

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	7.7819	0.0204
In_3R_Mo	4.8408	0.0889

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1974 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
3L	10756244	3L_10756244_SNP [dm3] 3L_10763144_SNP [dm6]	A	G	8.231e^-7	0.867	INTERGENIC
3R	20489343	3R_20489343_SNP [dm3] 3R_24663621_SNP [dm6]	G	A	1.208e^-6	0.867	INTRON slo	regulatory region REDfly_CRMs
3L	413912	3L_413912_SNP [dm3] 3L_413912_SNP [dm6]	C	T	2.157e^-6	0.867	INTERGENIC	TF binding site mE1_TFBS_Kr
3L	413923	3L_413923_SNP [dm3] 3L_413923_SNP [dm6]	A	G	2.787e^-6	0.867	INTERGENIC	TF binding site mE1_TFBS_Kr
2R	9134428	2R_9134428_SNP [dm3] 2R_13246923_SNP [dm6]	A	G	4.498e^-6	0.867	NON_SYNONYMOUS_CODING Mp20	TF binding site mE1_TFBS_cad
3L	5461675	3L_5461675_SNP [dm3] 3L_5468575_SNP [dm6]	G	C	5.174e^-6	0.867	INTERGENIC
X	3172280	X_3172280_SNP [dm3] X_3278247_SNP [dm6]	T	G	5.755e^-6	0.867	INTRON dnc
3R	20300904	3R_20300904_SNP [dm3] 3R_24475182_SNP [dm6]	T	G	8.622e^-6	0.867	INTERGENIC
X	5289897	X_5289897_SNP [dm3] X_5395864_SNP [dm6]	A	T	8.755e^-6	0.867	INTRON SK
3L	20888236	3L_20888236_SNP [dm3] 3L_20895136_SNP [dm6]	A	G	9.476e^-6	0.867	INTERGENIC
2L	9463855	2L_9463855_SNP [dm3] 2L_9463855_SNP [dm6]	C	T	1.014e^-5	0.867	UTR_3_PRIME numb DOWNSTREAM numb	TF binding site mE1_TFBS_kn
2L	718007	2L_718007_INS [dm3] 2L_718007_INS [dm6]	T	TT	1.123e^-5	0.867	INTERGENIC
2L	13325482	2L_13325482_SNP [dm3] 2L_13325482_SNP [dm6]	C	A	1.132e^-5	0.867	INTRON CG43778
X	14167285	X_14167285_SNP [dm3] X_14273252_SNP [dm6]	G	A	1.132e^-5	0.867	INTRON na
2L	22310213	2L_22310213_SNP [dm3] 2L_22310213_SNP [dm6]	A	T	1.183e^-5	0.867	INTRON CG17018	transposable element FlyBase
3L	14817116	3L_14817116_SNP [dm3] 3L_14824016_SNP [dm6]	A	T	1.265e^-5	0.867	INTRON CG17839
3R	10122626	3R_10122626_SNP [dm3] 3R_14296904_SNP [dm6]	G	A	1.347e^-5	0.867	INTRON CG12207
3R	10122629	3R_10122629_SNP [dm3] 3R_14296907_SNP [dm6]	T	C	1.347e^-5	0.867	INTRON CG12207
2R	19703974	2R_19703974_SNP [dm3] 2R_23816451_SNP [dm6]	G	T	1.349e^-5	0.867	INTRON CG4797
2L	13605161	2L_13605161_SNP [dm3] 2L_13605161_SNP [dm6]	T	A	1.423e^-5	0.867	INTRON kuz
X	9499586	X_9499586_SNP [dm3] X_9605553_SNP [dm6]	T	C	1.467e^-5	0.867	SYNONYMOUS_CODING Lst8 DOWNSTREAM Aats-lys	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Ubx
3R	10689502	3R_10689502_SNP [dm3] 3R_14863780_SNP [dm6]	A	G	1.703e^-5	0.867	INTRON btsz
3R	7273988	3R_7273988_SNP [dm3] 3R_11448266_SNP [dm6]	C	T	1.727e^-5	0.867	UTR_5_PRIME sals INTRON CG17230 & 1 other
3L	14811233	3L_14811233_SNP [dm3] 3L_14818133_SNP [dm6]	C	T	1.734e^-5	0.867	INTRON CG17839
2L	6851127	2L_6851127_SNP [dm3] 2L_6851127_SNP [dm6]	C	A	1.881e^-5	0.867	INTERGENIC
2L	13399308	2L_13399308_SNP [dm3] 2L_13399308_SNP [dm6]	T	C	1.978e^-5	0.867	NON_SYNONYMOUS_CODING CG7110 UPSTREAM CG10859 EXON CR44600	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_ttk
3R	10122627	3R_10122627_SNP [dm3] 3R_14296905_SNP [dm6]	A	T	1.985e^-5	0.867	INTRON CG12207
X	10719310	X_10719310_DEL [dm3] X_10825277_DEL [dm6]	AA	A	2.027e^-5	0.867	DOWNSTREAM CR45624 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	19156440	2L_19156440_SNP [dm3] 2L_19156440_SNP [dm6]	T	C	2.052e^-5	0.867	INTRON brat	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv
X	9500123	X_9500123_SNP [dm3] X_9606090_SNP [dm6]	C	T	2.072e^-5	0.867	UPSTREAM Lst8 DOWNSTREAM Aats-lys INTERGENIC
3R	21673753	3R_21673753_SNP [dm3] 3R_25848031_SNP [dm6]	T	G	2.133e^-5	0.867	UPSTREAM CR45657 & 1 other DOWNSTREAM CR45655 INTERGENIC
X	5291698	X_5291698_SNP [dm3] X_5397665_SNP [dm6]	T	A	2.153e^-5	0.867	DOWNSTREAM SK INTRON SK
2R	15906348	2R_15906348_SNP [dm3] 2R_20018843_SNP [dm6]	G	A	2.224e^-5	0.867	INTERGENIC
3R	23587733	3R_23587733_SNP [dm3] 3R_27762011_SNP [dm6]	A	G	2.508e^-5	0.867	INTERGENIC	TF binding site mE1_TFBS_chinmo
X	21946768	X_21946768_SNP [dm3] X_22544932_SNP [dm6]	T	C	2.522e^-5	0.867	UPSTREAM CG17599 INTERGENIC
2R	11575928	2R_11575928_SNP [dm3] 2R_15688423_SNP [dm6]	T	C	2.613e^-5	0.867	SYNONYMOUS_CODING Cep89	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	1604286	3L_1604286_SNP [dm3] 3L_1604286_SNP [dm6]	A	T	2.625e^-5	0.867	NON_SYNONYMOUS_CODING CG18170 UTR_5_PRIME CG33791 UPSTREAM CG33791
3L	5461676	3L_5461676_SNP [dm3] 3L_5468576_SNP [dm6]	A	C	2.762e^-5	0.867	INTERGENIC
X	9499442	X_9499442_SNP [dm3] X_9605409_SNP [dm6]	C	T	2.815e^-5	0.867	SYNONYMOUS_CODING Lst8 DOWNSTREAM Aats-lys	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Ubx
3R	14288446	3R_14288446_SNP [dm3] 3R_18462724_SNP [dm6]	C	T	2.931e^-5	0.867	INTRON fru
3L	18267088	3L_18267088_INS [dm3] 3L_18273988_INS [dm6]	T	TT	2.943e^-5	0.867	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_Kr
2R	19522673	2R_19522673_SNP [dm3] 2R_23635150_SNP [dm6]	G	T	2.990e^-5	0.867	INTRON retn	TF binding site mE1_TFBS_cad mE1_TFBS_sens
3L	14813948	3L_14813948_SNP [dm3] 3L_14820848_SNP [dm6]	G	A	3.031e^-5	0.867	INTRON CG17839
2R	14796431	2R_14796431_SNP [dm3] 2R_18908926_SNP [dm6]	A	C	3.160e^-5	0.867	DOWNSTREAM Vha100-3 INTRON sano
3R	5895134	3R_5895134_SNP [dm3] 3R_10069412_SNP [dm6]	C	A	3.175e^-5	0.867	DOWNSTREAM CG33784 INTERGENIC
3L	14815037	3L_14815037_SNP [dm3] 3L_14821937_SNP [dm6]	A	C	3.177e^-5	0.867	INTRON CG17839
3L	4857046	3L_4857046_SNP [dm3] 3L_4857046_SNP [dm6]	G	A	3.281e^-5	0.867	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	702597	2L_702597_INS [dm3] 2L_702597_INS [dm6]	C	CACCTAAGCACAAATATGC...	3.290e^-5	0.867	INTRON ds	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
3L	14817336	3L_14817336_SNP [dm3] 3L_14824236_SNP [dm6]	G	A	3.338e^-5	0.867	INTRON CG17839
2L	10940636	2L_10940636_SNP [dm3] 2L_10940636_SNP [dm6]	C	G	3.382e^-5	0.867	INTRON dpr2
X	5290172	X_5290172_SNP [dm3] X_5396139_SNP [dm6]	G	A	3.411e^-5	0.867	INTRON SK
3L	20875371	3L_20875371_SNP [dm3] 3L_20882271_SNP [dm6]	C	A	3.451e^-5	0.867	INTRON CG32432
2R	18259203	2R_18259203_SNP [dm3] 2R_22371698_SNP [dm6]	A	C	3.457e^-5	0.867	INTRON Liprin-gamma
2L	702629	2L_702629_SNP [dm3] 2L_702629_SNP [dm6]	C	A	3.559e^-5	0.867	INTRON ds	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
X	13204342	X_13204342_SNP [dm3] X_13310309_SNP [dm6]	C	G	3.619e^-5	0.867	INTRON IP3K2
X	14170491	X_14170491_SNP [dm3] X_14276458_SNP [dm6]	A	C	3.648e^-5	0.867	NON_SYNONYMOUS_CODING na	TF binding site mE1_TFBS_cad
3R	7278969	3R_7278969_SNP [dm3] 3R_11453247_SNP [dm6]	A	G	3.657e^-5	0.867	SYNONYMOUS_CODING PGRP-LB INTRON CG17230	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3L	712423	3L_712423_SNP [dm3] 3L_712423_SNP [dm6]	G	C	3.668e^-5	0.867	UPSTREAM CG13896 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_zfh1
3R	7278942	3R_7278942_SNP [dm3] 3R_11453220_SNP [dm6]	A	G	3.723e^-5	0.867	SYNONYMOUS_CODING PGRP-LB INTRON CG17230	TF binding site mE1_TFBS_chinmo
3L	9990656	3L_9990656_SNP [dm3] 3L_9997556_SNP [dm6]	A	G	3.753e^-5	0.867	INTRON dpr6
3L	14817946	3L_14817946_SNP [dm3] 3L_14824846_SNP [dm6]	A	G	3.787e^-5	0.867	INTRON CG17839
3R	22435414	3R_22435414_SNP [dm3] 3R_26609692_SNP [dm6]	G	T	3.881e^-5	0.867	INTERGENIC	TF binding site mE1_TFBS_chinmo
3R	25576930	3R_25576930_SNP [dm3] 3R_29751208_SNP [dm6]	T	C	3.898e^-5	0.867	SYNONYMOUS_CODING yata	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2R	15897808	2R_15897808_SNP [dm3] 2R_20010303_SNP [dm6]	G	C	3.931e^-5	0.867	INTERGENIC
2R	16543557	2R_16543557_SNP [dm3] 2R_20656052_SNP [dm6]	G	A	3.942e^-5	0.867	UPSTREAM CG16799 INTRON Lrt & 1 other
3R	10122680	3R_10122680_SNP [dm3] 3R_14296958_SNP [dm6]	T	A	3.975e^-5	0.867	INTRON CG12207
2R	9689880	2R_9689880_SNP [dm3] 2R_13802375_SNP [dm6]	C	A	4.082e^-5	0.867	INTRON Cpr50Cb
3L	413373	3L_413373_SNP [dm3] 3L_413373_SNP [dm6]	G	A	4.150e^-5	0.867	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_Kr
2R	9689881	2R_9689881_SNP [dm3] 2R_13802376_SNP [dm6]	T	A	4.186e^-5	0.867	INTRON Cpr50Cb
3L	14389469	3L_14389469_SNP [dm3] 3L_14396369_SNP [dm6]	C	G	4.194e^-5	0.867	INTERGENIC
2L	6520956	2L_6520956_SNP [dm3] 2L_6520956_SNP [dm6]	T	C	4.228e^-5	0.867	INTRON CG31637
2L	9577163	2L_9577163_DEL [dm3] 2L_9577163_DEL [dm6]	ACAA	G	4.234e^-5	0.867	UPSTREAM Mtpalpha DOWNSTREAM CG31709 INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_zfh1
2L	10940439	2L_10940439_SNP [dm3] 2L_10940439_SNP [dm6]	G	A	4.297e^-5	0.867	INTRON dpr2
3L	712399	3L_712399_SNP [dm3] 3L_712399_SNP [dm6]	A	T	4.318e^-5	0.867	UPSTREAM CG13896 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_zfh1
X	16685557	X_16685557_SNP [dm3] X_16791524_SNP [dm6]	T	A	4.357e^-5	0.867	UPSTREAM CG4768 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl
2L	9576858	2L_9576858_SNP [dm3] 2L_9576858_SNP [dm6]	T	G	4.367e^-5	0.867	UPSTREAM Mtpalpha INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_prd mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_zfh1
3L	837662	3L_837662_SNP [dm3] 3L_837662_SNP [dm6]	A	C	4.402e^-5	0.867	UPSTREAM CG13887 & 1 other DOWNSTREAM CG42554 INTRON CG13901	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 mE1_TFBS_cnc mE1_TFBS_D mE1_TFBS_HSA
2L	6520957	2L_6520957_DEL [dm3] 2L_6520957_DEL [dm6]	TT	T	4.435e^-5	0.867	INTRON CG31637
3L	14834277	3L_14834277_SNP [dm3] 3L_14841177_SNP [dm6]	T	A	4.438e^-5	0.867	INTRON CG17839
2L	702432	2L_702432_SNP [dm3] 2L_702432_SNP [dm6]	C	A	4.438e^-5	0.867	INTRON ds	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_shn BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_Trl
X	6736540	X_6736540_SNP [dm3] X_6842507_SNP [dm6]	C	T	4.449e^-5	0.867	INTRON CG14435	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	6851126	2L_6851126_SNP [dm3] 2L_6851126_SNP [dm6]	G	T	4.473e^-5	0.867	INTERGENIC
2R	16543558	2R_16543558_SNP [dm3] 2R_20656053_SNP [dm6]	T	C	4.576e^-5	0.867	UPSTREAM CG16799 INTRON Lrt & 1 other
2R	16794266	2R_16794266_SNP [dm3] 2R_20906761_SNP [dm6]	C	G	4.578e^-5	0.867	INTERGENIC	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_disco mE1_TFBS_zfh1
2R	16794363	2R_16794363_SNP [dm3] 2R_20906858_SNP [dm6]	T	A	4.578e^-5	0.867	INTERGENIC	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_disco mE1_TFBS_zfh1
2R	16794370	2R_16794370_SNP [dm3] 2R_20906865_SNP [dm6]	C	T	4.578e^-5	0.867	INTERGENIC	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_disco mE1_TFBS_zfh1
2R	16794579	2R_16794579_SNP [dm3] 2R_20907074_SNP [dm6]	T	A	4.578e^-5	0.867	INTERGENIC	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_kni BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_Trl mE1_TFBS_zfh1
2R	15839140	2R_15839140_SNP [dm3] 2R_19951635_SNP [dm6]	C	T	4.602e^-5	0.867	SYNONYMOUS_CODING CG10822
X	5594395	X_5594395_SNP [dm3] X_5700362_SNP [dm6]	G	T	4.668e^-5	0.867	INTRON CG4096
3L	837739	3L_837739_INS [dm3] 3L_837739_INS [dm6]	T	TA	4.672e^-5	0.867	UPSTREAM CG13887 & 1 other DOWNSTREAM CG42554 INTRON CG13901	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 mE1_TFBS_cnc mE1_TFBS_D mE1_TFBS_HSA
2R	16794328	2R_16794328_SNP [dm3] 2R_20906823_SNP [dm6]	G	A	4.692e^-5	0.867	INTERGENIC	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_disco mE1_TFBS_zfh1
2R	16794339	2R_16794339_SNP [dm3] 2R_20906834_SNP [dm6]	T	A	4.692e^-5	0.867	INTERGENIC	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_disco mE1_TFBS_zfh1
3R	5895763	3R_5895763_SNP [dm3] 3R_10070041_SNP [dm6]	C	A	4.743e^-5	0.867	INTERGENIC
2L	19143020	2L_19143020_SNP [dm3] 2L_19143020_SNP [dm6]	G	T	4.846e^-5	0.867	INTRON brat	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	20901821	3L_20901821_SNP [dm3] 3L_20908721_SNP [dm6]	T	C	4.888e^-5	0.867	INTERGENIC
2R	20161899	2R_20161899_SNP [dm3] 2R_24274376_SNP [dm6]	G	A	4.927e^-5	0.867	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo
2L	6520952	2L_6520952_SNP [dm3] 2L_6520952_SNP [dm6]	A	G	4.947e^-5	0.867	INTRON CG31637
3L	12571201	3L_12571201_DEL [dm3] 3L_12578101_DEL [dm6]	AGAAATATTAGGAATAGGCT...	A	5.011e^-5	0.867	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	15838613	2R_15838613_SNP [dm3] 2R_19951108_SNP [dm6]	G	A	5.033e^-5	0.867	UPSTREAM CG10822 INTERGENIC
X	15425490	X_15425490_SNP [dm3] X_15531457_SNP [dm6]	T	A	5.049e^-5	0.867	INTRON Ac13E	TF binding site BDTNP1_TFBS_twi

Showing 1 to 100 of 1,000 entries

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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=5.801e^-1)
Null hypothesis is not rejected (p>0.05).
Interpretation: 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	0.04159
In_3R_Mo	0.08845

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	6.6285	0.0364
In_3R_Mo	5.0085	0.0817

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1699 significant hits at p-value < 0.001. The 1000 top results are displayed in the table below.

Variant impact HIGH MODERATE LOW MODIFIER

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Chromosome	Position	ID	Reference	Variant	p-value	FDR_BH	Transcript annotation	Binding site annotation
2R	9134428	2R_9134428_SNP [dm3] 2R_13246923_SNP [dm6]	A	G	1.073e^-6	0.839	NON_SYNONYMOUS_CODING Mp20	TF binding site mE1_TFBS_cad
2L	13399308	2L_13399308_SNP [dm3] 2L_13399308_SNP [dm6]	T	C	1.482e^-6	0.839	NON_SYNONYMOUS_CODING CG7110 UPSTREAM CG10859 EXON CR44600	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_ttk
3L	10756244	3L_10756244_SNP [dm3] 3L_10763144_SNP [dm6]	A	G	3.174e^-6	0.839	INTERGENIC
X	3172280	X_3172280_SNP [dm3] X_3278247_SNP [dm6]	T	G	3.436e^-6	0.839	INTRON dnc
2R	15841021	2R_15841021_SNP [dm3] 2R_19953516_SNP [dm6]	C	T	5.250e^-6	0.839	UPSTREAM CG44622 INTERGENIC
2R	17920188	2R_17920188_DEL [dm3] 2R_22032683_DEL [dm6]	GGGCTGG	G	5.355e^-6	0.839	INTRON CG34370
2R	15838900	2R_15838900_SNP [dm3] 2R_19951395_SNP [dm6]	C	T	5.377e^-6	0.839	UTR_5_PRIME CG10822
2L	5548115	2L_5548115_SNP [dm3] 2L_5548115_SNP [dm6]	C	T	5.579e^-6	0.839	INTRON Oscillin	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z
2R	16289150	2R_16289150_SNP [dm3] 2R_20401645_SNP [dm6]	G	A	6.178e^-6	0.839	INTERGENIC
2L	5543816	2L_5543816_SNP [dm3] 2L_5543816_SNP [dm6]	C	T	6.217e^-6	0.839	INTRON Lam	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
2L	5544154	2L_5544154_SNP [dm3] 2L_5544154_SNP [dm6]	A	C	6.339e^-6	0.839	SYNONYMOUS_CODING Lam	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3L	7887500	3L_7887500_SNP [dm3] 3L_7894400_SNP [dm6]	C	T	7.160e^-6	0.839	NON_SYNONYMOUS_CODING CG32365 UPSTREAM eIF4E-5	TF binding site mE1_TFBS_cad
2R	15838903	2R_15838903_SNP [dm3] 2R_19951398_SNP [dm6]	A	C	7.436e^-6	0.839	UTR_5_PRIME CG10822
2R	15838896	2R_15838896_SNP [dm3] 2R_19951391_SNP [dm6]	C	T	8.038e^-6	0.839	START_GAINED CG10822 UTR_5_PRIME CG10822
2L	539849	2L_539849_SNP [dm3] 2L_539849_SNP [dm6]	C	T	8.785e^-6	0.839	NON_SYNONYMOUS_CODING ush DOWNSTREAM lwr	TF binding site mE1_TFBS_cad
2R	10925565	2R_10925565_SNP [dm3] 2R_15038060_SNP [dm6]	T	A	9.205e^-6	0.839	SYNONYMOUS_CODING hbs
3L	7887433	3L_7887433_SNP [dm3] 3L_7894333_SNP [dm6]	A	G	9.244e^-6	0.839	NON_SYNONYMOUS_CODING CG32365 UPSTREAM eIF4E-5	TF binding site mE1_TFBS_cad
2R	15841000	2R_15841000_SNP [dm3] 2R_19953495_SNP [dm6]	G	A	9.824e^-6	0.839	UPSTREAM CG44622 INTERGENIC
X	12264143	X_12264143_SNP [dm3] X_12370110_SNP [dm6]	C	A	1.039e^-5	0.839	INTERGENIC
3L	14817116	3L_14817116_SNP [dm3] 3L_14824016_SNP [dm6]	A	T	1.097e^-5	0.839	INTRON CG17839
3L	7887451	3L_7887451_SNP [dm3] 3L_7894351_SNP [dm6]	C	G	1.176e^-5	0.839	NON_SYNONYMOUS_CODING CG32365 UPSTREAM eIF4E-5	TF binding site mE1_TFBS_cad
X	16685557	X_16685557_SNP [dm3] X_16791524_SNP [dm6]	T	A	1.205e^-5	0.839	UPSTREAM CG4768 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl
3L	16983394	3L_16983394_SNP [dm3] 3L_16990294_SNP [dm6]	C	A	1.226e^-5	0.839	INTRON Exn
3L	16983298	3L_16983298_INS [dm3] 3L_16990198_INS [dm6]	A	AG	1.233e^-5	0.839	INTRON Exn
2R	19533244	2R_19533244_SNP [dm3] 2R_23645721_SNP [dm6]	G	A	1.247e^-5	0.839	UPSTREAM retn INTRON retn	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_kni BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_disco mE1_TFBS_eve mE1_TFBS_HSA mE1_TFBS_sens
X	12699254	X_12699254_SNP [dm3] X_12805221_SNP [dm6]	G	T	1.258e^-5	0.839	DOWNSTREAM CG3775 INTRON Pde9
2L	5544938	2L_5544938_SNP [dm3] 2L_5544938_SNP [dm6]	A	T	1.279e^-5	0.839	SYNONYMOUS_CODING Lam	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens
2L	4364449	2L_4364449_SNP [dm3] 2L_4364449_SNP [dm6]	T	A	1.285e^-5	0.839	UPSTREAM CR45363 INTRON Traf4	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3L	14815037	3L_14815037_SNP [dm3] 3L_14821937_SNP [dm6]	A	C	1.387e^-5	0.839	INTRON CG17839
2L	12923423	2L_12923423_SNP [dm3] 2L_12923423_SNP [dm6]	T	G	1.526e^-5	0.839	SYNONYMOUS_CODING ACXA UTR_3_PRIME ACXA
X	14756883	X_14756883_SNP [dm3] X_14862850_SNP [dm6]	C	T	1.590e^-5	0.839	DOWNSTREAM CG9518 INTRON Flo2
2R	11726154	2R_11726154_SNP [dm3] 2R_15838649_SNP [dm6]	G	A	1.754e^-5	0.839	INTRON tun	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA mE1_TFBS_Trl
2R	17920187	2R_17920187_SNP [dm3] 2R_22032682_SNP [dm6]	G	T	1.789e^-5	0.839	INTRON CG34370
2L	588419	2L_588419_SNP [dm3] 2L_588419_SNP [dm6]	T	A	1.794e^-5	0.839	INTRON Gsc	TF binding site BDTNP1_TFBS_dl
2L	5543811	2L_5543811_SNP [dm3] 2L_5543811_SNP [dm6]	T	A	1.820e^-5	0.839	INTRON Lam	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
X	14756893	X_14756893_SNP [dm3] X_14862860_SNP [dm6]	T	A	1.881e^-5	0.839	DOWNSTREAM CG9518 INTRON Flo2
3L	14817946	3L_14817946_SNP [dm3] 3L_14824846_SNP [dm6]	A	G	1.888e^-5	0.839	INTRON CG17839
2L	5550103	2L_5550103_SNP [dm3] 2L_5550103_SNP [dm6]	A	G	1.930e^-5	0.839	SYNONYMOUS_CODING CG14014 DOWNSTREAM Oscillin	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	14811233	3L_14811233_SNP [dm3] 3L_14818133_SNP [dm6]	C	T	1.947e^-5	0.839	INTRON CG17839
3L	14817336	3L_14817336_SNP [dm3] 3L_14824236_SNP [dm6]	G	A	1.957e^-5	0.839	INTRON CG17839
3L	7894419	3L_7894419_SNP [dm3] 3L_7901319_SNP [dm6]	T	C	1.959e^-5	0.839	SYNONYMOUS_CODING pbl INTRON pbl
3R	20489343	3R_20489343_SNP [dm3] 3R_24663621_SNP [dm6]	G	A	1.967e^-5	0.839	INTRON slo	regulatory region REDfly_CRMs
3L	14785088	3L_14785088_SNP [dm3] 3L_14791988_SNP [dm6]	A	G	2.016e^-5	0.839	INTRON CG9425
3L	14827396	3L_14827396_SNP [dm3] 3L_14834296_SNP [dm6]	G	A	2.027e^-5	0.839	INTRON CG17839
3R	19769710	3R_19769710_SNP [dm3] 3R_23943988_SNP [dm6]	G	A	2.167e^-5	0.839	SYNONYMOUS_CODING CG12268 UPSTREAM Gdh	TF binding site mE1_TFBS_cad
X	21063578	X_21063578_SNP [dm3] X_21192551_SNP [dm6]	G	A	2.207e^-5	0.839	UPSTREAM CG14579 INTERGENIC
X	18730960	X_18730960_SNP [dm3] X_18836927_SNP [dm6]	A	T	2.250e^-5	0.839	INTRON Pvf1	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	18663595	3L_18663595_SNP [dm3] 3L_18670495_SNP [dm6]	T	C	2.289e^-5	0.839	SYNONYMOUS_CODING Capr	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens
2R	15838910	2R_15838910_SNP [dm3] 2R_19951405_SNP [dm6]	T	A	2.302e^-5	0.839	UTR_5_PRIME CG10822
2L	5544156	2L_5544156_SNP [dm3] 2L_5544156_SNP [dm6]	A	C	2.311e^-5	0.839	NON_SYNONYMOUS_CODING Lam	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	13238951	2R_13238951_DEL [dm3] 2R_17351446_DEL [dm6]	GCGCGAAAATGAGTCAAAGA...	G	2.358e^-5	0.839	INTRON mbl
3L	12571201	3L_12571201_DEL [dm3] 3L_12578101_DEL [dm6]	AGAAATATTAGGAATAGGCT...	A	2.399e^-5	0.839	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
X	5064424	X_5064424_SNP [dm3] X_5170391_SNP [dm6]	G	A	2.425e^-5	0.839	INTRON rg & 1 other
2R	16253834	2R_16253834_SNP [dm3] 2R_20366329_SNP [dm6]	C	T	2.462e^-5	0.839	INTERGENIC
3L	14827010	3L_14827010_SNP [dm3] 3L_14833910_SNP [dm6]	G	T	2.462e^-5	0.839	INTRON CG17839
2R	16253858	2R_16253858_SNP [dm3] 2R_20366353_SNP [dm6]	A	G	2.541e^-5	0.839	INTERGENIC
2L	4364464	2L_4364464_SNP [dm3] 2L_4364464_SNP [dm6]	C	G	2.550e^-5	0.839	UPSTREAM CR45363 INTRON Traf4	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3L	17603716	3L_17603716_SNP [dm3] 3L_17610616_SNP [dm6]	T	G	2.595e^-5	0.839	INTRON Eip74EF	TF binding site BDTNP1_TFBS_dl
3R	2868311	3R_2868311_INS [dm3] 3R_7042589_INS [dm6]	C	CGGA	2.670e^-5	0.848	INTERGENIC	TF binding site BDTNP1_TFBS_da
X	14154319	X_14154319_SNP [dm3] X_14260286_SNP [dm6]	G	C	2.834e^-5	0.886	UPSTREAM CG1461 INTERGENIC
X	21160844	X_21160844_SNP [dm3] X_21289817_SNP [dm6]	G	C	3.076e^-5	0.945	INTRON CG1494	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
X	13504220	X_13504220_SNP [dm3] X_13610187_SNP [dm6]	T	C	3.347e^-5	0.961	SYNONYMOUS_CODING Ndc80 DOWNSTREAM CG11178	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3L	7874040	3L_7874040_SNP [dm3] 3L_7880940_SNP [dm6]	G	C	3.420e^-5	0.961	INTRON CG32365
X	14840917	X_14840917_SNP [dm3] X_14946884_SNP [dm6]	T	C	3.443e^-5	0.961	INTRON pdgy
2L	5543854	2L_5543854_SNP [dm3] 2L_5543854_SNP [dm6]	G	A	3.458e^-5	0.961	INTRON Lam	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
3L	14376180	3L_14376180_SNP [dm3] 3L_14383080_SNP [dm6]	C	T	3.475e^-5	0.961	UTR_3_PRIME CG43120
X	14182626	X_14182626_SNP [dm3] X_14288593_SNP [dm6]	G	A	3.475e^-5	0.961	DOWNSTREAM Muc12Ea INTRON CG9400
2R	12809255	2R_12809255_SNP [dm3] 2R_16921750_SNP [dm6]	C	T	3.498e^-5	0.961	INTERGENIC
3L	1604286	3L_1604286_SNP [dm3] 3L_1604286_SNP [dm6]	A	T	3.590e^-5	0.961	NON_SYNONYMOUS_CODING CG18170 UTR_5_PRIME CG33791 UPSTREAM CG33791
2L	588413	2L_588413_SNP [dm3] 2L_588413_SNP [dm6]	T	C	3.593e^-5	0.961	INTRON Gsc	TF binding site BDTNP1_TFBS_dl
X	4645841	X_4645841_SNP [dm3] X_4751808_SNP [dm6]	G	A	3.728e^-5	0.961	INTERGENIC
2L	13399279	2L_13399279_SNP [dm3] 2L_13399279_SNP [dm6]	G	C	3.833e^-5	0.961	SYNONYMOUS_CODING CG7110 UPSTREAM CG10859 EXON CR44600	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_ttk
2L	13399303	2L_13399303_SNP [dm3] 2L_13399303_SNP [dm6]	C	A	3.911e^-5	0.961	SYNONYMOUS_CODING CG7110 UPSTREAM CG10859 EXON CR44600	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_ttk
2R	7148303	2R_7148303_SNP [dm3] 2R_11260798_SNP [dm6]	C	G	4.050e^-5	0.961	UPSTREAM Cpr47Ec DOWNSTREAM Cpr47Ed INTERGENIC
2R	15839140	2R_15839140_SNP [dm3] 2R_19951635_SNP [dm6]	C	T	4.081e^-5	0.961	SYNONYMOUS_CODING CG10822
3L	9229668	3L_9229668_SNP [dm3] 3L_9236568_SNP [dm6]	T	C	4.113e^-5	0.961	NON_SYNONYMOUS_CODING CG4483
X	14167285	X_14167285_SNP [dm3] X_14273252_SNP [dm6]	G	A	4.154e^-5	0.961	INTRON na
3R	8477836	3R_8477836_SNP [dm3] 3R_12652114_SNP [dm6]	C	A	4.212e^-5	0.961	NON_SYNONYMOUS_CODING Dtg	TF binding site mE1_TFBS_sens
3L	15700947	3L_15700947_SNP [dm3] 3L_15707847_SNP [dm6]	A	G	4.270e^-5	0.961	INTERGENIC
2R	15838613	2R_15838613_SNP [dm3] 2R_19951108_SNP [dm6]	G	A	4.275e^-5	0.961	UPSTREAM CG10822 INTERGENIC
3L	12571356	3L_12571356_SNP [dm3] 3L_12578256_SNP [dm6]	C	T	4.503e^-5	0.961	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	14828782	3L_14828782_SNP [dm3] 3L_14835682_SNP [dm6]	A	C	4.624e^-5	0.961	INTRON CG17839
2R	7045208	2R_7045208_SNP [dm3] 2R_11157703_SNP [dm6]	C	A	4.666e^-5	0.961	INTRON CG13229
3L	14834278	3L_14834278_SNP [dm3] 3L_14841178_SNP [dm6]	G	T	4.695e^-5	0.961	INTRON CG17839
3R	25760016	3R_25760016_SNP [dm3] 3R_29934294_SNP [dm6]	A	C	4.719e^-5	0.961	NON_SYNONYMOUS_CODING CG42558 UTR_3_PRIME CG42557 DOWNSTREAM eIF2B-alpha	TF binding site mE1_TFBS_cad
2R	15839122	2R_15839122_SNP [dm3] 2R_19951617_SNP [dm6]	G	A	4.766e^-5	0.961	SYNONYMOUS_CODING CG10822
2L	5550121	2L_5550121_SNP [dm3] 2L_5550121_SNP [dm6]	A	G	4.768e^-5	0.961	SYNONYMOUS_CODING CG14014 DOWNSTREAM Oscillin	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	10925619	2R_10925619_SNP [dm3] 2R_15038114_SNP [dm6]	A	G	4.965e^-5	0.961	INTRON hbs
X	5289897	X_5289897_SNP [dm3] X_5395864_SNP [dm6]	A	T	4.988e^-5	0.961	INTRON SK
X	5826894	X_5826894_INS [dm3] X_5932861_INS [dm6]	T	TT	5.118e^-5	0.961	INTRON CG3726
3R	10122680	3R_10122680_SNP [dm3] 3R_14296958_SNP [dm6]	T	A	5.154e^-5	0.961	INTRON CG12207
X	13504292	X_13504292_SNP [dm3] X_13610259_SNP [dm6]	G	C	5.216e^-5	0.961	SYNONYMOUS_CODING Ndc80 DOWNSTREAM CG11178	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3L	11728415	3L_11728415_SNP [dm3] 3L_11735315_SNP [dm6]	C	T	5.288e^-5	0.961	UTR_3_PRIME CG6024 DOWNSTREAM CG6024
3L	7151754	3L_7151754_SNP [dm3] 3L_7158654_SNP [dm6]	G	A	5.301e^-5	0.961	SYNONYMOUS_CODING CG8620 UTR_3_PRIME CG8620 DOWNSTREAM Dscam2
2R	16289158	2R_16289158_DEL [dm3] 2R_20401653_DEL [dm6]	CCG	C	5.444e^-5	0.961	INTERGENIC
3L	14834277	3L_14834277_SNP [dm3] 3L_14841177_SNP [dm6]	T	A	5.484e^-5	0.961	INTRON CG17839
X	13504373	X_13504373_SNP [dm3] X_13610340_SNP [dm6]	C	T	5.552e^-5	0.961	SYNONYMOUS_CODING Ndc80 DOWNSTREAM CG11178	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
X	17441017	X_17441017_SNP [dm3] X_17546984_SNP [dm6]	G	A	5.650e^-5	0.961	INTRON CG43658
3R	19254668	3R_19254668_SNP [dm3] 3R_23428946_SNP [dm6]	G	A	5.676e^-5	0.961	INTRON CG4374	TF binding site BDTNP1_TFBS_prd
2L	6905302	2L_6905302_SNP [dm3] 2L_6905302_SNP [dm6]	C	T	5.695e^-5	0.961	SYNONYMOUS_CODING Nlg2	TF binding site mE1_TFBS_cad mE1_TFBS_HSA

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By genomic position
Variant impact
Gene name

Wing_Intervein_Area6 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results