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=4.288e^-15)
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	0.01261

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	4.8605	0.088
In_2R_NS	5.6771	0.0585

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

15179 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	11095321	2L_11095321_SNP [dm3] 2L_11095321_SNP [dm6]	G	T	0	0	UTR_3_PRIME Ge-1 DOWNSTREAM Ge-1 & 1 other
2L	17814951	2L_17814951_SNP [dm3] 2L_17814951_SNP [dm6]	T	A	0	0	INTRON CadN2
2L	4866008	2L_4866008_SNP [dm3] 2L_4866008_SNP [dm6]	T	C	0	0	NON_SYNONYMOUS_CODING pog
2L	9679476	2L_9679476_SNP [dm3] 2L_9679476_SNP [dm6]	A	G	0	0	INTERGENIC
2R	10135748	2R_10135748_SNP [dm3] 2R_14248243_SNP [dm6]	T	G	0	0	INTRON Mdr50
2R	16967555	2R_16967555_SNP [dm3] 2R_21080050_SNP [dm6]	A	G	0	0	UPSTREAM Treh INTRON Treh
3L	2298633	3L_2298633_SNP [dm3] 3L_2298633_SNP [dm6]	C	T	0	0	SYNONYMOUS_CODING MsR2	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3L	2902788	3L_2902788_SNP [dm3] 3L_2902788_SNP [dm6]	T	C	0	0	INTRON Shab
3L	501818	3L_501818_SNP [dm3] 3L_501818_SNP [dm6]	A	C	0	0	DOWNSTREAM CG34268 INTRON klar
3R	10799702	3R_10799702_SNP [dm3] 3R_14973980_SNP [dm6]	G	C	0	0	INTERGENIC
3R	14870466	3R_14870466_SNP [dm3] 3R_19044744_SNP [dm6]	C	T	0	0	DOWNSTREAM cdi & 1 other INTERGENIC	TF binding site mE1_TFBS_zfh1
3R	14870501	3R_14870501_SNP [dm3] 3R_19044779_SNP [dm6]	T	G	0	0	DOWNSTREAM cdi & 1 other INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_zfh1
3R	9416786	3R_9416786_SNP [dm3] 3R_13591064_SNP [dm6]	T	C	0	0	DOWNSTREAM CG14369 INTERGENIC
3L	2579779	3L_2579779_SNP [dm3] 3L_2579779_SNP [dm6]	A	T	6.170e^-69	7.653e^-64	INTRON msn	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	943561	3L_943561_SNP [dm3] 3L_943561_SNP [dm6]	G	T	6.170e^-69	7.653e^-64	INTRON Glut1
3L	2579911	3L_2579911_SNP [dm3] 3L_2579911_SNP [dm6]	C	T	6.194e^-68	6.170e^-63	INTRON msn	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	15417511	3R_15417511_SNP [dm3] 3R_19591789_SNP [dm6]	G	A	6.886e^-68	6.170e^-63	SYNONYMOUS_CODING Dys
X	8818976	X_8818976_SNP [dm3] X_8924943_SNP [dm6]	C	T	6.895e^-68	6.170e^-63	UPSTREAM rdgA DOWNSTREAM CG43255 INTRON rdgA
3L	2297155	3L_2297155_SNP [dm3] 3L_2297155_SNP [dm6]	A	C	6.935e^-68	6.170e^-63	INTRON MsR2
3L	2298624	3L_2298624_SNP [dm3] 3L_2298624_SNP [dm6]	T	G	6.935e^-68	6.170e^-63	SYNONYMOUS_CODING MsR2	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	20104710	3R_20104710_SNP [dm3] 3R_24278988_SNP [dm6]	A	C	6.964e^-68	6.170e^-63	UPSTREAM CG13611 DOWNSTREAM Orct INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad
3L	2296832	3L_2296832_SNP [dm3] 3L_2296832_SNP [dm6]	A	G	5.990e^-67	5.066e^-62	INTRON MsR2
3R	10297655	3R_10297655_SNP [dm3] 3R_14471933_SNP [dm6]	G	A	6.935e^-67	5.610e^-62	INTRON cv-c
3L	2298537	3L_2298537_SNP [dm3] 3L_2298537_SNP [dm6]	C	T	7.828e^-67	6.068e^-62	SYNONYMOUS_CODING MsR2	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2L	10282695	2L_10282695_SNP [dm3] 2L_10282695_SNP [dm6]	G	A	1.827e^-65	1.360e^-60	SYNONYMOUS_CODING CG5604	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	22911185	3L_22911185_SNP [dm3] 3L_22918085_SNP [dm6]	G	A	1.356e^-24	9.704e^-20	INTRON CG12768	TF binding site BDTNP1_TFBS_twi
3R	10130203	3R_10130203_SNP [dm3] 3R_14304481_SNP [dm6]	T	A	2.553e^-24	1.759e^-19	UTR_3_PRIME su_Hw_ DOWNSTREAM CG3259	TF binding site mE1_TFBS_cad
3L	2293909	3L_2293909_SNP [dm3] 3L_2293909_SNP [dm6]	A	G	6.228e^-23	4.138e^-18	INTRON MsR2
3R	10130223	3R_10130223_SNP [dm3] 3R_14304501_SNP [dm6]	T	A	8.484e^-22	5.443e^-17	UTR_3_PRIME su_Hw_ DOWNSTREAM CG3259	TF binding site mE1_TFBS_cad
2L	13179113	2L_13179113_SNP [dm3] 2L_13179113_SNP [dm6]	T	G	1.702e^-21	1.056e^-16	UPSTREAM CG5287 DOWNSTREAM CG5439 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_Ubx
2L	12130370	2L_12130370_SNP [dm3] 2L_12130370_SNP [dm6]	G	A	8.083e^-21	4.851e^-16	DOWNSTREAM rho-6 & 1 other INTERGENIC
2L	12130385	2L_12130385_SNP [dm3] 2L_12130385_SNP [dm6]	G	A	1.130e^-20	6.571e^-16	DOWNSTREAM rho-6 & 1 other INTERGENIC
2L	12130392	2L_12130392_SNP [dm3] 2L_12130392_SNP [dm6]	T	C	2.581e^-20	1.455e^-15	DOWNSTREAM rho-6 & 1 other INTERGENIC
2R	11957176	2R_11957176_SNP [dm3] 2R_16069671_SNP [dm6]	G	T	2.869e^-19	1.570e^-14	INTERGENIC
3L	2297987	3L_2297987_SNP [dm3] 3L_2297987_SNP [dm6]	T	A	2.775e^-17	1.395e^-12	INTRON MsR2
3L	2298016	3L_2298016_SNP [dm3] 3L_2298016_SNP [dm6]	C	G	2.775e^-17	1.395e^-12	INTRON MsR2	TF binding site mE1_TFBS_HSA
3L	2298023	3L_2298023_DEL [dm3] 3L_2298023_DEL [dm6]	GTTGTTTATTCGGTTTCTTT...	G	2.775e^-17	1.395e^-12	INTRON MsR2	TF binding site mE1_TFBS_HSA
3R	22863547	3R_22863547_INS [dm3] 3R_27037825_INS [dm6]	G	GG	8.970e^-17	4.391e^-12	INTRON RYa-R	TF binding site mE1_TFBS_cad
2L	18884734	2L_18884734_SNP [dm3] 2L_18884734_SNP [dm6]	C	T	2.591e^-16	1.236e^-11	INTERGENIC	TF binding site BDTNP1_TFBS_da
2R	17751335	2R_17751335_SNP [dm3] 2R_21863830_SNP [dm6]	G	A	3.608e^-16	1.678e^-11	INTERGENIC
2R	9398901	2R_9398901_SNP [dm3] 2R_13511396_SNP [dm6]	T	A	6.546e^-16	2.815e^-11	SYNONYMOUS_CODING mip120	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	2610329	3L_2610329_SNP [dm3] 3L_2610329_SNP [dm6]	A	G	6.546e^-16	2.815e^-11	UTR_3_PRIME Pxn INTRON Pxn	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	15413451	3R_15413451_SNP [dm3] 3R_19587729_SNP [dm6]	C	T	6.546e^-16	2.815e^-11	INTRON Dys
3L	2297759	3L_2297759_SNP [dm3] 3L_2297759_SNP [dm6]	A	T	6.899e^-16	2.815e^-11	INTRON MsR2
3L	8216207	3L_8216207_SNP [dm3] 3L_8223107_SNP [dm6]	A	T	6.899e^-16	2.815e^-11	DOWNSTREAM CG13678 INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
X	14755447	X_14755447_SNP [dm3] X_14861414_SNP [dm6]	G	T	6.960e^-16	2.815e^-11	INTRON Flo2
X	3891054	X_3891054_SNP [dm3] X_3997021_SNP [dm6]	A	T	7.407e^-16	2.932e^-11	INTERGENIC
2L	9099892	2L_9099892_SNP [dm3] 2L_9099892_SNP [dm6]	T	C	8.816e^-16	3.254e^-11	DOWNSTREAM CR44482 INTERGENIC
3R	22864150	3R_22864150_SNP [dm3] 3R_27038428_SNP [dm6]	C	T	9.444e^-16	3.254e^-11	INTRON RYa-R
3R	22864168	3R_22864168_SNP [dm3] 3R_27038446_SNP [dm6]	A	C	9.444e^-16	3.254e^-11	INTRON RYa-R
3R	22865359	3R_22865359_SNP [dm3] 3R_27039637_SNP [dm6]	G	A	9.444e^-16	3.254e^-11	INTRON RYa-R
3R	22865360	3R_22865360_SNP [dm3] 3R_27039638_SNP [dm6]	G	A	9.444e^-16	3.254e^-11	INTRON RYa-R
3R	22866568	3R_22866568_SNP [dm3] 3R_27040846_SNP [dm6]	A	G	9.444e^-16	3.254e^-11	INTRON RYa-R
3R	22867152	3R_22867152_SNP [dm3] 3R_27041430_SNP [dm6]	A	T	9.444e^-16	3.254e^-11	INTRON RYa-R
3R	15415190	3R_15415190_SNP [dm3] 3R_19589468_SNP [dm6]	A	G	1.066e^-15	3.304e^-11	INTRON Dys	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2R	9396953	2R_9396953_SNP [dm3] 2R_13509448_SNP [dm6]	T	A	1.088e^-15	3.304e^-11	UPSTREAM mip120 DOWNSTREAM EfTuM INTRON mip120	TF binding site BDTNP1_TFBS_dl mE1_TFBS_D mE1_TFBS_GATAe mE1_TFBS_h mE1_TFBS_HSA
3L	6593206	3L_6593206_SNP [dm3] 3L_6600106_SNP [dm6]	C	T	1.100e^-15	3.304e^-11	SYNONYMOUS_CODING ndl	TF binding site mE1_TFBS_cad
3R	23534910	3R_23534910_SNP [dm3] 3R_27709188_SNP [dm6]	T	C	1.100e^-15	3.304e^-11	SYNONYMOUS_CODING CG12877	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_eve mE1_TFBS_HSA
3L	3562229	3L_3562229_SNP [dm3] 3L_3562229_SNP [dm6]	A	G	1.101e^-15	3.304e^-11	INTRON Eip63E
3L	3562231	3L_3562231_INS [dm3] 3L_3562231_INS [dm6]	G	GAAG	1.101e^-15	3.304e^-11	INTRON Eip63E
X	8704505	X_8704505_SNP [dm3] X_8810472_SNP [dm6]	G	T	1.101e^-15	3.304e^-11	INTERGENIC
X	8704600	X_8704600_SNP [dm3] X_8810567_SNP [dm6]	C	T	1.101e^-15	3.304e^-11	INTERGENIC
3L	15414060	3L_15414060_SNP [dm3] 3L_15420960_SNP [dm6]	G	T	1.119e^-15	3.304e^-11	INTERGENIC
2L	11239374	2L_11239374_SNP [dm3] 2L_11239374_SNP [dm6]	C	A	1.299e^-15	3.775e^-11	INTRON ab
3R	5847231	3R_5847231_SNP [dm3] 3R_10021509_SNP [dm6]	T	G	1.492e^-15	4.272e^-11	UPSTREAM Mical INTRON Mical	TF binding site BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_HSA
3R	22863486	3R_22863486_SNP [dm3] 3R_27037764_SNP [dm6]	A	G	1.661e^-15	4.422e^-11	INTRON RYa-R	TF binding site mE1_TFBS_cad
3R	15438220	3R_15438220_SNP [dm3] 3R_19612498_SNP [dm6]	T	G	1.722e^-15	4.422e^-11	UPSTREAM CG16727 DOWNSTREAM CG17752 INTERGENIC
3R	15438229	3R_15438229_DEL [dm3] 3R_19612507_DEL [dm6]	GG	G	1.722e^-15	4.422e^-11	UPSTREAM CG16727 DOWNSTREAM CG17752 INTERGENIC
2R	9921793	2R_9921793_SNP [dm3] 2R_14034288_SNP [dm6]	T	C	1.722e^-15	4.422e^-11	INTRON mam
X	14763129	X_14763129_DEL [dm3] X_14869096_DEL [dm6]	AA	A	1.766e^-15	4.422e^-11	INTRON Flo2 & 1 other
2R	8880829	2R_8880829_DEL [dm3] 2R_12993324_DEL [dm6]	TGATACAGT	T	1.800e^-15	4.422e^-11	UPSTREAM CG33798 INTERGENIC
2R	8880852	2R_8880852_SNP [dm3] 2R_12993347_SNP [dm6]	G	A	1.800e^-15	4.422e^-11	UPSTREAM CG33798 INTERGENIC
3R	10139020	3R_10139020_SNP [dm3] 3R_14313298_SNP [dm6]	C	T	1.800e^-15	4.422e^-11	SYNONYMOUS_CODING CG31321
3R	10143727	3R_10143727_SNP [dm3] 3R_14318005_SNP [dm6]	C	T	1.800e^-15	4.422e^-11	SYNONYMOUS_CODING pr-set7	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	10297887	3R_10297887_SNP [dm3] 3R_14472165_SNP [dm6]	G	T	1.800e^-15	4.422e^-11	INTRON cv-c
2R	1800180	2R_1800180_SNP [dm3] 2R_5912675_SNP [dm6]	C	A	1.829e^-15	4.422e^-11	INTRON CG43366	TF binding site mE1_TFBS_chinmo
3L	2298844	3L_2298844_SNP [dm3] 3L_2298844_SNP [dm6]	T	G	1.851e^-15	4.422e^-11	NON_SYNONYMOUS_CODING MsR2	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3R	5859809	3R_5859809_SNP [dm3] 3R_10034087_SNP [dm6]	C	A	1.854e^-15	4.422e^-11	INTRON Mical
2L	6809833	2L_6809833_SNP [dm3] 2L_6809833_SNP [dm6]	G	A	2.045e^-15	4.815e^-11	INTERGENIC
2R	7836874	2R_7836874_SNP [dm3] 2R_11949369_SNP [dm6]	C	A	2.241e^-15	5.212e^-11	INTRON CG13188
2L	16181135	2L_16181135_SNP [dm3] 2L_16181135_SNP [dm6]	G	A	2.363e^-15	5.362e^-11	INTRON Ca-alpha1D
2L	16181222	2L_16181222_SNP [dm3] 2L_16181222_SNP [dm6]	A	T	2.363e^-15	5.362e^-11	INTRON Ca-alpha1D
2L	14457306	2L_14457306_SNP [dm3] 2L_14457306_SNP [dm6]	G	A	2.482e^-15	5.564e^-11	EXON CR44730	TF binding site mE1_TFBS_cad
3R	15435481	3R_15435481_SNP [dm3] 3R_19609759_SNP [dm6]	T	C	2.848e^-15	6.250e^-11	UPSTREAM CG17752 DOWNSTREAM CG17751 INTERGENIC
3R	15438189	3R_15438189_SNP [dm3] 3R_19612467_SNP [dm6]	T	A	2.855e^-15	6.250e^-11	UPSTREAM CG16727 DOWNSTREAM CG17752 INTERGENIC
3R	10550079	3R_10550079_SNP [dm3] 3R_14724357_SNP [dm6]	C	A	2.965e^-15	6.261e^-11	UPSTREAM kibra DOWNSTREAM CG7530 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_sens mE1_TFBS_Trl
3L	2295283	3L_2295283_SNP [dm3] 3L_2295283_SNP [dm6]	G	T	2.981e^-15	6.261e^-11	INTRON MsR2
3L	2297113	3L_2297113_SNP [dm3] 3L_2297113_SNP [dm6]	C	T	2.981e^-15	6.261e^-11	INTRON MsR2
3R	10299485	3R_10299485_SNP [dm3] 3R_14473763_SNP [dm6]	G	A	2.995e^-15	6.261e^-11	INTRON cv-c	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2L	9370505	2L_9370505_INS [dm3] 2L_9370505_INS [dm6]	T	TGT	3.206e^-15	6.627e^-11	UTR_3_PRIME Shawl
3L	22899521	3L_22899521_SNP [dm3] 3L_22906421_SNP [dm6]	A	T	3.323e^-15	6.793e^-11	DOWNSTREAM BoYb INTERGENIC
2L	20414506	2L_20414506_SNP [dm3] 2L_20414506_SNP [dm6]	T	A	3.407e^-15	6.873e^-11	UTR_5_PRIME CG10947 DOWNSTREAM CG10949
2R	10074949	2R_10074949_SNP [dm3] 2R_14187444_SNP [dm6]	A	G	3.436e^-15	6.873e^-11	INTRON CG30069
2L	19778608	2L_19778608_SNP [dm3] 2L_19778608_SNP [dm6]	G	T	3.730e^-15	7.382e^-11	SYNONYMOUS_CODING CdGAPr	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	11519462	3L_11519462_SNP [dm3] 3L_11526362_SNP [dm6]	G	A	4.219e^-15	8.177e^-11	INTRON Mob2
3R	3460857	3R_3460857_SNP [dm3] 3R_7635135_SNP [dm6]	T	G	4.219e^-15	8.177e^-11	INTRON CG34127
3R	22864726	3R_22864726_SNP [dm3] 3R_27039004_SNP [dm6]	C	G	4.343e^-15	8.238e^-11	INTRON RYa-R
3R	22863339	3R_22863339_SNP [dm3] 3R_27037617_SNP [dm6]	C	T	4.384e^-15	8.238e^-11	INTRON RYa-R	TF binding site mE1_TFBS_cad
3R	22867841	3R_22867841_SNP [dm3] 3R_27042119_SNP [dm6]	G	A	4.384e^-15	8.238e^-11	INTRON RYa-R
3R	18898068	3R_18898068_SNP [dm3] 3R_23072346_SNP [dm6]	G	T	4.735e^-15	8.722e^-11	UTR_3_PRIME CG13830 DOWNSTREAM CG13830

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By genomic position
Variant impact
Gene name

Microbiota_OTU009 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results