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=1.771e^-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

Covariate	p-value	Significance
In_2L_t	0.05824

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
wolba	2.8968	0.0888

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

4850 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	6310552	3R_6310552_SNP [dm3] 3R_10484830_SNP [dm6]	T	A	3.235e^-10	6.019e^-4	INTERGENIC	TF binding site mE1_TFBS_cad
X	13546773	X_13546773_SNP [dm3] X_13652740_SNP [dm6]	T	A	6.139e^-9	0.004	INTRON NFAT	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
X	13546786	X_13546786_SNP [dm3] X_13652753_SNP [dm6]	A	C	6.139e^-9	0.004	INTRON NFAT	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
X	13546822	X_13546822_SNP [dm3] X_13652789_SNP [dm6]	A	T	8.060e^-9	0.004	INTRON NFAT	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA
X	13546673	X_13546673_SNP [dm3] X_13652640_SNP [dm6]	A	G	9.968e^-9	0.004	INTRON NFAT	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
3R	6269077	3R_6269077_DEL [dm3] 3R_10443355_DEL [dm6]	AA	A	4.886e^-8	0.01	INTERGENIC
X	15336941	X_15336941_SNP [dm3] X_15442908_SNP [dm6]	T	A	5.696e^-8	0.01	INTERGENIC
X	15337231	X_15337231_SNP [dm3] X_15443198_SNP [dm6]	C	T	5.696e^-8	0.01	INTERGENIC
3R	4806578	3R_4806578_SNP [dm3] 3R_8980856_SNP [dm6]	C	A	6.088e^-8	0.01	UPSTREAM CAHbeta INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
3R	6269871	3R_6269871_SNP [dm3] 3R_10444149_SNP [dm6]	C	G	6.817e^-8	0.01	INTERGENIC
3R	4837047	3R_4837047_SNP [dm3] 3R_9011325_SNP [dm6]	A	T	6.859e^-8	0.01	INTRON CG11984	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3R	4815968	3R_4815968_SNP [dm3] 3R_8990246_SNP [dm6]	G	C	7.847e^-8	0.01	NON_SYNONYMOUS_CODING CG11970 DOWNSTREAM E_var_3-9
3R	4817823	3R_4817823_SNP [dm3] 3R_8992101_SNP [dm6]	G	A	7.847e^-8	0.01	NON_SYNONYMOUS_CODING E_var_3-9	TF binding site BDTNP1_TFBS_Med mE1_TFBS_sens
X	15335426	X_15335426_SNP [dm3] X_15441393_SNP [dm6]	G	A	8.395e^-8	0.01	UPSTREAM Cngl INTERGENIC	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	4801916	3R_4801916_SNP [dm3] 3R_8976194_SNP [dm6]	G	T	8.435e^-8	0.01	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_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_eve mE1_TFBS_HSA mE1_TFBS_Kr
3R	4801289	3R_4801289_SNP [dm3] 3R_8975567_SNP [dm6]	C	T	8.512e^-8	0.01	INTERGENIC	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_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Kr
3R	4822806	3R_4822806_SNP [dm3] 3R_8997084_SNP [dm6]	C	T	9.777e^-8	0.01	UPSTREAM CG11977 INTRON CG31100
X	13546717	X_13546717_SNP [dm3] X_13652684_SNP [dm6]	A	G	9.954e^-8	0.01	INTRON NFAT	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
3R	10852253	3R_10852253_SNP [dm3] 3R_15026531_SNP [dm6]	C	T	1.072e^-7	0.01	INTERGENIC
3R	4820467	3R_4820467_SNP [dm3] 3R_8994745_SNP [dm6]	T	A	1.096e^-7	0.01	UTR_3_PRIME CG11975 DOWNSTREAM CG31100
3R	4823780	3R_4823780_SNP [dm3] 3R_8998058_SNP [dm6]	G	A	1.096e^-7	0.01	NON_SYNONYMOUS_CODING CG11977 INTRON CG31100
3R	4802597	3R_4802597_SNP [dm3] 3R_8976875_SNP [dm6]	G	A	1.271e^-7	0.01	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Kr
3R	4806554	3R_4806554_SNP [dm3] 3R_8980832_SNP [dm6]	C	G	1.291e^-7	0.01	UPSTREAM CAHbeta INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
3R	6310553	3R_6310553_DEL [dm3] 3R_10484831_DEL [dm6]	CACCCCATCATCC...	C	1.521e^-7	0.012	INTERGENIC	TF binding site mE1_TFBS_cad
3R	4826860	3R_4826860_SNP [dm3] 3R_9001138_SNP [dm6]	G	T	1.631e^-7	0.012	INTRON CG31100
3R	4826964	3R_4826964_SNP [dm3] 3R_9001242_SNP [dm6]	A	G	1.631e^-7	0.012	INTRON CG31100
2L	8847267	2L_8847267_SNP [dm3] 2L_8847267_SNP [dm6]	C	G	1.826e^-7	0.012	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_disco mE1_TFBS_HSA
3R	10851092	3R_10851092_SNP [dm3] 3R_15025370_SNP [dm6]	C	A	1.912e^-7	0.012	INTERGENIC
3L	6807580	3L_6807580_SNP [dm3] 3L_6814480_SNP [dm6]	C	T	2.010e^-7	0.012	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_Trl
3R	10851234	3R_10851234_SNP [dm3] 3R_15025512_SNP [dm6]	G	C	2.052e^-7	0.012	INTERGENIC
3R	10851500	3R_10851500_SNP [dm3] 3R_15025778_SNP [dm6]	A	G	2.052e^-7	0.012	INTERGENIC
3R	10851117	3R_10851117_SNP [dm3] 3R_15025395_SNP [dm6]	A	G	2.052e^-7	0.012	INTERGENIC
3R	4823553	3R_4823553_SNP [dm3] 3R_8997831_SNP [dm6]	C	G	2.451e^-7	0.014	INTRON CG31100 & 1 other
2R	6506247	2R_6506247_DEL [dm3] 2R_10618742_DEL [dm6]	AA	A	2.960e^-7	0.016	INTRON CG11883	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
3L	15732484	3L_15732484_SNP [dm3] 3L_15739384_SNP [dm6]	G	A	2.988e^-7	0.016	INTERGENIC
3L	16701502	3L_16701502_SNP [dm3] 3L_16708402_SNP [dm6]	C	A	3.107e^-7	0.016	INTRON Lasp & 1 other
3R	10014982	3R_10014982_SNP [dm3] 3R_14189260_SNP [dm6]	C	T	3.239e^-7	0.016	INTRON Dop1R1
3L	567556	3L_567556_SNP [dm3] 3L_567556_SNP [dm6]	G	A	3.255e^-7	0.016	INTRON hipk
3L	16818936	3L_16818936_SNP [dm3] 3L_16825836_SNP [dm6]	T	A	3.801e^-7	0.018	INTRON CG13024
3R	10859063	3R_10859063_SNP [dm3] 3R_15033341_SNP [dm6]	T	A	3.893e^-7	0.018	INTERGENIC
3R	8140244	3R_8140244_SNP [dm3] 3R_12314522_SNP [dm6]	T	C	3.931e^-7	0.018	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	6692399	3R_6692399_SNP [dm3] 3R_10866677_SNP [dm6]	G	A	4.363e^-7	0.019	SYNONYMOUS_CODING SelR	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	18482203	3R_18482203_SNP [dm3] 3R_22656481_SNP [dm6]	T	A	4.429e^-7	0.019	INTRON CG45058
3R	9988295	3R_9988295_SNP [dm3] 3R_14162573_SNP [dm6]	G	A	4.699e^-7	0.02	UPSTREAM CG3199 INTERGENIC
3R	4243979	3R_4243979_SNP [dm3] 3R_8418257_SNP [dm6]	T	G	4.780e^-7	0.02	INTRON CG45263
3L	12845668	3L_12845668_SNP [dm3] 3L_12852568_SNP [dm6]	A	G	5.047e^-7	0.02	DOWNSTREAM Wbp2 INTRON Wbp2
X	10957741	X_10957741_DEL [dm3] X_11063708_DEL [dm6]	TGCA	T	5.354e^-7	0.021	UPSTREAM CG1537 INTERGENIC
3R	5450555	3R_5450555_SNP [dm3] 3R_9624833_SNP [dm6]	G	A	5.575e^-7	0.021	UTR_3_PRIME CG8312 DOWNSTREAM CG9427	TF binding site BDTNP1_TFBS_sna BDTNP1_TFBS_twi
3R	10850965	3R_10850965_SNP [dm3] 3R_15025243_SNP [dm6]	A	C	5.653e^-7	0.021	INTERGENIC
3R	6310539	3R_6310539_DEL [dm3] 3R_10484817_DEL [dm6]	GCTCACA	G	7.082e^-7	0.026	INTERGENIC	TF binding site mE1_TFBS_cad
3R	14652073	3R_14652073_DEL [dm3] 3R_18826351_DEL [dm6]	CG	C	8.562e^-7	0.031	INTRON CG18208
X	13576453	X_13576453_DEL [dm3] X_13682420_DEL [dm6]	AAAATCAGCTTA...	A	9.764e^-7	0.035	UPSTREAM CG11158 INTERGENIC
2L	11190066	2L_11190066_SNP [dm3] 2L_11190066_SNP [dm6]	G	A	9.885e^-7	0.035	INTRON Ca-beta	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	14780321	X_14780321_SNP [dm3] X_14886288_SNP [dm6]	C	T	1.156e^-6	0.04	UTR_3_PRIME CG9514 INTRON Flo2	TF binding site mE1_TFBS_chinmo
3L	6807742	3L_6807742_SNP [dm3] 3L_6814642_SNP [dm6]	G	T	1.175e^-6	0.04	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_chinmo mE1_TFBS_HSA
3R	10789177	3R_10789177_SNP [dm3] 3R_14963455_SNP [dm6]	G	A	1.203e^-6	0.04	INTERGENIC
3L	17311406	3L_17311406_SNP [dm3] 3L_17318306_SNP [dm6]	A	G	1.266e^-6	0.041	INTERGENIC
3R	6020356	3R_6020356_SNP [dm3] 3R_10194634_SNP [dm6]	A	T	1.467e^-6	0.044	INTRON Syn
X	15336058	X_15336058_SNP [dm3] X_15442025_SNP [dm6]	T	C	1.490e^-6	0.044	UPSTREAM Cngl INTERGENIC
X	15336059	X_15336059_SNP [dm3] X_15442026_SNP [dm6]	G	A	1.490e^-6	0.044	UPSTREAM Cngl INTERGENIC
3R	10865964	3R_10865964_INS [dm3] 3R_15040242_INS [dm6]	A	AA	1.546e^-6	0.044	DOWNSTREAM CR44944 INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	9802372	2R_9802372_SNP [dm3] 2R_13914867_SNP [dm6]	A	T	1.615e^-6	0.044	INTRON shot
X	15337193	X_15337193_INS [dm3] X_15443160_INS [dm6]	T	TAAATGCTTTAAATAAATGC...	1.629e^-6	0.044	INTERGENIC
2L	20660246	2L_20660246_SNP [dm3] 2L_20660246_SNP [dm6]	G	T	1.631e^-6	0.044	SYNONYMOUS_CODING CG31678	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3R	4799846	3R_4799846_SNP [dm3] 3R_8974124_SNP [dm6]	C	G	1.652e^-6	0.044	INTERGENIC
3R	4802404	3R_4802404_SNP [dm3] 3R_8976682_SNP [dm6]	T	C	1.652e^-6	0.044	INTERGENIC	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_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Kr
3R	4804535	3R_4804535_SNP [dm3] 3R_8978813_SNP [dm6]	T	C	1.652e^-6	0.044	INTERGENIC	TF binding site BDTNP1_TFBS_dl
3R	4806703	3R_4806703_SNP [dm3] 3R_8980981_SNP [dm6]	T	C	1.652e^-6	0.044	UTR_5_PRIME CAHbeta	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
3R	6247377	3R_6247377_SNP [dm3] 3R_10421655_SNP [dm6]	G	A	1.693e^-6	0.044	INTERGENIC
2R	6524696	2R_6524696_SNP [dm3] 2R_10637191_SNP [dm6]	T	C	1.695e^-6	0.044	INTRON CG11883
3R	16904402	3R_16904402_SNP [dm3] 3R_21078680_SNP [dm6]	T	C	1.704e^-6	0.044	INTRON HHEX
2L	7955222	2L_7955222_SNP [dm3] 2L_7955222_SNP [dm6]	A	T	1.734e^-6	0.044	INTRON Snoo
3L	15863770	3L_15863770_SNP [dm3] 3L_15870670_SNP [dm6]	C	T	1.762e^-6	0.044	NON_SYNONYMOUS_CODING pHCl	TF binding site mE1_TFBS_cad
2L	13147743	2L_13147743_SNP [dm3] 2L_13147743_SNP [dm6]	T	C	1.782e^-6	0.044	DOWNSTREAM CR44199 INTERGENIC
3R	4888057	3R_4888057_SNP [dm3] 3R_9062335_SNP [dm6]	G	T	1.803e^-6	0.044	UTR_3_PRIME Kdm2 DOWNSTREAM beag	TF binding site mE1_TFBS_cad
X	15336929	X_15336929_SNP [dm3] X_15442896_SNP [dm6]	A	C	1.832e^-6	0.044	INTERGENIC
X	15336944	X_15336944_SNP [dm3] X_15442911_SNP [dm6]	C	T	1.832e^-6	0.044	INTERGENIC
2L	7485073	2L_7485073_SNP [dm3] 2L_7485073_SNP [dm6]	G	A	1.862e^-6	0.044	INTRON Ziz
3R	10609797	3R_10609797_SNP [dm3] 3R_14784075_SNP [dm6]	A	C	1.885e^-6	0.044	INTRON jvl
3R	10864690	3R_10864690_SNP [dm3] 3R_15038968_SNP [dm6]	T	C	1.915e^-6	0.044	DOWNSTREAM RpL10Aa EXON CR44944	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	5549884	2L_5549884_SNP [dm3] 2L_5549884_SNP [dm6]	G	A	1.931e^-6	0.044	SYNONYMOUS_CODING CG14014 DOWNSTREAM Oscillin	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_twi
3L	20065100	3L_20065100_SNP [dm3] 3L_20072000_SNP [dm6]	T	C	1.939e^-6	0.044	INTRON sNPF-R	TF binding site mE1_TFBS_chinmo
3R	14594357	3R_14594357_SNP [dm3] 3R_18768635_SNP [dm6]	A	T	1.984e^-6	0.044	INTRON CG7720
3R	12709396	3R_12709396_SNP [dm3] 3R_16883674_SNP [dm6]	T	A	2.002e^-6	0.044	INTRON iab-8	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_gt
3R	4824360	3R_4824360_SNP [dm3] 3R_8998638_SNP [dm6]	A	C	2.025e^-6	0.044	SYNONYMOUS_CODING CG11977 INTRON CG31100
X	15336946	X_15336946_INS [dm3] X_15442913_INS [dm6]	A	TC	2.088e^-6	0.044	INTERGENIC
X	15336960	X_15336960_SNP [dm3] X_15442927_SNP [dm6]	A	T	2.088e^-6	0.044	INTERGENIC
2L	19833109	2L_19833109_SNP [dm3] 2L_19833109_SNP [dm6]	G	T	2.122e^-6	0.044	INTRON sick
X	5903923	X_5903923_SNP [dm3] X_6009890_SNP [dm6]	T	A	2.164e^-6	0.044	INTRON mab-21
2L	10958104	2L_10958104_SNP [dm3] 2L_10958104_SNP [dm6]	A	T	2.185e^-6	0.044	INTRON dpr2	TF binding site BDTNP1_TFBS_twi
3R	4807098	3R_4807098_SNP [dm3] 3R_8981376_SNP [dm6]	C	A	2.255e^-6	0.044	INTRON CAHbeta	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
X	15336936	X_15336936_SNP [dm3] X_15442903_SNP [dm6]	A	T	2.276e^-6	0.044	INTERGENIC
3R	4847172	3R_4847172_SNP [dm3] 3R_9021450_SNP [dm6]	C	T	2.287e^-6	0.044	UTR_3_PRIME neur UPSTREAM CR31429	TF binding site BDTNP1_TFBS_twi
3R	4848076	3R_4848076_SNP [dm3] 3R_9022354_SNP [dm6]	G	T	2.287e^-6	0.044	NON_SYNONYMOUS_CODING neur EXON CR31429	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3R	4851259	3R_4851259_SNP [dm3] 3R_9025537_SNP [dm6]	A	C	2.287e^-6	0.044	INTRON neur	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3R	14577770	3R_14577770_SNP [dm3] 3R_18752048_SNP [dm6]	C	G	2.346e^-6	0.044	SYNONYMOUS_CODING CG14299
X	12362318	X_12362318_SNP [dm3] X_12468285_SNP [dm6]	C	T	2.353e^-6	0.044	INTRON CG42258	TF binding site mE1_TFBS_HSA
3R	4810104	3R_4810104_SNP [dm3] 3R_8984382_SNP [dm6]	A	T	2.356e^-6	0.044	UPSTREAM CG11970 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_Ubx
4	911848	4_911848_SNP [dm3] 4_891222_SNP [dm6]	T	G	2.364e^-6	0.044	SYNONYMOUS_CODING unc-13 INTRON unc-13
3L	7046082	3L_7046082_SNP [dm3] 3L_7052982_SNP [dm6]	T	G	2.436e^-6	0.045	UTR_3_PRIME Mp DOWNSTREAM Mp

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By genomic position
Variant impact
Gene name

Microbiota_OTU115 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results