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=5.130e^-12)
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

3448 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	4243979	3R_4243979_SNP [dm3] 3R_8418257_SNP [dm6]	T	G	2.976e^-10	2.751e^-4	INTRON CG45263
3R	4244453	3R_4244453_SNP [dm3] 3R_8418731_SNP [dm6]	G	A	4.437e^-10	2.751e^-4	INTRON CG45263
3R	4244456	3R_4244456_DEL [dm3] 3R_8418734_DEL [dm6]	AGACAACTATCATTTGCTTT...	A	4.437e^-10	2.751e^-4	INTRON CG45263
3R	4254654	3R_4254654_SNP [dm3] 3R_8428932_SNP [dm6]	T	A	6.222e^-10	2.894e^-4	INTRON CG45263
3R	4249440	3R_4249440_SNP [dm3] 3R_8423718_SNP [dm6]	A	T	3.098e^-9	0.001	INTRON CG45263
3R	4249357	3R_4249357_SNP [dm3] 3R_8423635_SNP [dm6]	G	C	3.355e^-9	0.001	INTRON CG45263
2R	11750561	2R_11750561_SNP [dm3] 2R_15863056_SNP [dm6]	T	G	4.815e^-9	0.001	UPSTREAM Gpo-1 INTERGENIC	TF binding site BDTNP1_TFBS_dl
3R	4244441	3R_4244441_DEL [dm3] 3R_8418719_DEL [dm6]	GATACAGCAAA...	G	6.669e^-9	0.002	INTRON CG45263
2L	13437368	2L_13437368_SNP [dm3] 2L_13437368_SNP [dm6]	A	G	8.817e^-9	0.002	DOWNSTREAM CR45683 INTRON CG42784 & 1 other
2L	20531806	2L_20531806_DEL [dm3] 2L_20531806_DEL [dm6]	AA	A	1.860e^-8	0.003	UTR_3_PRIME CG44270
2R	16498623	2R_16498623_SNP [dm3] 2R_20611118_SNP [dm6]	G	T	2.160e^-8	0.004	INTRON Hil
2L	13071572	2L_13071572_SNP [dm3] 2L_13071572_SNP [dm6]	A	T	2.390e^-8	0.004	INTERGENIC
3R	4241479	3R_4241479_SNP [dm3] 3R_8415757_SNP [dm6]	C	T	3.390e^-8	0.005	INTRON CG45263
3R	4252841	3R_4252841_SNP [dm3] 3R_8427119_SNP [dm6]	T	C	4.200e^-8	0.005	INTRON CG45263
2L	9485911	2L_9485911_SNP [dm3] 2L_9485911_SNP [dm6]	C	T	4.332e^-8	0.005	INTERGENIC
3R	4239087	3R_4239087_SNP [dm3] 3R_8413365_SNP [dm6]	G	C	6.477e^-8	0.008	INTRON CG45263
3R	4239795	3R_4239795_SNP [dm3] 3R_8414073_SNP [dm6]	C	T	9.054e^-8	0.01	INTRON CG45263
3L	4449309	3L_4449309_SNP [dm3] 3L_4449309_SNP [dm6]	T	C	1.089e^-7	0.011	INTERGENIC
3R	9817421	3R_9817421_DEL [dm3] 3R_13991699_DEL [dm6]	AA	A	1.158e^-7	0.011	INTRON rdx
2L	19833264	2L_19833264_SNP [dm3] 2L_19833264_SNP [dm6]	A	G	1.262e^-7	0.012	INTRON sick
3R	4225435	3R_4225435_SNP [dm3] 3R_8399713_SNP [dm6]	C	T	1.391e^-7	0.012	INTRON CG45263
3R	5468480	3R_5468480_SNP [dm3] 3R_9642758_SNP [dm6]	T	C	1.857e^-7	0.016	INTRON Dh44
2L	20571051	2L_20571051_SNP [dm3] 2L_20571051_SNP [dm6]	G	C	2.345e^-7	0.018	INTRON CR45347
3R	5474860	3R_5474860_SNP [dm3] 3R_9649138_SNP [dm6]	A	T	2.379e^-7	0.018	NON_SYNONYMOUS_CODING Dh44
2R	7022382	2R_7022382_SNP [dm3] 2R_11134877_SNP [dm6]	T	A	2.653e^-7	0.019	INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_zfh1
3R	4955554	3R_4955554_SNP [dm3] 3R_9129832_SNP [dm6]	G	A	2.760e^-7	0.019	INTRON pum
2L	19833109	2L_19833109_SNP [dm3] 2L_19833109_SNP [dm6]	G	T	2.764e^-7	0.019	INTRON sick
2L	10200111	2L_10200111_SNP [dm3] 2L_10200111_SNP [dm6]	A	G	3.113e^-7	0.02	SYNONYMOUS_CODING Ripalpha UPSTREAM Sur & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
2L	11892860	2L_11892860_SNP [dm3] 2L_11892860_SNP [dm6]	T	G	3.114e^-7	0.02	INTRON Pde1c
3L	20078602	3L_20078602_SNP [dm3] 3L_20085502_SNP [dm6]	G	A	3.813e^-7	0.023	INTRON sNPF-R
3R	4248989	3R_4248989_SNP [dm3] 3R_8423267_SNP [dm6]	C	G	3.914e^-7	0.023	INTRON CG45263	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2L	20641769	2L_20641769_SNP [dm3] 2L_20641769_SNP [dm6]	G	C	4.216e^-7	0.025	UTR_3_PRIME Sfp38D DOWNSTREAM CG17470 & 1 other
2R	10860126	2R_10860126_SNP [dm3] 2R_14972621_SNP [dm6]	T	C	4.648e^-7	0.026	SYNONYMOUS_CODING ckn	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	20535232	2L_20535232_DEL [dm3] 2L_20535232_DEL [dm6]	TTT	G	4.690e^-7	0.026	INTERGENIC
X	10813791	X_10813791_SNP [dm3] X_10919758_SNP [dm6]	A	C	5.099e^-7	0.027	INTRON CG43901	TF binding site BDTNP1_TFBS_dl
X	10812640	X_10812640_SNP [dm3] X_10918607_SNP [dm6]	C	G	5.517e^-7	0.028	INTRON CG43901	TF binding site mE1_TFBS_cad
3R	4225439	3R_4225439_DEL [dm3] 3R_8399717_DEL [dm6]	TA	T	5.634e^-7	0.028	INTRON CG45263
3R	5473945	3R_5473945_SNP [dm3] 3R_9648223_SNP [dm6]	C	T	5.931e^-7	0.028	INTRON Dh44
X	15325839	X_15325839_SNP [dm3] X_15431806_SNP [dm6]	A	C	5.953e^-7	0.028	INTRON Cngl
X	10811040	X_10811040_SNP [dm3] X_10917007_SNP [dm6]	A	C	6.254e^-7	0.029	SYNONYMOUS_CODING CG43901	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	4249875	3R_4249875_SNP [dm3] 3R_8424153_SNP [dm6]	G	C	6.302e^-7	0.029	INTRON CG45263
2L	14245853	2L_14245853_SNP [dm3] 2L_14245853_SNP [dm6]	G	A	6.591e^-7	0.029	INTERGENIC
3R	4348621	3R_4348621_SNP [dm3] 3R_8522899_SNP [dm6]	A	T	6.695e^-7	0.029	NON_SYNONYMOUS_CODING CG31454
2L	9485973	2L_9485973_SNP [dm3] 2L_9485973_SNP [dm6]	T	A	7.013e^-7	0.03	INTERGENIC
2R	4784166	2R_4784166_SNP [dm3] 2R_8896661_SNP [dm6]	G	A	7.301e^-7	0.03	SYNONYMOUS_CODING Sec31	TF binding site BDTNP1_TFBS_sna mE1_TFBS_chinmo mE1_TFBS_HSA
3R	4252790	3R_4252790_SNP [dm3] 3R_8427068_SNP [dm6]	T	C	7.390e^-7	0.03	INTRON CG45263
X	10812753	X_10812753_SNP [dm3] X_10918720_SNP [dm6]	T	C	7.704e^-7	0.03	INTRON CG43901
3R	5475718	3R_5475718_SNP [dm3] 3R_9649996_SNP [dm6]	G	A	8.460e^-7	0.033	UTR_3_PRIME Dh44
3R	4239799	3R_4239799_SNP [dm3] 3R_8414077_SNP [dm6]	T	A	8.774e^-7	0.033	INTRON CG45263
2L	15863957	2L_15863957_SNP [dm3] 2L_15863957_SNP [dm6]	G	C	8.885e^-7	0.033	DOWNSTREAM CR42791 & 1 other INTERGENIC
2R	12010657	2R_12010657_SNP [dm3] 2R_16123152_SNP [dm6]	G	T	9.063e^-7	0.033	UPSTREAM CG30095 DOWNSTREAM Jhe INTERGENIC
3L	14755656	3L_14755656_SNP [dm3] 3L_14762556_SNP [dm6]	G	T	9.873e^-7	0.035	UPSTREAM CG33260 INTRON CG9384	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
X	16146855	X_16146855_SNP [dm3] X_16252822_SNP [dm6]	C	T	1.028e^-6	0.036	INTERGENIC
3R	4867877	3R_4867877_SNP [dm3] 3R_9042155_SNP [dm6]	G	T	1.110e^-6	0.038	UTR_3_PRIME hyx DOWNSTREAM Nmdmc
3R	8358365	3R_8358365_SNP [dm3] 3R_12532643_SNP [dm6]	G	C	1.140e^-6	0.038	INTRON Octbeta3R
3R	5472939	3R_5472939_INS [dm3] 3R_9647217_INS [dm6]	A	AA	1.170e^-6	0.038	INTRON Dh44
2L	17963860	2L_17963860_SNP [dm3] 2L_17963860_SNP [dm6]	T	C	1.191e^-6	0.038	INTRON btv & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_GATAe mE1_TFBS_HSA mE1_TFBS_sens
2L	19833135	2L_19833135_SNP [dm3] 2L_19833135_SNP [dm6]	A	G	1.200e^-6	0.038	INTRON sick
3R	5156128	3R_5156128_SNP [dm3] 3R_9330406_SNP [dm6]	A	G	1.278e^-6	0.038	UPSTREAM CG12951 DOWNSTREAM CG16749 INTERGENIC
3R	5156140	3R_5156140_SNP [dm3] 3R_9330418_SNP [dm6]	C	A	1.278e^-6	0.038	UPSTREAM CG12951 DOWNSTREAM CG16749 INTERGENIC
3R	5156177	3R_5156177_SNP [dm3] 3R_9330455_SNP [dm6]	A	G	1.278e^-6	0.038	UPSTREAM CG12951 DOWNSTREAM CG16749 INTERGENIC
3R	5156198	3R_5156198_SNP [dm3] 3R_9330476_SNP [dm6]	A	T	1.278e^-6	0.038	UPSTREAM CG12951 DOWNSTREAM CG16749 INTERGENIC
2R	15312220	2R_15312220_SNP [dm3] 2R_19424715_SNP [dm6]	G	T	1.282e^-6	0.038	UPSTREAM CalpA & 1 other INTRON hts	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_sens mE1_TFBS_Trl mE1_TFBS_zfh1
3R	5472884	3R_5472884_SNP [dm3] 3R_9647162_SNP [dm6]	T	C	1.314e^-6	0.038	INTRON Dh44
3R	5472937	3R_5472937_SNP [dm3] 3R_9647215_SNP [dm6]	G	A	1.390e^-6	0.039	INTRON Dh44
2L	18023481	2L_18023481_SNP [dm3] 2L_18023481_SNP [dm6]	C	T	1.398e^-6	0.039	INTRON rdo
3R	5477861	3R_5477861_SNP [dm3] 3R_9652139_SNP [dm6]	G	A	1.480e^-6	0.041	DOWNSTREAM CG43441 INTRON CG9492	TF binding site BDTNP1_TFBS_da
2L	7839406	2L_7839406_INS [dm3] 2L_7839406_INS [dm6]	T	TCGGTT	1.651e^-6	0.044	DOWNSTREAM CR43100 INTERGENIC
3R	5477233	3R_5477233_SNP [dm3] 3R_9651511_SNP [dm6]	G	T	1.662e^-6	0.044	UTR_3_PRIME CG9492 DOWNSTREAM Dh44
3R	5156176	3R_5156176_SNP [dm3] 3R_9330454_SNP [dm6]	A	G	1.707e^-6	0.044	UPSTREAM CG12951 DOWNSTREAM CG16749 INTERGENIC
3R	5464454	3R_5464454_SNP [dm3] 3R_9638732_SNP [dm6]	C	T	1.714e^-6	0.044	INTRON Dh44
X	11267803	X_11267803_SNP [dm3] X_11373770_SNP [dm6]	G	A	1.738e^-6	0.044	INTRON dlg1	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
2L	7643704	2L_7643704_SNP [dm3] 2L_7643704_SNP [dm6]	A	G	1.751e^-6	0.044	SYNONYMOUS_CODING Slob UTR_3_PRIME Slob
2R	17306363	2R_17306363_SNP [dm3] 2R_21418858_SNP [dm6]	T	A	1.763e^-6	0.044	INTRON Sdc
3R	4257485	3R_4257485_SNP [dm3] 3R_8431763_SNP [dm6]	C	A	1.796e^-6	0.044	INTRON CG45263
3L	4462398	3L_4462398_SNP [dm3] 3L_4462398_SNP [dm6]	T	C	1.809e^-6	0.044	UPSTREAM CG15023 DOWNSTREAM CG15024 INTERGENIC
3R	4257601	3R_4257601_SNP [dm3] 3R_8431879_SNP [dm6]	C	T	1.862e^-6	0.044	INTRON CG45263
3R	4257602	3R_4257602_SNP [dm3] 3R_8431880_SNP [dm6]	G	T	1.862e^-6	0.044	INTRON CG45263
3L	3893381	3L_3893381_SNP [dm3] 3L_3893381_SNP [dm6]	C	T	1.899e^-6	0.045	UPSTREAM snRNA:U11 INTRON Fie
3R	5156196	3R_5156196_SNP [dm3] 3R_9330474_SNP [dm6]	C	A	1.944e^-6	0.045	UPSTREAM CG12951 DOWNSTREAM CG16749 INTERGENIC
2L	20571642	2L_20571642_SNP [dm3] 2L_20571642_SNP [dm6]	G	A	1.987e^-6	0.045	INTRON CR45347
X	10812644	X_10812644_SNP [dm3] X_10918611_SNP [dm6]	G	A	1.990e^-6	0.045	INTRON CG43901	TF binding site mE1_TFBS_cad
2L	2867778	2L_2867778_SNP [dm3] 2L_2867778_SNP [dm6]	T	C	2.149e^-6	0.048	UTR_3_PRIME CG2991 DOWNSTREAM CG31694
3R	5474426	3R_5474426_SNP [dm3] 3R_9648704_SNP [dm6]	A	T	2.157e^-6	0.048	INTRON Dh44
3R	5429744	3R_5429744_SNP [dm3] 3R_9604022_SNP [dm6]	G	T	2.283e^-6	0.05	INTRON CG8312	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_cnc
3L	20550655	3L_20550655_SNP [dm3] 3L_20557555_SNP [dm6]	G	A	2.374e^-6	0.051	INTERGENIC
3L	5478981	3L_5478981_SNP [dm3] 3L_5485881_SNP [dm6]	G	T	2.632e^-6	0.056	INTERGENIC
2L	13147743	2L_13147743_SNP [dm3] 2L_13147743_SNP [dm6]	T	C	2.733e^-6	0.058	DOWNSTREAM CR44199 INTERGENIC
2R	10603166	2R_10603166_SNP [dm3] 2R_14715661_SNP [dm6]	A	C	2.790e^-6	0.058	INTERGENIC	TF binding site BDTNP1_TFBS_dl
2R	17567744	2R_17567744_SNP [dm3] 2R_21680239_SNP [dm6]	A	G	2.825e^-6	0.058	NON_SYNONYMOUS_CODING CG30263	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	4579333	3R_4579333_SNP [dm3] 3R_8753611_SNP [dm6]	T	C	2.890e^-6	0.059	NON_SYNONYMOUS_CODING CG8223 UTR_5_PRIME CG34135 UTR_3_PRIME CG11768 UPSTREAM CG34135 & 1 other DOWNSTREAM CG11768	TF binding site mE1_TFBS_cad
2L	20789742	2L_20789742_SNP [dm3] 2L_20789742_SNP [dm6]	C	T	2.957e^-6	0.06	SYNONYMOUS_CODING vari DOWNSTREAM Pomp	TF binding site mE1_TFBS_sens
3R	4748701	3R_4748701_SNP [dm3] 3R_8922979_SNP [dm6]	A	G	2.984e^-6	0.06	INTRON pyd
3R	4348614	3R_4348614_SNP [dm3] 3R_8522892_SNP [dm6]	G	T	3.187e^-6	0.063	NON_SYNONYMOUS_CODING CG31454
2L	3150282	2L_3150282_SNP [dm3] 2L_3150282_SNP [dm6]	C	T	3.229e^-6	0.063	INTRON Mad
3L	5479040	3L_5479040_SNP [dm3] 3L_5485940_SNP [dm6]	G	A	3.328e^-6	0.064	INTERGENIC
X	4430947	X_4430947_SNP [dm3] X_4536914_SNP [dm6]	C	T	3.343e^-6	0.064	SYNONYMOUS_CODING rb INTRON CR32773	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	13231535	2R_13231535_SNP [dm3] 2R_17344030_SNP [dm6]	C	T	3.538e^-6	0.067	INTRON mbl
3R	4834000	3R_4834000_SNP [dm3] 3R_9008278_SNP [dm6]	C	A	3.829e^-6	0.072	UPSTREAM CG11983 DOWNSTREAM CG11982 INTERGENIC
3R	4572598	3R_4572598_SNP [dm3] 3R_8746876_SNP [dm6]	C	G	4.015e^-6	0.073	UPSTREAM CG8223 INTRON CG9801	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi

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By genomic position
Variant impact
Gene name

Microbiota_OTU005 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results