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=3.165e^-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

Covariate	p-value	Significance
In_2R_NS	0.002694

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2R_NS	6.0453	0.0487

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2957 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
X	5143766	X_5143766_SNP [dm3] X_5249733_SNP [dm6]	G	T	2.948e^-9	0.005	INTRON CG15465 & 1 other
3R	23522392	3R_23522392_SNP [dm3] 3R_27696670_SNP [dm6]	G	A	9.744e^-9	0.006	UTR_3_PRIME ALiX DOWNSTREAM CG43320
3R	25147951	3R_25147951_SNP [dm3] 3R_29322229_SNP [dm6]	G	T	1.169e^-8	0.006	INTERGENIC
3R	23522336	3R_23522336_SNP [dm3] 3R_27696614_SNP [dm6]	C	T	1.312e^-8	0.006	UTR_3_PRIME ALiX DOWNSTREAM CG43320
X	21205575	X_21205575_SNP [dm3] X_21334548_SNP [dm6]	C	A	3.087e^-8	0.009	INTRON tty
X	21205542	X_21205542_SNP [dm3] X_21334515_SNP [dm6]	C	T	3.105e^-8	0.009	INTRON tty
3R	13915897	3R_13915897_DEL [dm3] 3R_18090175_DEL [dm6]	TTCT	T	3.401e^-8	0.009	UPSTREAM sr INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	8701623	3L_8701623_SNP [dm3] 3L_8708523_SNP [dm6]	A	G	4.022e^-8	0.009	INTERGENIC	regulatory region REDfly_CRMs
3R	19530992	3R_19530992_SNP [dm3] 3R_23705270_SNP [dm6]	G	A	5.383e^-8	0.009	DOWNSTREAM CG31413 INTRON CG31414	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi
3R	19531011	3R_19531011_SNP [dm3] 3R_23705289_SNP [dm6]	T	C	5.383e^-8	0.009	DOWNSTREAM CG31413 INTRON CG31414	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi
X	21867866	X_21867866_SNP [dm3] X_22466030_SNP [dm6]	T	C	5.411e^-8	0.009	UPSTREAM CG14619 INTRON CG14619
3R	25147954	3R_25147954_SNP [dm3] 3R_29322232_SNP [dm6]	C	A	6.643e^-8	0.01	INTERGENIC
X	20689714	X_20689714_SNP [dm3] X_20818687_SNP [dm6]	C	A	7.157e^-8	0.01	INTRON shakB
X	17006816	X_17006816_SNP [dm3] X_17112783_SNP [dm6]	A	T	1.030e^-7	0.013	INTRON CG5004	TF binding site BDTNP1_TFBS_twi
X	21205728	X_21205728_SNP [dm3] X_21334701_SNP [dm6]	G	A	1.142e^-7	0.013	INTRON tty
X	21205735	X_21205735_SNP [dm3] X_21334708_SNP [dm6]	T	A	1.142e^-7	0.013	INTRON tty
3R	21980529	3R_21980529_SNP [dm3] 3R_26154807_SNP [dm6]	C	T	1.331e^-7	0.013	INTERGENIC
X	12402257	X_12402257_SNP [dm3] X_12508224_SNP [dm6]	A	G	1.332e^-7	0.013	INTRON CG2556	TF binding site BDTNP1_TFBS_da
3R	23081744	3R_23081744_SNP [dm3] 3R_27256022_SNP [dm6]	C	T	1.342e^-7	0.013	DOWNSTREAM woc INTRON TfIIA-L	TF binding site BDTNP1_TFBS_z
3L	12032724	3L_12032724_SNP [dm3] 3L_12039624_SNP [dm6]	T	C	1.489e^-7	0.014	INTRON rols	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
X	16985273	X_16985273_DEL [dm3] X_17091240_DEL [dm6]	CTA	C	1.960e^-7	0.017	UPSTREAM CG16700 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl
3R	14309178	3R_14309178_SNP [dm3] 3R_18483456_SNP [dm6]	C	T	2.599e^-7	0.022	INTRON fru
X	21205205	X_21205205_SNP [dm3] X_21334178_SNP [dm6]	G	A	3.669e^-7	0.027	INTRON tty	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
X	5145629	X_5145629_INS [dm3] X_5251596_INS [dm6]	C	CGC	3.859e^-7	0.027	UTR_3_PRIME CG15465 & 1 other DOWNSTREAM rg
X	8781242	X_8781242_SNP [dm3] X_8887209_SNP [dm6]	G	A	3.975e^-7	0.027	INTRON Moe	TF binding site BDTNP1_TFBS_dl
X	17016398	X_17016398_SNP [dm3] X_17122365_SNP [dm6]	C	A	4.048e^-7	0.027	INTRON CG5004	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad
3L	10826558	3L_10826558_SNP [dm3] 3L_10833458_SNP [dm6]	A	G	4.149e^-7	0.027	INTERGENIC
3R	21189594	3R_21189594_SNP [dm3] 3R_25363872_SNP [dm6]	T	A	4.240e^-7	0.027	INTRON Fur1
2R	14801302	2R_14801302_INS [dm3] 2R_18913797_INS [dm6]	T	TCGTTT	4.357e^-7	0.027	INTRON sano
3R	10139170	3R_10139170_SNP [dm3] 3R_14313448_SNP [dm6]	G	A	4.363e^-7	0.027	INTRON CG31321
3L	10827443	3L_10827443_INS [dm3] 3L_10834343_INS [dm6]	C	CTA	4.433e^-7	0.027	INTERGENIC
3L	12032949	3L_12032949_SNP [dm3] 3L_12039849_SNP [dm6]	C	T	4.775e^-7	0.028	INTRON rols	TF binding site mE1_TFBS_inv
3L	10823837	3L_10823837_SNP [dm3] 3L_10830737_SNP [dm6]	A	T	5.236e^-7	0.03	INTERGENIC
3L	10378149	3L_10378149_SNP [dm3] 3L_10385049_SNP [dm6]	C	T	6.706e^-7	0.036	INTERGENIC
X	21203559	X_21203559_SNP [dm3] X_21332532_SNP [dm6]	G	A	6.741e^-7	0.036	DOWNSTREAM tty INTRON tty	transposable element FlyBase
3L	10826598	3L_10826598_SNP [dm3] 3L_10833498_SNP [dm6]	T	A	6.972e^-7	0.036	INTERGENIC
3R	21980745	3R_21980745_SNP [dm3] 3R_26155023_SNP [dm6]	G	C	7.796e^-7	0.039	INTERGENIC
3L	12263187	3L_12263187_SNP [dm3] 3L_12270087_SNP [dm6]	A	T	8.074e^-7	0.039	UTR_3_PRIME Pbgs DOWNSTREAM CG32100
2L	16963413	2L_16963413_SNP [dm3] 2L_16963413_SNP [dm6]	G	C	8.275e^-7	0.039	INTERGENIC
3R	24495726	3R_24495726_SNP [dm3] 3R_28670004_SNP [dm6]	C	T	9.081e^-7	0.042	SYNONYMOUS_CODING CG33346 UPSTREAM CG9989
3L	4684942	3L_4684942_SNP [dm3] 3L_4684942_SNP [dm6]	C	G	9.824e^-7	0.043	INTRON axo
3R	26789545	3R_26789545_SNP [dm3] 3R_30963823_SNP [dm6]	A	C	9.862e^-7	0.043	SYNONYMOUS_CODING Ctr1C
3L	10378368	3L_10378368_SNP [dm3] 3L_10385268_SNP [dm6]	G	A	1.004e^-6	0.043	INTERGENIC
2R	3895822	2R_3895822_SNP [dm3] 2R_8008317_SNP [dm6]	A	G	1.151e^-6	0.049	DOWNSTREAM CG14762 INTRON Odc2	TF binding site mE1_TFBS_cad
2L	1346974	2L_1346974_INS [dm3] 2L_1346974_INS [dm6]	G	GAGACACG	1.230e^-6	0.049	UPSTREAM CR45006 INTERGENIC
3L	8701631	3L_8701631_SNP [dm3] 3L_8708531_SNP [dm6]	G	A	1.248e^-6	0.049	INTERGENIC	regulatory region REDfly_CRMs
3L	1440619	3L_1440619_SNP [dm3] 3L_1440619_SNP [dm6]	T	C	1.263e^-6	0.049	INTRON Ptp61F	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3L	10823747	3L_10823747_SNP [dm3] 3L_10830647_SNP [dm6]	C	G	1.288e^-6	0.049	INTERGENIC
3L	10823749	3L_10823749_SNP [dm3] 3L_10830649_SNP [dm6]	A	G	1.288e^-6	0.049	INTERGENIC
3L	1440587	3L_1440587_SNP [dm3] 3L_1440587_SNP [dm6]	C	G	1.320e^-6	0.049	INTRON Ptp61F	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	21980522	3R_21980522_SNP [dm3] 3R_26154800_SNP [dm6]	A	T	1.361e^-6	0.049	INTERGENIC
X	16993590	X_16993590_DEL [dm3] X_17099557_DEL [dm6]	GG	G	1.382e^-6	0.049	INTRON CG4991
X	21461411	X_21461411_SNP [dm3] X_21590384_SNP [dm6]	G	A	1.413e^-6	0.049	INTERGENIC
3L	1444377	3L_1444377_SNP [dm3] 3L_1444377_SNP [dm6]	C	A	1.454e^-6	0.049	INTRON Ptp61F	TF binding site mE1_TFBS_sens
2L	2332995	2L_2332995_SNP [dm3] 2L_2332995_SNP [dm6]	T	G	1.466e^-6	0.049	INTRON CG9967 & 1 other
3R	24658738	3R_24658738_SNP [dm3] 3R_28833016_SNP [dm6]	A	G	1.470e^-6	0.049	UTR_3_PRIME Apc UPSTREAM WASp
3L	1444406	3L_1444406_SNP [dm3] 3L_1444406_SNP [dm6]	C	T	1.653e^-6	0.054	INTRON Ptp61F	TF binding site mE1_TFBS_sens
X	5996137	X_5996137_SNP [dm3] X_6102104_SNP [dm6]	C	G	1.690e^-6	0.054	SYNONYMOUS_CODING Nep1	TF binding site mE1_TFBS_chinmo
2L	17214212	2L_17214212_SNP [dm3] 2L_17214212_SNP [dm6]	A	T	1.749e^-6	0.054	INTRON beat-IIIc	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	21205388	X_21205388_SNP [dm3] X_21334361_SNP [dm6]	A	T	1.753e^-6	0.054	INTRON tty	TF binding site mE1_TFBS_cad
X	2436390	X_2436390_SNP [dm3] X_2542357_SNP [dm6]	G	A	1.884e^-6	0.057	INTRON trol	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_inv
3L	9302746	3L_9302746_SNP [dm3] 3L_9309646_SNP [dm6]	T	C	1.907e^-6	0.057	INTERGENIC
X	5145585	X_5145585_SNP [dm3] X_5251552_SNP [dm6]	C	T	1.985e^-6	0.058	UTR_3_PRIME CG15465 & 1 other DOWNSTREAM rg
X	4427889	X_4427889_SNP [dm3] X_4533856_SNP [dm6]	A	G	2.011e^-6	0.058	UTR_3_PRIME CG3556 DOWNSTREAM CG3556 INTRON CR32773
3L	7746389	3L_7746389_SNP [dm3] 3L_7753289_SNP [dm6]	A	T	2.094e^-6	0.06	INTRON CG32373
3R	23629995	3R_23629995_SNP [dm3] 3R_27804273_SNP [dm6]	G	C	2.197e^-6	0.062	INTRON CG34353
3L	1438367	3L_1438367_SNP [dm3] 3L_1438367_SNP [dm6]	C	T	2.277e^-6	0.063	UPSTREAM SA-2 INTRON Ptp61F	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cnc mE1_TFBS_HSA
3L	1078027	3L_1078027_SNP [dm3] 3L_1078027_SNP [dm6]	G	A	2.359e^-6	0.065	INTRON bab1	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	2389985	3L_2389985_SNP [dm3] 3L_2389985_SNP [dm6]	C	A	2.496e^-6	0.065	SYNONYMOUS_CODING CG32299 UTR_3_PRIME CG32298 DOWNSTREAM CG42787 INTRON CG45186	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	2809724	3L_2809724_INS [dm3] 3L_2809724_INS [dm6]	A	AAAGA	2.496e^-6	0.065	INTRON CG43444	TF binding site mE1_TFBS_cad
3L	1438368	3L_1438368_SNP [dm3] 3L_1438368_SNP [dm6]	C	T	2.515e^-6	0.065	UPSTREAM SA-2 INTRON Ptp61F	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cnc mE1_TFBS_HSA
3R	14024155	3R_14024155_SNP [dm3] 3R_18198433_SNP [dm6]	T	C	2.520e^-6	0.065	INTRON Ssdp	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3L	10825992	3L_10825992_SNP [dm3] 3L_10832892_SNP [dm6]	C	T	2.561e^-6	0.065	INTERGENIC
3L	10828632	3L_10828632_SNP [dm3] 3L_10835532_SNP [dm6]	G	A	2.676e^-6	0.066	INTERGENIC
X	21093246	X_21093246_SNP [dm3] X_21222219_SNP [dm6]	T	G	2.703e^-6	0.066	INTRON CG32521
3L	2390024	3L_2390024_SNP [dm3] 3L_2390024_SNP [dm6]	G	A	2.737e^-6	0.066	SYNONYMOUS_CODING CG32299 UTR_3_PRIME CG32298 DOWNSTREAM CG42787 INTRON CG45186	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	2390083	3L_2390083_SNP [dm3] 3L_2390083_SNP [dm6]	T	G	2.737e^-6	0.066	NON_SYNONYMOUS_CODING CG32299 UTR_3_PRIME CG32298 DOWNSTREAM CG42787 INTRON CG45186	TF binding site mE1_TFBS_sens
X	21203952	X_21203952_SNP [dm3] X_21332925_SNP [dm6]	T	C	2.906e^-6	0.069	DOWNSTREAM tty INTRON tty	TF binding site mE1_TFBS_cad
3L	2477290	3L_2477290_SNP [dm3] 3L_2477290_SNP [dm6]	G	A	2.954e^-6	0.07	SYNONYMOUS_CODING Cyp4d20 INTRON CG45186	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2R	3896164	2R_3896164_SNP [dm3] 2R_8008659_SNP [dm6]	G	A	3.076e^-6	0.07	DOWNSTREAM CG14762 INTRON Odc2	TF binding site mE1_TFBS_cad
3L	4807267	3L_4807267_SNP [dm3] 3L_4807267_SNP [dm6]	T	G	3.080e^-6	0.07	NON_SYNONYMOUS_CODING CG18808 DOWNSTREAM Dhc64C
X	5145625	X_5145625_SNP [dm3] X_5251592_SNP [dm6]	A	C	3.153e^-6	0.07	UTR_3_PRIME CG15465 & 1 other DOWNSTREAM rg
X	21093211	X_21093211_SNP [dm3] X_21222184_SNP [dm6]	G	A	3.180e^-6	0.07	INTRON CG32521
X	16979309	X_16979309_SNP [dm3] X_17085276_SNP [dm6]	A	G	3.181e^-6	0.07	SYNONYMOUS_CODING CG8945
3R	24650791	3R_24650791_INS [dm3] 3R_28825069_INS [dm6]	A	AA	3.265e^-6	0.071	UTR_3_PRIME WASp DOWNSTREAM CG1647
3R	21189772	3R_21189772_SNP [dm3] 3R_25364050_SNP [dm6]	A	T	3.327e^-6	0.072	INTRON Fur1
3R	24706749	3R_24706749_SNP [dm3] 3R_28881027_SNP [dm6]	G	A	3.405e^-6	0.073	SYNONYMOUS_CODING CG14527 UPSTREAM CG14523 INTRON CG33203
2R	20299587	2R_20299587_SNP [dm3] 2R_24412064_SNP [dm6]	C	T	3.823e^-6	0.08	SYNONYMOUS_CODING CG45068 UTR_5_PRIME CG45069 UPSTREAM SerT	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_sens
2L	7631063	2L_7631063_SNP [dm3] 2L_7631063_SNP [dm6]	T	C	3.832e^-6	0.08	INTERGENIC
3L	4684945	3L_4684945_SNP [dm3] 3L_4684945_SNP [dm6]	C	A	3.914e^-6	0.08	INTRON axo
X	4427892	X_4427892_SNP [dm3] X_4533859_SNP [dm6]	A	T	3.929e^-6	0.08	UTR_3_PRIME CG3556 DOWNSTREAM CG3556 INTRON CR32773
3L	1443549	3L_1443549_SNP [dm3] 3L_1443549_SNP [dm6]	T	C	4.013e^-6	0.081	INTRON Ptp61F	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Trl
3R	7950202	3R_7950202_SNP [dm3] 3R_12124480_SNP [dm6]	C	G	4.144e^-6	0.083	INTRON CG4702	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
X	21201017	X_21201017_INS [dm3] X_21329990_INS [dm6]	A	AA	4.368e^-6	0.086	UTR_3_PRIME tty	TF binding site BDTNP1_TFBS_prd
3L	4830511	3L_4830511_SNP [dm3] 3L_4830511_SNP [dm6]	G	A	4.405e^-6	0.086	SYNONYMOUS_CODING CG13708	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	13420389	3L_13420389_SNP [dm3] 3L_13427289_SNP [dm6]	G	T	4.561e^-6	0.087	UPSTREAM CG14105 INTERGENIC
X	16997599	X_16997599_SNP [dm3] X_17103566_SNP [dm6]	C	T	4.607e^-6	0.087	SYNONYMOUS_CODING CG4991
X	16999025	X_16999025_SNP [dm3] X_17104992_SNP [dm6]	A	G	4.607e^-6	0.087	DOWNSTREAM CG4991 INTRON Arpc3B
X	8282358	X_8282358_INS [dm3] X_8388325_INS [dm6]	A	AATCGCA	4.669e^-6	0.088		TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
X	16979108	X_16979108_SNP [dm3] X_17085075_SNP [dm6]	T	A	4.714e^-6	0.088	SYNONYMOUS_CODING CG8945

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By genomic position
Variant impact
Gene name

Microbiota_OTU060 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results