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=2.511e^-13)
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
No significant result.

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

6086 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	22958910	3R_22958910_SNP [dm3] 3R_27133188_SNP [dm6]	C	A	3.748e^-15	6.972e^-9	INTRON CG6051
2R	10325701	2R_10325701_SNP [dm3] 2R_14438196_SNP [dm6]	G	A	8.268e^-15	7.692e^-9	INTRON Oaz	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	10325695	2R_10325695_SNP [dm3] 2R_14438190_SNP [dm6]	T	A	1.428e^-14	8.853e^-9	INTRON Oaz	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	14356281	2R_14356281_SNP [dm3] 2R_18468776_SNP [dm6]	G	A	7.224e^-14	3.360e^-8	INTRON CG30116
2R	10325825	2R_10325825_SNP [dm3] 2R_14438320_SNP [dm6]	G	A	7.730e^-12	2.876e^-6	INTRON Oaz	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
3L	3495470	3L_3495470_SNP [dm3] 3L_3495470_SNP [dm6]	T	C	1.004e^-11	3.103e^-6	INTRON CG42324
3L	5894052	3L_5894052_SNP [dm3] 3L_5900952_SNP [dm6]	G	A	1.170e^-11	3.103e^-6	NON_SYNONYMOUS_CODING QC DOWNSTREAM CG32409	TF binding site mE1_TFBS_cad
2L	5788435	2L_5788435_SNP [dm3] 2L_5788435_SNP [dm6]	C	G	1.334e^-11	3.103e^-6	INTRON CG9171	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	13076905	2L_13076905_SNP [dm3] 2L_13076905_SNP [dm6]	C	G	1.667e^-11	3.446e^-6	INTERGENIC
3L	3496821	3L_3496821_SNP [dm3] 3L_3496821_SNP [dm6]	G	T	2.327e^-11	4.330e^-6	INTRON CG42324
2R	17132532	2R_17132532_SNP [dm3] 2R_21245027_SNP [dm6]	A	T	4.436e^-11	7.503e^-6	INTRON ASPP	TF binding site BDTNP1_TFBS_prd
2R	17132455	2R_17132455_SNP [dm3] 2R_21244950_SNP [dm6]	C	G	5.718e^-11	8.865e^-6	INTRON ASPP	TF binding site BDTNP1_TFBS_prd
3L	3817734	3L_3817734_SNP [dm3] 3L_3817734_SNP [dm6]	A	G	8.157e^-11	1.167e^-5	UPSTREAM enc INTRON Scsalpha	TF binding site mE1_TFBS_sens
3L	1356011	3L_1356011_SNP [dm3] 3L_1356011_SNP [dm6]	G	A	4.342e^-10	5.770e^-5	INTRON Ptp61F	TF binding site mE1_TFBS_inv
2R	3687625	2R_3687625_SNP [dm3] 2R_7800120_SNP [dm6]	A	C	7.249e^-10	8.449e^-5	DOWNSTREAM Nop17l INTRON mus205	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	3495875	3L_3495875_SNP [dm3] 3L_3495875_SNP [dm6]	G	A	7.482e^-10	8.449e^-5	INTRON CG42324
3R	22981837	3R_22981837_SNP [dm3] 3R_27156115_SNP [dm6]	A	G	7.932e^-10	8.449e^-5	INTRON Men-b
2R	3677687	2R_3677687_SNP [dm3] 2R_7790182_SNP [dm6]	C	T	8.175e^-10	8.449e^-5	UPSTREAM CG12824 DOWNSTREAM CG12825 INTERGENIC
2R	16689395	2R_16689395_SNP [dm3] 2R_20801890_SNP [dm6]	C	G	1.075e^-9	1.053e^-4	INTERGENIC
2R	3677701	2R_3677701_SNP [dm3] 2R_7790196_SNP [dm6]	C	A	1.152e^-9	1.071e^-4	UPSTREAM CG12824 DOWNSTREAM CG12825 INTERGENIC
3L	3494056	3L_3494056_SNP [dm3] 3L_3494056_SNP [dm6]	G	A	1.320e^-9	1.143e^-4	INTRON CG42324	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
3L	20065216	3L_20065216_SNP [dm3] 3L_20072116_SNP [dm6]	C	A	1.568e^-9	1.143e^-4	INTRON sNPF-R
2R	3677708	2R_3677708_SNP [dm3] 2R_7790203_SNP [dm6]	C	G	1.663e^-9	1.143e^-4	UPSTREAM CG12824 DOWNSTREAM CG12825 INTERGENIC
3L	3493832	3L_3493832_SNP [dm3] 3L_3493832_SNP [dm6]	C	A	1.738e^-9	1.143e^-4	INTRON CG42324	TF binding site mE1_TFBS_inv
3L	10778787	3L_10778787_SNP [dm3] 3L_10785687_SNP [dm6]	G	A	1.776e^-9	1.143e^-4	DOWNSTREAM CR44544 INTERGENIC
3L	10786874	3L_10786874_SNP [dm3] 3L_10793774_SNP [dm6]	T	C	1.776e^-9	1.143e^-4	INTERGENIC	TF binding site mE1_TFBS_Trl
X	5211003	X_5211003_SNP [dm3] X_5316970_SNP [dm6]	T	C	1.776e^-9	1.143e^-4	NON_SYNONYMOUS_CODING CG15930 UPSTREAM Sas10	TF binding site mE1_TFBS_HSA
3L	16473582	3L_16473582_SNP [dm3] 3L_16480482_SNP [dm6]	G	C	1.812e^-9	1.143e^-4	INTRON CG33158 & 1 other	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3L	3492230	3L_3492230_SNP [dm3] 3L_3492230_SNP [dm6]	T	G	1.828e^-9	1.143e^-4	INTRON CG42324
2L	1705201	2L_1705201_SNP [dm3] 2L_1705201_SNP [dm6]	T	G	1.844e^-9	1.143e^-4	UTR_5_PRIME cpb DOWNSTREAM chinmo INTRON cpb	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_h mE1_TFBS_HSA
3L	3494050	3L_3494050_SNP [dm3] 3L_3494050_SNP [dm6]	C	G	1.994e^-9	1.197e^-4	INTRON CG42324	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2L	10114553	2L_10114553_SNP [dm3] 2L_10114553_SNP [dm6]	C	G	2.266e^-9	1.276e^-4	INTRON CG44153 & 1 other
3L	3494073	3L_3494073_DEL [dm3] 3L_3494073_DEL [dm6]	TTTGTTA	T	2.319e^-9	1.276e^-4	INTRON CG42324	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
3L	10787041	3L_10787041_SNP [dm3] 3L_10793941_SNP [dm6]	C	T	2.332e^-9	1.276e^-4	INTERGENIC
3L	3495213	3L_3495213_SNP [dm3] 3L_3495213_SNP [dm6]	A	C	2.441e^-9	1.298e^-4	INTRON CG42324
2L	12476821	2L_12476821_SNP [dm3] 2L_12476821_SNP [dm6]	T	A	2.572e^-9	1.329e^-4	INTRON bun
2L	12197299	2L_12197299_SNP [dm3] 2L_12197299_SNP [dm6]	T	A	3.389e^-9	1.682e^-4	INTRON aret	TF binding site mE1_TFBS_inv
2L	6955557	2L_6955557_SNP [dm3] 2L_6955557_SNP [dm6]	C	T	3.436e^-9	1.682e^-4	SYNONYMOUS_CODING CG13775 DOWNSTREAM SA	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	3496841	3L_3496841_SNP [dm3] 3L_3496841_SNP [dm6]	T	A	3.881e^-9	1.851e^-4	INTRON CG42324
2R	18749420	2R_18749420_SNP [dm3] 2R_22861897_SNP [dm6]	G	A	4.772e^-9	2.220e^-4	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
2L	9412370	2L_9412370_SNP [dm3] 2L_9412370_SNP [dm6]	C	T	5.517e^-9	2.503e^-4	INTRON Shawl
2R	5868148	2R_5868148_SNP [dm3] 2R_9980643_SNP [dm6]	C	A	6.481e^-9	2.827e^-4	UTR_3_PRIME eve	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	10200111	2L_10200111_SNP [dm3] 2L_10200111_SNP [dm6]	A	G	6.534e^-9	2.827e^-4	SYNONYMOUS_CODING Ripalpha UPSTREAM Sur & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
2L	18751259	2L_18751259_SNP [dm3] 2L_18751259_SNP [dm6]	G	A	6.841e^-9	2.893e^-4	INTERGENIC
3L	3496160	3L_3496160_SNP [dm3] 3L_3496160_SNP [dm6]	T	C	8.422e^-9	3.482e^-4	INTRON CG42324
X	18289521	X_18289521_SNP [dm3] X_18395488_SNP [dm6]	T	C	8.788e^-9	3.554e^-4	INTRON CG32549	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	3497066	3L_3497066_SNP [dm3] 3L_3497066_SNP [dm6]	T	C	9.490e^-9	3.756e^-4	INTRON CG42324
3L	3494818	3L_3494818_SNP [dm3] 3L_3494818_SNP [dm6]	C	T	1.003e^-8	3.887e^-4	INTRON CG42324
3R	20314411	3R_20314411_SNP [dm3] 3R_24488689_SNP [dm6]	G	T	1.066e^-8	4.048e^-4	DOWNSTREAM mir-1017 INTRON nAChRalpha2
3L	2602466	3L_2602466_SNP [dm3] 3L_2602466_SNP [dm6]	G	A	1.104e^-8	4.109e^-4	SYNONYMOUS_CODING Pxn DOWNSTREAM CG16986	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_sens
X	14504402	X_14504402_SNP [dm3] X_14610369_SNP [dm6]	G	A	1.152e^-8	4.204e^-4	INTRON NetA	TF binding site mE1_TFBS_cad
2L	4854057	2L_4854057_SNP [dm3] 2L_4854057_SNP [dm6]	A	C	1.187e^-8	4.248e^-4	INTRON pog
2L	13039818	2L_13039818_SNP [dm3] 2L_13039818_SNP [dm6]	A	C	1.325e^-8	4.650e^-4	INTRON CG9932
2L	12174887	2L_12174887_SNP [dm3] 2L_12174887_SNP [dm6]	T	G	1.502e^-8	5.175e^-4	UPSTREAM aret & 1 other DOWNSTREAM crok & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_slp1
X	6883570	X_6883570_SNP [dm3] X_6989537_SNP [dm6]	G	A	1.720e^-8	5.817e^-4	INTRON ogre	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
2L	13559605	2L_13559605_SNP [dm3] 2L_13559605_SNP [dm6]	G	A	1.863e^-8	6.190e^-4	INTRON kuz
3L	5343108	3L_5343108_SNP [dm3] 3L_5350008_SNP [dm6]	A	C	2.306e^-8	7.526e^-4	INTRON lama
2L	9485911	2L_9485911_SNP [dm3] 2L_9485911_SNP [dm6]	C	T	2.510e^-8	8.052e^-4	INTERGENIC
3L	5502457	3L_5502457_SNP [dm3] 3L_5509357_SNP [dm6]	T	G	2.594e^-8	8.178e^-4	INTRON CG34342	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
3L	1355941	3L_1355941_SNP [dm3] 3L_1355941_SNP [dm6]	C	T	2.704e^-8	8.384e^-4	INTRON Ptp61F	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2R	14282663	2R_14282663_SNP [dm3] 2R_18395158_SNP [dm6]	G	A	2.883e^-8	8.773e^-4	SYNONYMOUS_CODING Idgf5
2L	3910842	2L_3910842_SNP [dm3] 2L_3910842_SNP [dm6]	C	T	2.932e^-8	8.773e^-4	DOWNSTREAM CG31773 INTRON fred
2R	6744568	2R_6744568_SNP [dm3] 2R_10857063_SNP [dm6]	C	T	3.013e^-8	8.773e^-4	INTRON CG30015
2L	6956593	2L_6956593_SNP [dm3] 2L_6956593_SNP [dm6]	C	T	3.018e^-8	8.773e^-4	UPSTREAM CG3430 & 1 other INTRON CG13775	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_ttk mE1_TFBS_Ubx
X	6882779	X_6882779_SNP [dm3] X_6988746_SNP [dm6]	G	A	3.067e^-8	8.779e^-4	INTRON ogre	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
2L	4523206	2L_4523206_SNP [dm3] 2L_4523206_SNP [dm6]	C	T	3.206e^-8	9.038e^-4	SYNONYMOUS_CODING dp INTRON dp	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	18387290	3L_18387290_INS [dm3] 3L_18394190_INS [dm6]	A	AGGGCC	3.291e^-8	9.140e^-4	INTERGENIC	TF binding site mE1_TFBS_cad
2L	14149696	2L_14149696_SNP [dm3] 2L_14149696_SNP [dm6]	C	T	3.714e^-8	0.001	INTRON CG17341
2L	6955793	2L_6955793_SNP [dm3] 2L_6955793_SNP [dm6]	C	T	3.793e^-8	0.001	NON_SYNONYMOUS_CODING CG13775	TF binding site mE1_TFBS_sens
2L	6957085	2L_6957085_SNP [dm3] 2L_6957085_SNP [dm6]	C	T	3.793e^-8	0.001	START_GAINED CG3430 UTR_5_PRIME CG3430 UPSTREAM CG13775	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_ttk
2L	4520995	2L_4520995_SNP [dm3] 2L_4520995_SNP [dm6]	T	C	3.927e^-8	0.001	INTRON dp	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	18475154	2L_18475154_SNP [dm3] 2L_18475154_SNP [dm6]	C	T	4.554e^-8	0.001	SPLICE_SITE_REGION CG10283 SYNONYMOUS_CODING CG10283	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad
2L	18475175	2L_18475175_SNP [dm3] 2L_18475175_SNP [dm6]	G	T	4.554e^-8	0.001	SYNONYMOUS_CODING CG10283	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad
2L	6956327	2L_6956327_SNP [dm3] 2L_6956327_SNP [dm6]	C	T	5.000e^-8	0.001	UTR_5_PRIME CG13775 UPSTREAM CG3430 INTRON CG13775	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_ttk
2L	5316869	2L_5316869_SNP [dm3] 2L_5316869_SNP [dm6]	G	C	5.185e^-8	0.001	UTR_3_PRIME Ncoa6	TF binding site mE1_TFBS_cad
2R	11401143	2R_11401143_SNP [dm3] 2R_15513638_SNP [dm6]	T	C	5.202e^-8	0.001	INTRON GalNAc-T1
2L	4532444	2L_4532444_SNP [dm3] 2L_4532444_SNP [dm6]	T	A	5.204e^-8	0.001	INTRON dp
2R	14148023	2R_14148023_SNP [dm3] 2R_18260518_SNP [dm6]	T	A	5.304e^-8	0.001	INTERGENIC
2R	15949601	2R_15949601_SNP [dm3] 2R_20062096_SNP [dm6]	A	G	5.691e^-8	0.001	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_chinmo mE1_TFBS_HSA
2R	10321738	2R_10321738_SNP [dm3] 2R_14434233_SNP [dm6]	A	C	6.142e^-8	0.001	UPSTREAM CR45277 INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_zfh1
3R	22989209	3R_22989209_SNP [dm3] 3R_27163487_SNP [dm6]	C	T	6.159e^-8	0.001	DOWNSTREAM CG5909 INTRON ppk31
2L	9409270	2L_9409270_SNP [dm3] 2L_9409270_SNP [dm6]	G	A	6.308e^-8	0.001	INTRON Shawl
2R	20252047	2R_20252047_INS [dm3] 2R_24364524_INS [dm6]	C	CAAAAC	6.464e^-8	0.001	INTRON bs & 1 other	TF binding site mE1_TFBS_cad
3L	3513309	3L_3513309_SNP [dm3] 3L_3513309_SNP [dm6]	T	G	6.704e^-8	0.001	UPSTREAM ImpE2 INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	11750561	2R_11750561_SNP [dm3] 2R_15863056_SNP [dm6]	T	G	6.793e^-8	0.001	UPSTREAM Gpo-1 INTERGENIC	TF binding site BDTNP1_TFBS_dl
3L	11577895	3L_11577895_SNP [dm3] 3L_11584795_SNP [dm6]	C	T	7.283e^-8	0.002	SYNONYMOUS_CODING rt UPSTREAM CG32086	TF binding site mE1_TFBS_cad mE1_TFBS_sens
3L	718924	3L_718924_SNP [dm3] 3L_718924_SNP [dm6]	T	C	7.669e^-8	0.002	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
2L	13118713	2L_13118713_SNP [dm3] 2L_13118713_SNP [dm6]	A	G	7.854e^-8	0.002	UPSTREAM CG43050 DOWNSTREAM CR44198 INTERGENIC
2R	18986084	2R_18986084_SNP [dm3] 2R_23098561_SNP [dm6]	C	T	7.947e^-8	0.002	INTERGENIC
2L	22069499	2L_22069499_SNP [dm3] 2L_22069499_SNP [dm6]	T	G	7.982e^-8	0.002	INTERGENIC	TF binding site mE1_TFBS_sens
3R	15122404	3R_15122404_SNP [dm3] 3R_19296682_SNP [dm6]	A	C	8.467e^-8	0.002	DOWNSTREAM CG44174 INTERGENIC
X	6282812	X_6282812_SNP [dm3] X_6388779_SNP [dm6]	A	G	8.644e^-8	0.002	INTERGENIC
2L	22121076	2L_22121076_SNP [dm3] 2L_22121076_SNP [dm6]	G	A	9.049e^-8	0.002	UPSTREAM CG3651 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	10765122	3L_10765122_SNP [dm3] 3L_10772022_SNP [dm6]	G	T	9.233e^-8	0.002	UTR_5_PRIME CG43245	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	9406683	2L_9406683_SNP [dm3] 2L_9406683_SNP [dm6]	A	C	9.485e^-8	0.002	INTRON Shawl
3R	26169320	3R_26169320_SNP [dm3] 3R_30343598_SNP [dm6]	C	A	9.521e^-8	0.002	INTRON hdc
3R	22003398	3R_22003398_SNP [dm3] 3R_26177676_SNP [dm6]	A	G	9.672e^-8	0.002	INTRON CG31323
3R	8236513	3R_8236513_SNP [dm3] 3R_12410791_SNP [dm6]	A	T	9.915e^-8	0.002	SYNONYMOUS_CODING CG5196	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	7907847	2L_7907847_SNP [dm3] 2L_7907847_SNP [dm6]	T	A	1.035e^-7	0.002	INTRON Snoo
2L	13354828	2L_13354828_SNP [dm3] 2L_13354828_SNP [dm6]	T	C	1.040e^-7	0.002	UTR_5_PRIME CG9395 INTRON CG9395	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl

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By genomic position
Variant impact
Gene name

Microbiota_OTU154 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results