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=3.525e^-9)
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

3634 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	3617483	2L_3617483_SNP [dm3] 2L_3617483_SNP [dm6]	A	T	8.253e^-9	0.015	EXON CR44310	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_cad
3L	7768125	3L_7768125_INS [dm3] 3L_7775025_INS [dm6]	A	AA	1.915e^-8	0.015	INTRON Clk	regulatory region REDfly_CRMs
2L	14673008	2L_14673008_SNP [dm3] 2L_14673008_SNP [dm6]	T	C	2.495e^-8	0.015	INTRON osp
3L	15989963	3L_15989963_SNP [dm3] 3L_15996863_SNP [dm6]	T	C	3.930e^-8	0.018	INTRON CG5830
2R	14399164	2R_14399164_SNP [dm3] 2R_18511659_SNP [dm6]	C	G	9.888e^-8	0.035	INTERGENIC
X	7609515	X_7609515_SNP [dm3] X_7715482_SNP [dm6]	T	C	1.227e^-7	0.035	UPSTREAM CG15478 INTRON CG15478
2R	8773471	2R_8773471_DEL [dm3] 2R_12885966_DEL [dm6]	CGACCTAATTC...	C	1.342e^-7	0.035	INTRON vg	TF binding site BDTNP1_TFBS_dl
3R	4442768	3R_4442768_SNP [dm3] 3R_8617046_SNP [dm6]	C	T	1.488e^-7	0.035	INTRON 5-HT2B	TF binding site mE1_TFBS_inv
2L	14673011	2L_14673011_SNP [dm3] 2L_14673011_SNP [dm6]	C	T	1.901e^-7	0.039	INTRON osp
2L	14706263	2L_14706263_SNP [dm3] 2L_14706263_SNP [dm6]	G	A	2.328e^-7	0.041	INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_cnc mE1_TFBS_HSA mE1_TFBS_zfh1
3L	20417121	3L_20417121_SNP [dm3] 3L_20424021_SNP [dm6]	A	C	2.881e^-7	0.041	NON_SYNONYMOUS_CODING zye DOWNSTREAM CG5282	TF binding site mE1_TFBS_cad
2R	8782385	2R_8782385_SNP [dm3] 2R_12894880_SNP [dm6]	T	C	2.968e^-7	0.041	INTRON vg	TF binding site BDTNP1_TFBS_dl
3L	8508655	3L_8508655_SNP [dm3] 3L_8515555_SNP [dm6]	G	C	3.001e^-7	0.041	SYNONYMOUS_CODING CG6765 UPSTREAM CG6683	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	3615495	2L_3615495_SNP [dm3] 2L_3615495_SNP [dm6]	T	C	3.117e^-7	0.041	UPSTREAM CR44310 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_ftz BDTNP1_TFBS_hb BDTNP1_TFBS_kni BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	8788232	2R_8788232_SNP [dm3] 2R_12900727_SNP [dm6]	G	A	3.437e^-7	0.043	INTERGENIC
3L	14800328	3L_14800328_DEL [dm3] 3L_14807228_DEL [dm6]	CC	C	4.034e^-7	0.047	INTRON CG17839	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2R	8778729	2R_8778729_SNP [dm3] 2R_12891224_SNP [dm6]	A	G	4.448e^-7	0.047	INTRON vg	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3R	13569252	3R_13569252_SNP [dm3] 3R_17743530_SNP [dm6]	G	A	4.550e^-7	0.047	INTRON TyrRII	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	14706269	2L_14706269_SNP [dm3] 2L_14706269_SNP [dm6]	A	C	4.912e^-7	0.048	INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_cnc mE1_TFBS_HSA mE1_TFBS_zfh1
3L	20416307	3L_20416307_SNP [dm3] 3L_20423207_SNP [dm6]	C	A	5.623e^-7	0.052	NON_SYNONYMOUS_CODING zye	TF binding site mE1_TFBS_cad mE1_TFBS_sens
X	9389916	X_9389916_SNP [dm3] X_9495883_SNP [dm6]	A	G	5.889e^-7	0.052	UTR_5_PRIME mgl INTRON mgl	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA
2L	14706252	2L_14706252_SNP [dm3] 2L_14706252_SNP [dm6]	T	A	6.148e^-7	0.052	INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_cnc mE1_TFBS_HSA mE1_TFBS_zfh1
3R	20848750	3R_20848750_SNP [dm3] 3R_25023028_SNP [dm6]	C	A	6.924e^-7	0.052	UPSTREAM beta4GalT7 DOWNSTREAM tnc INTERGENIC
3L	15253928	3L_15253928_SNP [dm3] 3L_15260828_SNP [dm6]	G	A	6.932e^-7	0.052	INTERGENIC	TF binding site mE1_TFBS_cad
X	10143299	X_10143299_SNP [dm3] X_10249266_SNP [dm6]	G	C	7.214e^-7	0.052	INTRON Hk	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	14906853	3R_14906853_DEL [dm3] 3R_19081131_DEL [dm6]	TTCT	T	7.261e^-7	0.052	INTRON cdi
3L	12314795	3L_12314795_SNP [dm3] 3L_12321695_SNP [dm6]	T	A	7.964e^-7	0.052	INTERGENIC
3R	17450634	3R_17450634_SNP [dm3] 3R_21624912_SNP [dm6]	T	G	7.996e^-7	0.052	INTRON E2f	TF binding site mE1_TFBS_cad
2R	14399150	2R_14399150_SNP [dm3] 2R_18511645_SNP [dm6]	T	C	8.078e^-7	0.052	INTERGENIC
2L	3617439	2L_3617439_SNP [dm3] 2L_3617439_SNP [dm6]	A	G	8.443e^-7	0.052	EXON CR44310	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_cad
2L	14694436	2L_14694436_SNP [dm3] 2L_14694436_SNP [dm6]	A	T	8.768e^-7	0.052	INTERGENIC
2L	15741236	2L_15741236_INS [dm3] 2L_15741236_INS [dm6]	A	ATA	9.648e^-7	0.052	INTRON CycE	regulatory region FlyBase REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
X	4222485	X_4222485_SNP [dm3] X_4328452_SNP [dm6]	A	C	1.038e^-6	0.052	NON_SYNONYMOUS_CODING CG12693 INTRON norpA	TF binding site BDTNP1_TFBS_twi
3L	6338299	3L_6338299_SNP [dm3] 3L_6345199_SNP [dm6]	C	T	1.050e^-6	0.052	INTRON CG13300	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3L	12300442	3L_12300442_SNP [dm3] 3L_12307342_SNP [dm6]	G	C	1.087e^-6	0.052	INTERGENIC
3L	19058997	3L_19058997_SNP [dm3] 3L_19065897_SNP [dm6]	A	T	1.091e^-6	0.052	UTR_3_PRIME CG6812 DOWNSTREAM Mkp3
3R	13411515	3R_13411515_SNP [dm3] 3R_17585793_SNP [dm6]	G	A	1.151e^-6	0.052	INTERGENIC
3R	13411516	3R_13411516_SNP [dm3] 3R_17585794_SNP [dm6]	T	G	1.151e^-6	0.052	INTERGENIC
3L	20412140	3L_20412140_SNP [dm3] 3L_20419040_SNP [dm6]	C	G	1.161e^-6	0.052	NON_SYNONYMOUS_CODING zye	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3L	20421612	3L_20421612_SNP [dm3] 3L_20428512_SNP [dm6]	A	G	1.161e^-6	0.052	SYNONYMOUS_CODING CG5262 UPSTREAM CG5274
3L	20421849	3L_20421849_SNP [dm3] 3L_20428749_SNP [dm6]	G	T	1.161e^-6	0.052	SYNONYMOUS_CODING CG5262
X	9389878	X_9389878_SNP [dm3] X_9495845_SNP [dm6]	G	A	1.201e^-6	0.052	UTR_5_PRIME mgl INTRON mgl	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
2L	14681456	2L_14681456_SNP [dm3] 2L_14681456_SNP [dm6]	G	A	1.225e^-6	0.052	INTRON osp
3L	20424719	3L_20424719_SNP [dm3] 3L_20431619_SNP [dm6]	T	A	1.226e^-6	0.052	UPSTREAM Psn INTRON Las	TF binding site BDTNP1_TFBS_dl mE1_TFBS_sens
3L	16885963	3L_16885963_SNP [dm3] 3L_16892863_SNP [dm6]	C	A	1.246e^-6	0.052	INTRON Lmpt
2L	2315973	2L_2315973_SNP [dm3] 2L_2315973_SNP [dm6]	A	G	1.301e^-6	0.053	INTRON CG9967 & 1 other
2L	16820612	2L_16820612_SNP [dm3] 2L_16820612_SNP [dm6]	A	G	1.518e^-6	0.058	SYNONYMOUS_CODING mdy DOWNSTREAM Cas INTRON CG13280
3L	7766183	3L_7766183_SNP [dm3] 3L_7773083_SNP [dm6]	A	T	1.554e^-6	0.058	INTRON Clk	regulatory region REDfly_CRMs
3L	20416909	3L_20416909_SNP [dm3] 3L_20423809_SNP [dm6]	C	T	1.627e^-6	0.058	NON_SYNONYMOUS_CODING zye DOWNSTREAM CG5282	TF binding site mE1_TFBS_cad
3L	20419376	3L_20419376_SNP [dm3] 3L_20426276_SNP [dm6]	T	C	1.627e^-6	0.058	UTR_3_PRIME CG5274 UPSTREAM CG5282	TF binding site mE1_TFBS_chinmo
3L	20419434	3L_20419434_SNP [dm3] 3L_20426334_SNP [dm6]	T	A	1.627e^-6	0.058	UTR_3_PRIME CG5274 UPSTREAM CG5282	TF binding site mE1_TFBS_chinmo
3L	20420767	3L_20420767_SNP [dm3] 3L_20427667_SNP [dm6]	T	C	1.627e^-6	0.058	UPSTREAM CG5274 DOWNSTREAM CG5262 INTERGENIC	TF binding site BDTNP1_TFBS_Med
2R	8337493	2R_8337493_SNP [dm3] 2R_12449988_SNP [dm6]	A	T	1.673e^-6	0.058	INTRON Dyb	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	20414535	3L_20414535_SNP [dm3] 3L_20421435_SNP [dm6]	T	C	1.693e^-6	0.058	SYNONYMOUS_CODING zye	TF binding site mE1_TFBS_cad
3L	7763828	3L_7763828_SNP [dm3] 3L_7770728_SNP [dm6]	C	T	1.740e^-6	0.059	INTRON Clk	regulatory region REDfly_CRMs
3L	5897346	3L_5897346_SNP [dm3] 3L_5904246_SNP [dm6]	C	T	1.889e^-6	0.063	UTR_3_PRIME CG10486 UPSTREAM CG32413
3L	11590842	3L_11590842_DEL [dm3] 3L_11597742_DEL [dm6]	TTTTTGATGACT...	T	2.078e^-6	0.068	INTRON CG7368
3R	10553699	3R_10553699_SNP [dm3] 3R_14727977_SNP [dm6]	G	T	2.310e^-6	0.074	INTRON CG7530
3L	12300369	3L_12300369_DEL [dm3] 3L_12307269_DEL [dm6]	GG	G	2.393e^-6	0.075	INTERGENIC
3L	13125081	3L_13125081_SNP [dm3] 3L_13131981_SNP [dm6]	G	A	2.517e^-6	0.078	INTERGENIC	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA mE1_TFBS_sens
3L	12300456	3L_12300456_SNP [dm3] 3L_12307356_SNP [dm6]	T	G	2.661e^-6	0.078	INTERGENIC
2L	9547725	2L_9547725_SNP [dm3] 2L_9547725_SNP [dm6]	T	C	2.714e^-6	0.078	UTR_3_PRIME jp DOWNSTREAM jp & 1 other
2L	12542479	2L_12542479_SNP [dm3] 2L_12542479_SNP [dm6]	T	C	2.730e^-6	0.078	UPSTREAM CR42746 INTRON bun	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
X	6009292	X_6009292_SNP [dm3] X_6115259_SNP [dm6]	T	C	2.800e^-6	0.078	INTRON Ca-alpha1T
3R	10287983	3R_10287983_SNP [dm3] 3R_14462261_SNP [dm6]	C	T	2.808e^-6	0.078	INTRON cv-c	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	8778785	2R_8778785_DEL [dm3] 2R_12891280_DEL [dm6]	AA	A	2.835e^-6	0.078	INTRON vg	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
X	11830572	X_11830572_SNP [dm3] X_11936539_SNP [dm6]	A	C	2.936e^-6	0.078	INTRON cac	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	19944608	3R_19944608_SNP [dm3] 3R_24118886_SNP [dm6]	T	C	2.966e^-6	0.078	UTR_5_PRIME Rootletin INTRON Rootletin
3L	1657831	3L_1657831_SNP [dm3] 3L_1657831_SNP [dm6]	G	C	2.982e^-6	0.078	SYNONYMOUS_CODING CG7971
2R	7043523	2R_7043523_SNP [dm3] 2R_11156018_SNP [dm6]	C	A	3.023e^-6	0.078	DOWNSTREAM CG13230 INTRON CG13229
3R	12840070	3R_12840070_INS [dm3] 3R_17014348_INS [dm6]	A	AAA	3.032e^-6	0.078	UPSTREAM Pxd INTERGENIC
3R	12840422	3R_12840422_SNP [dm3] 3R_17014700_SNP [dm6]	C	T	3.032e^-6	0.078	UTR_5_PRIME Pxd
3R	12846847	3R_12846847_SNP [dm3] 3R_17021125_SNP [dm6]	G	C	3.089e^-6	0.079	UPSTREAM AdSL INTRON Pxd	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Ubx
2R	10096818	2R_10096818_SNP [dm3] 2R_14209313_SNP [dm6]	T	C	3.190e^-6	0.08	INTRON Sox15	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl
3L	105174	3L_105174_SNP [dm3] 3L_105174_SNP [dm6]	C	T	3.286e^-6	0.082	INTERGENIC
X	8660776	X_8660776_SNP [dm3] X_8766743_SNP [dm6]	A	C	3.553e^-6	0.084	INTRON Lim1	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3L	7609923	3L_7609923_SNP [dm3] 3L_7616823_SNP [dm6]	C	G	3.563e^-6	0.084	INTRON CG33275
3L	13612493	3L_13612493_SNP [dm3] 3L_13619393_SNP [dm6]	A	T	3.599e^-6	0.084	INTRON bru-3
3L	7409318	3L_7409318_SNP [dm3] 3L_7416218_SNP [dm6]	A	T	3.643e^-6	0.084	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_inv
2R	12344202	2R_12344202_SNP [dm3] 2R_16456697_SNP [dm6]	T	C	3.648e^-6	0.084	INTERGENIC
3R	12840256	3R_12840256_SNP [dm3] 3R_17014534_SNP [dm6]	T	C	3.658e^-6	0.084	UPSTREAM Pxd INTERGENIC
3R	14351116	3R_14351116_SNP [dm3] 3R_18525394_SNP [dm6]	A	T	3.815e^-6	0.087	INTRON fru	TF binding site mE1_TFBS_inv
3L	7775681	3L_7775681_SNP [dm3] 3L_7782581_SNP [dm6]	C	T	3.946e^-6	0.088	INTRON CG32369	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
3R	13411505	3R_13411505_MNP [dm3] 3R_17585783_MNP [dm6]	TTC	CAA	4.214e^-6	0.091	INTERGENIC
2R	8808667	2R_8808667_SNP [dm3] 2R_12921162_SNP [dm6]	G	A	4.384e^-6	0.091	SYNONYMOUS_CODING NAT1	TF binding site mE1_TFBS_cad mE1_TFBS_sens
3L	20424569	3L_20424569_SNP [dm3] 3L_20431469_SNP [dm6]	G	A	4.387e^-6	0.091	SYNONYMOUS_CODING Las UPSTREAM CG5262 & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_sens
3L	20425816	3L_20425816_SNP [dm3] 3L_20432716_SNP [dm6]	T	C	4.387e^-6	0.091	UPSTREAM Las INTRON Psn	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Ubx
3L	20426709	3L_20426709_SNP [dm3] 3L_20433609_SNP [dm6]	T	G	4.387e^-6	0.091	INTRON Psn
X	14571199	X_14571199_SNP [dm3] X_14677166_SNP [dm6]	T	C	4.407e^-6	0.091	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	7520406	2L_7520406_SNP [dm3] 2L_7520406_SNP [dm6]	G	T	4.473e^-6	0.091	DOWNSTREAM CR44082 INTRON RapGAP1	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	16817521	2L_16817521_SNP [dm3] 2L_16817521_SNP [dm6]	G	A	4.488e^-6	0.091	INTRON CG13280 & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
2L	8650691	2L_8650691_SNP [dm3] 2L_8650691_SNP [dm6]	G	A	4.570e^-6	0.091	INTRON Sema-1a
3L	20856998	3L_20856998_SNP [dm3] 3L_20863898_SNP [dm6]	C	A	4.644e^-6	0.091	INTRON CG32432
3R	13569251	3R_13569251_SNP [dm3] 3R_17743529_SNP [dm6]	G	A	4.713e^-6	0.091	INTRON TyrRII	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	13569300	3R_13569300_SNP [dm3] 3R_17743578_SNP [dm6]	C	T	4.713e^-6	0.091	INTRON TyrRII	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	13569303	3R_13569303_SNP [dm3] 3R_17743581_SNP [dm6]	T	C	4.713e^-6	0.091	INTRON TyrRII	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	7770156	2L_7770156_DEL [dm3] 2L_7770156_DEL [dm6]	CAAGCCCTT	C	5.080e^-6	0.096	INTRON CG7191
2R	18885976	2R_18885976_DEL [dm3] 2R_22998453_DEL [dm6]	AA	A	5.428e^-6	0.096	INTRON twi & 1 other
2L	9349017	2L_9349017_SNP [dm3] 2L_9349017_SNP [dm6]	T	C	5.428e^-6	0.096	UPSTREAM CG43350 EXON CR44802
2R	18318828	2R_18318828_SNP [dm3] 2R_22431323_SNP [dm6]	G	A	5.473e^-6	0.096	INTERGENIC

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By genomic position
Variant impact
Gene name

Microbiota_OTU016 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results