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=4.809e^-5)
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	0.0188987
In_3R_Mo	0.0749795

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_3R_Mo	5.0955	0.0783

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1768 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	8371319	2L_8371319_INS [dm3] 2L_8371319_INS [dm6]	A	ATCTA	1.302e^-6	0.946	UPSTREAM CR45341 INTRON CG17292
3R	9973092	3R_9973092_SNP [dm3] 3R_14147370_SNP [dm6]	A	T	2.989e^-6	0.946	INTERGENIC
2R	2882279	2R_2882279_SNP [dm3] 2R_6994774_SNP [dm6]	T	C	3.267e^-6	0.946	DOWNSTREAM CG30159 INTRON Tsp42Ea	TF binding site mE1_TFBS_Trl
2L	8398451	2L_8398451_DEL [dm3] 2L_8398451_DEL [dm6]	CAATAC	C	6.146e^-6	0.946	UPSTREAM CG13386 DOWNSTREAM CG13385 INTERGENIC
3L	5350075	3L_5350075_SNP [dm3] 3L_5356975_SNP [dm6]	A	G	8.389e^-6	0.946	UTR_3_PRIME Klp64D UPSTREAM tRNA:CR32421 DOWNSTREAM tRNA:CR32420
X	16226823	X_16226823_SNP [dm3] X_16332790_SNP [dm6]	A	C	9.196e^-6	0.946	UPSTREAM CG9921 & 1 other INTRON CG9921	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_Trl mE1_TFBS_zfh1
3L	4357029	3L_4357029_SNP [dm3] 3L_4357029_SNP [dm6]	C	G	1.163e^-5	0.946	INTRON Cip4
3R	9855212	3R_9855212_SNP [dm3] 3R_14029490_SNP [dm6]	T	A	1.167e^-5	0.946	SYNONYMOUS_CODING Cyp6d5 INTRON rdx	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb mE1_TFBS_HSA mE1_TFBS_sens
2R	2570058	2R_2570058_SNP [dm3] 2R_6682553_SNP [dm6]	C	T	1.178e^-5	0.946	UPSTREAM CG15909 DOWNSTREAM CR44164 INTRON CG9422 EXON CR44165
X	3136845	X_3136845_SNP [dm3] X_3242812_SNP [dm6]	A	G	1.257e^-5	0.946	UTR_3_PRIME ng1 UPSTREAM ng3 INTRON dnc
3L	4722156	3L_4722156_SNP [dm3] 3L_4722156_SNP [dm6]	T	A	1.304e^-5	0.946	INTRON RhoGEF64C
3L	7221082	3L_7221082_SNP [dm3] 3L_7227982_SNP [dm6]	T	A	1.500e^-5	0.946	INTERGENIC
X	3875217	X_3875217_SNP [dm3] X_3981184_SNP [dm6]	G	C	1.563e^-5	0.946	INTERGENIC
2L	15759696	2L_15759696_SNP [dm3] 2L_15759696_SNP [dm6]	G	A	1.578e^-5	0.946	SYNONYMOUS_CODING Gli	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2L	21882791	2L_21882791_SNP [dm3] 2L_21882791_SNP [dm6]	G	C	1.596e^-5	0.946	INTERGENIC
3R	11181742	3R_11181742_SNP [dm3] 3R_15356020_SNP [dm6]	C	T	1.672e^-5	0.946	SYNONYMOUS_CODING Atg4b	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3R	14239542	3R_14239542_INS [dm3] 3R_18413820_INS [dm6]	C	CCATCAGAAAAGTAAACTAG...	1.907e^-5	0.946	UPSTREAM CG31122 DOWNSTREAM fru INTERGENIC	TF binding site BDTNP1_TFBS_dl
X	15486296	X_15486296_INS [dm3] X_15592263_INS [dm6]	G	GAGG	1.944e^-5	0.946	INTRON CG9220	TF binding site BDTNP1_TFBS_dl
3R	14856001	3R_14856001_SNP [dm3] 3R_19030279_SNP [dm6]	T	C	2.010e^-5	0.946	SYNONYMOUS_CODING Prp18 DOWNSTREAM P5cr	TF binding site mE1_TFBS_cad mE1_TFBS_sens
X	8471036	X_8471036_SNP [dm3] X_8577003_SNP [dm6]	G	T	2.030e^-5	0.946	INTRON CG12065
2R	6726485	2R_6726485_SNP [dm3] 2R_10838980_SNP [dm6]	A	C	2.033e^-5	0.946	UPSTREAM CG7686 DOWNSTREAM CG30015 INTERGENIC	TF binding site BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	12175390	3L_12175390_SNP [dm3] 3L_12182290_SNP [dm6]	T	C	2.145e^-5	0.946	SYNONYMOUS_CODING CAH2
3L	12173728	3L_12173728_SNP [dm3] 3L_12180628_SNP [dm6]	T	C	2.270e^-5	0.946	INTRON CAH2
3L	16872533	3L_16872533_SNP [dm3] 3L_16879433_SNP [dm6]	C	T	2.309e^-5	0.946	DOWNSTREAM CG32170 INTRON Lmpt
X	3136851	X_3136851_SNP [dm3] X_3242818_SNP [dm6]	G	C	2.425e^-5	0.946	UTR_3_PRIME ng1 UPSTREAM ng3 INTRON dnc
2L	11295413	2L_11295413_SNP [dm3] 2L_11295413_SNP [dm6]	C	A	2.491e^-5	0.946	INTERGENIC
2R	6555381	2R_6555381_SNP [dm3] 2R_10667876_SNP [dm6]	C	T	2.527e^-5	0.946	INTERGENIC
3R	16005337	3R_16005337_INS [dm3] 3R_20179615_INS [dm6]	A	ATGTA	2.865e^-5	0.946	INTERGENIC	TF binding site mE1_TFBS_sbb
3L	10241531	3L_10241531_INS [dm3] 3L_10248431_INS [dm6]	C	CTTTTTTTGTT...	2.947e^-5	0.946	DOWNSTREAM CR44539 EXON CR44540
3R	9868203	3R_9868203_SNP [dm3] 3R_14042481_SNP [dm6]	G	C	3.031e^-5	0.946	INTERGENIC
2L	20336420	2L_20336420_SNP [dm3] 2L_20336420_SNP [dm6]	G	A	3.033e^-5	0.946	INTRON spir
3L	16673300	3L_16673300_SNP [dm3] 3L_16680200_SNP [dm6]	G	A	3.040e^-5	0.946	INTRON Lasp & 1 other	TF binding site BDTNP1_TFBS_dl
2R	17772302	2R_17772302_INS [dm3] 2R_21884797_INS [dm6]	A	AA	3.041e^-5	0.946	INTRON Fili	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	11292363	2L_11292363_SNP [dm3] 2L_11292363_SNP [dm6]	G	A	3.120e^-5	0.946	INTERGENIC
X	17346119	X_17346119_SNP [dm3] X_17452086_SNP [dm6]	A	G	3.140e^-5	0.946	SYNONYMOUS_CODING CG8568
3R	12922495	3R_12922495_SNP [dm3] 3R_17096773_SNP [dm6]	A	G	3.199e^-5	0.946	INTRON cher
2R	5801867	2R_5801867_SNP [dm3] 2R_9914362_SNP [dm6]	G	A	3.199e^-5	0.946	UTR_3_PRIME Mef2 DOWNSTREAM Etf-QO
3R	15992223	3R_15992223_SNP [dm3] 3R_20166501_SNP [dm6]	A	G	3.287e^-5	0.946	INTERGENIC
3L	7395815	3L_7395815_SNP [dm3] 3L_7402715_SNP [dm6]	C	A	3.329e^-5	0.946	INTRON CG8560	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	12306884	3L_12306884_SNP [dm3] 3L_12313784_SNP [dm6]	C	T	3.381e^-5	0.946	INTERGENIC
2L	20331677	2L_20331677_SNP [dm3] 2L_20331677_SNP [dm6]	A	G	3.447e^-5	0.946	INTRON spir
3R	16005541	3R_16005541_SNP [dm3] 3R_20179819_SNP [dm6]	G	T	3.457e^-5	0.946	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2L	8098939	2L_8098939_SNP [dm3] 2L_8098939_SNP [dm6]	T	C	3.654e^-5	0.946	INTRON Bsg	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad
3L	16673400	3L_16673400_SNP [dm3] 3L_16680300_SNP [dm6]	G	A	3.742e^-5	0.946	INTRON Lasp & 1 other
3L	8115095	3L_8115095_SNP [dm3] 3L_8121995_SNP [dm6]	T	A	3.869e^-5	0.946	NON_SYNONYMOUS_CODING ldbr DOWNSTREAM msk	TF binding site BDTNP1_TFBS_Med mE1_TFBS_HSA
2L	8113189	2L_8113189_SNP [dm3] 2L_8113189_SNP [dm6]	C	A	3.988e^-5	0.946	UTR_3_PRIME Bsg
3R	25451499	3R_25451499_SNP [dm3] 3R_29625777_SNP [dm6]	A	G	3.995e^-5	0.946	INTERGENIC	TF binding site mE1_TFBS_chinmo
3L	10287406	3L_10287406_SNP [dm3] 3L_10294306_SNP [dm6]	C	G	4.087e^-5	0.946	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	8895277	3L_8895277_SNP [dm3] 3L_8902177_SNP [dm6]	G	A	4.395e^-5	0.946	UPSTREAM TrpA1 INTRON TrpA1
3L	12478358	3L_12478358_SNP [dm3] 3L_12485258_SNP [dm6]	C	T	4.400e^-5	0.946	UPSTREAM CG33725 & 1 other INTRON CG33725	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
X	18358953	X_18358953_SNP [dm3] X_18464920_SNP [dm6]	C	G	4.421e^-5	0.946	INTRON CG32547	TF binding site mE1_TFBS_chinmo
2R	16042681	2R_16042681_SNP [dm3] 2R_20155176_SNP [dm6]	C	A	4.423e^-5	0.946	INTERGENIC
2L	8371537	2L_8371537_SNP [dm3] 2L_8371537_SNP [dm6]	T	A	4.513e^-5	0.946	UPSTREAM CR45341 & 1 other INTRON CG17292
3L	10712198	3L_10712198_SNP [dm3] 3L_10719098_SNP [dm6]	G	A	4.736e^-5	0.946	INTERGENIC
2L	4073253	2L_4073253_SNP [dm3] 2L_4073253_SNP [dm6]	C	G	4.757e^-5	0.946	INTRON ed
2L	8234171	2L_8234171_SNP [dm3] 2L_8234171_SNP [dm6]	C	T	4.771e^-5	0.946	INTRON Pvr
3R	11342771	3R_11342771_DEL [dm3] 3R_15517049_DEL [dm6]	TCTCCACAGACT...	T	4.779e^-5	0.946	INTERGENIC	TF binding site mE1_TFBS_chinmo
X	5582697	X_5582697_SNP [dm3] X_5688664_SNP [dm6]	C	G	4.999e^-5	0.946	SYNONYMOUS_CODING CG3160	TF binding site BDTNP1_TFBS_dl mE1_TFBS_sens
3L	11804001	3L_11804001_SNP [dm3] 3L_11810901_SNP [dm6]	A	T	5.023e^-5	0.946	SYNONYMOUS_CODING CG42255
3L	18820962	3L_18820962_SNP [dm3] 3L_18827862_SNP [dm6]	C	T	5.127e^-5	0.946	SYNONYMOUS_CODING Cat DOWNSTREAM Indy	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA
3R	18531658	3R_18531658_SNP [dm3] 3R_22705936_SNP [dm6]	G	A	5.141e^-5	0.946	SYNONYMOUS_CODING CG13842
3L	20587062	3L_20587062_SNP [dm3] 3L_20593962_SNP [dm6]	T	C	5.350e^-5	0.946	INTERGENIC
3L	3823377	3L_3823377_SNP [dm3] 3L_3823377_SNP [dm6]	T	C	5.367e^-5	0.946	INTRON enc	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
3R	12386148	3R_12386148_SNP [dm3] 3R_16560426_SNP [dm6]	C	G	5.450e^-5	0.946	INTRON CG42342	TF binding site BDTNP1_TFBS_twi
2L	3238057	2L_3238057_SNP [dm3] 2L_3238057_SNP [dm6]	C	T	5.473e^-5	0.946	INTERGENIC
X	9507713	X_9507713_SNP [dm3] X_9613680_SNP [dm6]	C	G	5.527e^-5	0.946	INTRON CG42797
X	9507717	X_9507717_SNP [dm3] X_9613684_SNP [dm6]	T	G	5.527e^-5	0.946	INTRON CG42797
2L	8372336	2L_8372336_SNP [dm3] 2L_8372336_SNP [dm6]	C	A	5.586e^-5	0.946	UPSTREAM CG17292 INTRON CG17292
3R	26620810	3R_26620810_SNP [dm3] 3R_30795088_SNP [dm6]	C	T	5.806e^-5	0.946	INTRON wts	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2L	11296751	2L_11296751_SNP [dm3] 2L_11296751_SNP [dm6]	T	A	5.902e^-5	0.946	INTERGENIC	TF binding site BDTNP1_TFBS_prd
3R	25264539	3R_25264539_SNP [dm3] 3R_29438817_SNP [dm6]	T	A	6.004e^-5	0.946	INTRON Ptp99A
3L	10427905	3L_10427905_SNP [dm3] 3L_10434805_SNP [dm6]	C	T	6.040e^-5	0.946	UPSTREAM Ir67c INTERGENIC
3L	7200704	3L_7200704_SNP [dm3] 3L_7207604_SNP [dm6]	C	G	6.050e^-5	0.946	INTERGENIC
2R	11472329	2R_11472329_SNP [dm3] 2R_15584824_SNP [dm6]	T	A	6.080e^-5	0.946	INTERGENIC
3R	25069064	3R_25069064_SNP [dm3] 3R_29243342_SNP [dm6]	A	G	6.116e^-5	0.946	INTRON CG31445
2L	16794067	2L_16794067_SNP [dm3] 2L_16794067_SNP [dm6]	G	A	6.175e^-5	0.946	UPSTREAM Ugt36Ba DOWNSTREAM CG17928 INTERGENIC	TF binding site mE1_TFBS_Trl
X	6728895	X_6728895_SNP [dm3] X_6834862_SNP [dm6]	T	C	6.177e^-5	0.946	SYNONYMOUS_CODING nonC	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3R	12210089	3R_12210089_SNP [dm3] 3R_16384367_SNP [dm6]	C	T	6.200e^-5	0.946	INTRON ss	regulatory region REDfly_CRMs
3R	5307674	3R_5307674_SNP [dm3] 3R_9481952_SNP [dm6]	C	G	6.235e^-5	0.946	INTRON CG16779
X	16160435	X_16160435_SNP [dm3] X_16266402_SNP [dm6]	A	G	6.248e^-5	0.946	SYNONYMOUS_CODING CG12507 DOWNSTREAM kat80
2R	13505616	2R_13505616_DEL [dm3] 2R_17618111_DEL [dm6]	CC	C	6.332e^-5	0.946	UPSTREAM CG44403 INTRON CG10936
X	20847874	X_20847874_SNP [dm3] X_20976847_SNP [dm6]	T	C	6.366e^-5	0.946	INTERGENIC
X	8471071	X_8471071_SNP [dm3] X_8577038_SNP [dm6]	C	A	6.586e^-5	0.946	INTRON CG12065
3R	25451580	3R_25451580_SNP [dm3] 3R_29625858_SNP [dm6]	C	A	6.642e^-5	0.946	INTERGENIC	TF binding site mE1_TFBS_chinmo
3R	25451581	3R_25451581_SNP [dm3] 3R_29625859_SNP [dm6]	C	A	6.642e^-5	0.946	INTERGENIC	TF binding site mE1_TFBS_chinmo
3R	10047101	3R_10047101_SNP [dm3] 3R_14221379_SNP [dm6]	C	T	6.651e^-5	0.946	SYNONYMOUS_CODING CG33109 DOWNSTREAM Sp212
3R	25460307	3R_25460307_SNP [dm3] 3R_29634585_SNP [dm6]	T	C	6.698e^-5	0.946	INTRON Dop1R2
2L	8353554	2L_8353554_SNP [dm3] 2L_8353554_SNP [dm6]	C	T	6.718e^-5	0.946	INTRON Mur29B	TF binding site mE1_TFBS_sens
2L	6488827	2L_6488827_SNP [dm3] 2L_6488827_SNP [dm6]	A	C	6.720e^-5	0.946	UPSTREAM epsilonCOP & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Ubx
3L	12478303	3L_12478303_SNP [dm3] 3L_12485203_SNP [dm6]	G	T	6.774e^-5	0.946	UPSTREAM CG33725 & 1 other INTRON CG33725	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	8378512	2L_8378512_SNP [dm3] 2L_8378512_SNP [dm6]	T	C	6.828e^-5	0.946	SYNONYMOUS_CODING Aats-ala DOWNSTREAM CG17294	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	1508198	2L_1508198_SNP [dm3] 2L_1508198_SNP [dm6]	C	T	6.843e^-5	0.946	INTERGENIC	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	10414181	3L_10414181_SNP [dm3] 3L_10421081_SNP [dm6]	T	C	6.940e^-5	0.946	INTERGENIC
2L	13433604	2L_13433604_SNP [dm3] 2L_13433604_SNP [dm6]	G	C	6.987e^-5	0.946	INTRON CG42784
3L	7921417	3L_7921417_SNP [dm3] 3L_7928317_SNP [dm6]	G	T	7.157e^-5	0.946	SYNONYMOUS_CODING syd	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2L	20336415	2L_20336415_SNP [dm3] 2L_20336415_SNP [dm6]	C	G	7.333e^-5	0.946	INTRON spir
3R	15051899	3R_15051899_SNP [dm3] 3R_19226177_SNP [dm6]	T	G	7.390e^-5	0.946	DOWNSTREAM CG11703 INTRON vib	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_prd mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_hkb mE1_TFBS_HSA mE1_TFBS_Trl
3R	12897186	3R_12897186_SNP [dm3] 3R_17071464_SNP [dm6]	T	A	7.400e^-5	0.946	SYNONYMOUS_CODING Ns1
3R	12897210	3R_12897210_SNP [dm3] 3R_17071488_SNP [dm6]	G	A	7.400e^-5	0.946	SYNONYMOUS_CODING Ns1
3R	12904883	3R_12904883_SNP [dm3] 3R_17079161_SNP [dm6]	A	G	7.422e^-5	0.946	INTRON Keap1	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_Trl mE1_TFBS_zfh1

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By genomic position
Variant impact
Gene name

Microbiota_OTU160 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results