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=3.325e^-8)
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_Mo	0.06741

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_3R_Mo	7.252	0.0266

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

3526 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	12797216	2L_12797216_SNP [dm3] 2L_12797216_SNP [dm6]	A	T	1.136e^-8	0.017	INTERGENIC
2R	13021002	2R_13021002_SNP [dm3] 2R_17133497_SNP [dm6]	C	T	4.692e^-8	0.017	UTR_5_PRIME Acp54A1 UPSTREAM CG11400
2R	13021999	2R_13021999_SNP [dm3] 2R_17134494_SNP [dm6]	C	T	4.692e^-8	0.017	NON_SYNONYMOUS_CODING CG11400 DOWNSTREAM Acp54A1
2R	13022020	2R_13022020_SNP [dm3] 2R_17134515_SNP [dm6]	C	T	4.692e^-8	0.017	NON_SYNONYMOUS_CODING CG11400 DOWNSTREAM Acp54A1
2R	13022123	2R_13022123_SNP [dm3] 2R_17134618_SNP [dm6]	C	G	4.692e^-8	0.017	SYNONYMOUS_CODING CG11400 UPSTREAM CR44391 DOWNSTREAM Acp54A1
2R	13021746	2R_13021746_SNP [dm3] 2R_17134241_SNP [dm6]	C	G	5.649e^-8	0.018	NON_SYNONYMOUS_CODING CG11400 DOWNSTREAM Acp54A1
2R	13049508	2R_13049508_SNP [dm3] 2R_17162003_SNP [dm6]	C	T	1.526e^-7	0.039	INTERGENIC
3L	5416444	3L_5416444_DEL [dm3] 3L_5423344_DEL [dm6]	CAAG	T	1.865e^-7	0.039	UPSTREAM CG34391 INTERGENIC
2L	20505649	2L_20505649_SNP [dm3] 2L_20505649_SNP [dm6]	C	A	1.999e^-7	0.039	INTERGENIC
3L	16674021	3L_16674021_SNP [dm3] 3L_16680921_SNP [dm6]	A	C	2.228e^-7	0.039	SYNONYMOUS_CODING Lasp UTR_5_PRIME CG43954	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	13049077	2R_13049077_SNP [dm3] 2R_17161572_SNP [dm6]	C	A	2.316e^-7	0.039	UPSTREAM CG30457 INTERGENIC
X	22235222	X_22235222_DEL [dm3] X_22833386_DEL [dm6]	AA	A	3.259e^-7	0.047	DOWNSTREAM mir-2491 INTRON fog & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad transposable element FlyBase
2R	13049096	2R_13049096_SNP [dm3] 2R_17161591_SNP [dm6]	T	A	3.575e^-7	0.047	UPSTREAM CG30457 INTERGENIC
2R	13019968	2R_13019968_SNP [dm3] 2R_17132463_SNP [dm6]	T	C	3.807e^-7	0.047	UPSTREAM CR45273 & 1 other INTERGENIC
2R	13019973	2R_13019973_SNP [dm3] 2R_17132468_SNP [dm6]	A	G	3.807e^-7	0.047	UPSTREAM CR45273 & 1 other INTERGENIC
2L	12797315	2L_12797315_SNP [dm3] 2L_12797315_SNP [dm6]	A	T	4.756e^-7	0.047	INTERGENIC
X	18019403	X_18019403_SNP [dm3] X_18125370_SNP [dm6]	C	A	4.865e^-7	0.047	NON_SYNONYMOUS_CODING CG32553 DOWNSTREAM mir-969
2R	17343694	2R_17343694_SNP [dm3] 2R_21456189_SNP [dm6]	T	C	5.268e^-7	0.047	INTRON Sdc
X	18018859	X_18018859_DEL [dm3] X_18124826_DEL [dm6]	TGT	T	5.300e^-7	0.047	UTR_3_PRIME CG32553 DOWNSTREAM mir-969
2L	12798146	2L_12798146_INS [dm3] 2L_12798146_INS [dm6]	T	TTTT	5.345e^-7	0.047	INTERGENIC
2L	10460566	2L_10460566_SNP [dm3] 2L_10460566_SNP [dm6]	G	T	5.436e^-7	0.047	INTRON LM408
2R	13019907	2R_13019907_SNP [dm3] 2R_17132402_SNP [dm6]	G	T	5.541e^-7	0.047	UPSTREAM CR45273 INTERGENIC
2R	18447017	2R_18447017_SNP [dm3] 2R_22559512_SNP [dm6]	C	T	6.681e^-7	0.054	INTRON px
2R	13020340	2R_13020340_SNP [dm3] 2R_17132835_SNP [dm6]	G	A	7.032e^-7	0.054	UPSTREAM Acp54A1 INTERGENIC
X	18019438	X_18019438_SNP [dm3] X_18125405_SNP [dm6]	T	C	7.302e^-7	0.054	NON_SYNONYMOUS_CODING CG32553 DOWNSTREAM mir-969
3L	16661482	3L_16661482_SNP [dm3] 3L_16668382_SNP [dm6]	T	A	7.786e^-7	0.054	UPSTREAM Galphaf INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Trl
2R	12608266	2R_12608266_SNP [dm3] 2R_16720761_SNP [dm6]	C	A	7.796e^-7	0.054	INTRON CG30463	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2L	14764769	2L_14764769_SNP [dm3] 2L_14764769_SNP [dm6]	C	T	8.382e^-7	0.056	DOWNSTREAM CSN1a INTERGENIC
2R	10251028	2R_10251028_SNP [dm3] 2R_14363523_SNP [dm6]	T	C	9.671e^-7	0.061	DOWNSTREAM Arc2 INTRON Tfb1	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_sens
3L	5692330	3L_5692330_SNP [dm3] 3L_5699230_SNP [dm6]	C	T	1.032e^-6	0.061	INTRON sif	TF binding site mE1_TFBS_chinmo
2L	12798143	2L_12798143_SNP [dm3] 2L_12798143_SNP [dm6]	T	A	1.085e^-6	0.061	INTERGENIC
2L	14615175	2L_14615175_SNP [dm3] 2L_14615175_SNP [dm6]	G	T	1.151e^-6	0.061	UPSTREAM Adhr & 1 other INTRON osp
X	18018538	X_18018538_SNP [dm3] X_18124505_SNP [dm6]	G	A	1.165e^-6	0.061	DOWNSTREAM CG32553 & 1 other INTERGENIC
X	18018598	X_18018598_SNP [dm3] X_18124565_SNP [dm6]	C	G	1.165e^-6	0.061	DOWNSTREAM CG32553 & 1 other INTERGENIC
X	22237358	X_22237358_SNP [dm3] X_22835522_SNP [dm6]	A	G	1.196e^-6	0.061	INTRON fog & 1 other	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi
2R	19090961	2R_19090961_INS [dm3] 2R_23203438_INS [dm6]	G	GA	1.202e^-6	0.061	INTRON CG34371	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
X	18018808	X_18018808_INS [dm3] X_18124775_INS [dm6]	TG	AAA	1.217e^-6	0.061	UTR_3_PRIME CG32553 DOWNSTREAM mir-969
3L	6164678	3L_6164678_SNP [dm3] 3L_6171578_SNP [dm6]	T	C	1.372e^-6	0.063	NON_SYNONYMOUS_CODING CG10289	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv
3L	5262905	3L_5262905_SNP [dm3] 3L_5269805_SNP [dm6]	T	A	1.378e^-6	0.063	INTRON shep
X	18018694	X_18018694_SNP [dm3] X_18124661_SNP [dm6]	T	A	1.457e^-6	0.063	UTR_3_PRIME CG32553 DOWNSTREAM mir-969
2R	12420476	2R_12420476_SNP [dm3] 2R_16532971_SNP [dm6]	G	T	1.460e^-6	0.063	UTR_3_PRIME Sema-2a
2L	1070442	2L_1070442_SNP [dm3] 2L_1070442_SNP [dm6]	A	G	1.569e^-6	0.063	INTRON S	TF binding site mE1_TFBS_cad
2R	13005656	2R_13005656_SNP [dm3] 2R_17118151_SNP [dm6]	T	G	1.642e^-6	0.063	DOWNSTREAM Amy-p INTERGENIC
3L	16672662	3L_16672662_SNP [dm3] 3L_16679562_SNP [dm6]	C	T	1.647e^-6	0.063	SYNONYMOUS_CODING Lasp UTR_5_PRIME CG43954 INTRON Lasp	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
3L	16666710	3L_16666710_SNP [dm3] 3L_16673610_SNP [dm6]	A	T	1.713e^-6	0.063	UPSTREAM CG13032 & 1 other INTERGENIC	regulatory region REDfly_CRMs
3L	16668713	3L_16668713_SNP [dm3] 3L_16675613_SNP [dm6]	G	T	1.713e^-6	0.063	SYNONYMOUS_CODING CG13032 DOWNSTREAM Lasp	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
3R	7684139	3R_7684139_SNP [dm3] 3R_11858417_SNP [dm6]	C	A	1.743e^-6	0.063	INTRON CG6959
X	18018299	X_18018299_DEL [dm3] X_18124266_DEL [dm6]	AC	A	1.907e^-6	0.063	UPSTREAM mir-969 DOWNSTREAM CG32553 INTERGENIC
X	18018482	X_18018482_SNP [dm3] X_18124449_SNP [dm6]	C	T	1.907e^-6	0.063	DOWNSTREAM CG32553 & 1 other EXON mir-969
X	18018591	X_18018591_SNP [dm3] X_18124558_SNP [dm6]	A	G	1.907e^-6	0.063	DOWNSTREAM CG32553 & 1 other INTERGENIC
X	18018592	X_18018592_SNP [dm3] X_18124559_SNP [dm6]	A	G	1.907e^-6	0.063	DOWNSTREAM CG32553 & 1 other INTERGENIC
X	18018784	X_18018784_INS [dm3] X_18124751_INS [dm6]	A	AC	1.907e^-6	0.063	UTR_3_PRIME CG32553 DOWNSTREAM mir-969
2L	1070109	2L_1070109_SNP [dm3] 2L_1070109_SNP [dm6]	C	T	1.930e^-6	0.063	INTRON S	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad
3L	5344210	3L_5344210_SNP [dm3] 3L_5351110_SNP [dm6]	T	A	1.944e^-6	0.063	INTRON lama
2L	10685807	2L_10685807_SNP [dm3] 2L_10685807_SNP [dm6]	A	G	1.999e^-6	0.063	DOWNSTREAM CG7296 INTERGENIC	TF binding site mE1_TFBS_zfh1
2L	12766906	2L_12766906_INS [dm3] 2L_12766906_INS [dm6]	A	AA	2.030e^-6	0.063	INTERGENIC
3L	6164651	3L_6164651_SNP [dm3] 3L_6171551_SNP [dm6]	C	T	2.047e^-6	0.063	NON_SYNONYMOUS_CODING CG10289	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv
3L	16666709	3L_16666709_SNP [dm3] 3L_16673609_SNP [dm6]	G	T	2.051e^-6	0.063	UPSTREAM CG13032 & 1 other INTERGENIC	regulatory region REDfly_CRMs
2L	10685765	2L_10685765_SNP [dm3] 2L_10685765_SNP [dm6]	T	A	2.131e^-6	0.063	DOWNSTREAM CG7296 INTERGENIC	TF binding site mE1_TFBS_zfh1
3L	5719080	3L_5719080_SNP [dm3] 3L_5725980_SNP [dm6]	T	A	2.147e^-6	0.063	INTRON sif
3L	4056180	3L_4056180_SNP [dm3] 3L_4056180_SNP [dm6]	T	C	2.174e^-6	0.063	INTRON CG1136
3L	4056192	3L_4056192_SNP [dm3] 3L_4056192_SNP [dm6]	T	A	2.174e^-6	0.063	INTRON CG1136
X	18018680	X_18018680_SNP [dm3] X_18124647_SNP [dm6]	C	T	2.209e^-6	0.063	UTR_3_PRIME CG32553 DOWNSTREAM mir-969
X	18018685	X_18018685_SNP [dm3] X_18124652_SNP [dm6]	G	T	2.209e^-6	0.063	UTR_3_PRIME CG32553 DOWNSTREAM mir-969
X	18018686	X_18018686_SNP [dm3] X_18124653_SNP [dm6]	T	A	2.209e^-6	0.063	UTR_3_PRIME CG32553 DOWNSTREAM mir-969
2L	16999755	2L_16999755_SNP [dm3] 2L_16999755_SNP [dm6]	G	A	2.408e^-6	0.063	DOWNSTREAM CR45357 INTERGENIC
X	12267352	X_12267352_SNP [dm3] X_12373319_SNP [dm6]	T	C	2.436e^-6	0.063	SYNONYMOUS_CODING CG2577
2L	12797478	2L_12797478_SNP [dm3] 2L_12797478_SNP [dm6]	C	T	2.470e^-6	0.063	INTERGENIC
3L	5345133	3L_5345133_SNP [dm3] 3L_5352033_SNP [dm6]	T	C	2.493e^-6	0.063	UPSTREAM lama INTRON lama	TF binding site mE1_TFBS_HSA
3L	16665315	3L_16665315_DEL [dm3] 3L_16672215_DEL [dm6]	CTTGT	C	2.506e^-6	0.063	UTR_3_PRIME zetaCOP INTRON zetaCOP
3L	16665323	3L_16665323_SNP [dm3] 3L_16672223_SNP [dm6]	C	T	2.506e^-6	0.063	UTR_3_PRIME zetaCOP INTRON zetaCOP
3L	16667156	3L_16667156_SNP [dm3] 3L_16674056_SNP [dm6]	A	T	2.556e^-6	0.063	UTR_5_PRIME CG13032 UPSTREAM zetaCOP	regulatory region REDfly_CRMs
3L	16670236	3L_16670236_SNP [dm3] 3L_16677136_SNP [dm6]	G	A	2.556e^-6	0.063	UTR_3_PRIME Lasp DOWNSTREAM CG13032 & 2 others
3L	16674247	3L_16674247_SNP [dm3] 3L_16681147_SNP [dm6]	C	A	2.556e^-6	0.063	INTRON Lasp & 1 other	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3L	16674389	3L_16674389_SNP [dm3] 3L_16681289_SNP [dm6]	G	A	2.583e^-6	0.063	SYNONYMOUS_CODING Lasp UTR_5_PRIME CG43954	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
X	18018246	X_18018246_SNP [dm3] X_18124213_SNP [dm6]	T	G	2.627e^-6	0.063	UPSTREAM mir-969 DOWNSTREAM CG32553 INTERGENIC
X	18019227	X_18019227_SNP [dm3] X_18125194_SNP [dm6]	A	T	2.627e^-6	0.063	SYNONYMOUS_CODING CG32553 DOWNSTREAM mir-969
3L	5426345	3L_5426345_SNP [dm3] 3L_5433245_SNP [dm6]	G	A	2.653e^-6	0.063	INTRON CG34391
2R	12967998	2R_12967998_SNP [dm3] 2R_17080493_SNP [dm6]	C	A	2.750e^-6	0.065	INTRON CG30460
2R	13020226	2R_13020226_DEL [dm3] 2R_17132721_DEL [dm6]	TTCGTTGTATT...	T	2.867e^-6	0.067	UPSTREAM Acp54A1 INTERGENIC
3L	5344218	3L_5344218_SNP [dm3] 3L_5351118_SNP [dm6]	G	A	2.957e^-6	0.067	INTRON lama
2L	12766907	2L_12766907_INS [dm3] 2L_12766907_INS [dm6]	T	TT	2.994e^-6	0.067	INTERGENIC
X	18019141	X_18019141_SNP [dm3] X_18125108_SNP [dm6]	G	A	3.007e^-6	0.067	UTR_3_PRIME CG32553 DOWNSTREAM mir-969
3L	5344231	3L_5344231_SNP [dm3] 3L_5351131_SNP [dm6]	T	A	3.012e^-6	0.067	INTRON lama
2R	17343270	2R_17343270_SNP [dm3] 2R_21455765_SNP [dm6]	A	G	3.044e^-6	0.067	INTRON Sdc	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	5691965	3L_5691965_SNP [dm3] 3L_5698865_SNP [dm6]	G	A	3.112e^-6	0.067	SYNONYMOUS_CODING sif INTRON sif	TF binding site mE1_TFBS_chinmo
2R	15539060	2R_15539060_INS [dm3] 2R_19651555_INS [dm6]	A	ATA	3.269e^-6	0.069	UPSTREAM Ir56e DOWNSTREAM CR44212 INTERGENIC
2L	4338426	2L_4338426_SNP [dm3] 2L_4338426_SNP [dm6]	A	C	3.287e^-6	0.069	UPSTREAM Atet INTRON Atet
2L	2735023	2L_2735023_INS [dm3] 2L_2735023_INS [dm6]	G	TA	3.549e^-6	0.074	UPSTREAM CG31689 INTRON CG31689
X	12267361	X_12267361_SNP [dm3] X_12373328_SNP [dm6]	C	T	3.594e^-6	0.074	SYNONYMOUS_CODING CG2577
X	22251662	X_22251662_SNP [dm3] X_22849826_SNP [dm6]	T	C	3.731e^-6	0.076	INTRON fog & 1 other
2R	12967974	2R_12967974_SNP [dm3] 2R_17080469_SNP [dm6]	C	T	3.822e^-6	0.077	INTRON CG30460
X	6624836	X_6624836_DEL [dm3] X_6730803_DEL [dm6]	CATTTTTCCTC...	C	3.840e^-6	0.077	UPSTREAM CG3168 INTRON CG3168
3L	3889047	3L_3889047_SNP [dm3] 3L_3889047_SNP [dm6]	T	C	3.872e^-6	0.077	INTERGENIC
3L	5301451	3L_5301451_SNP [dm3] 3L_5308351_SNP [dm6]	C	A	3.943e^-6	0.077	INTERGENIC
3L	15618088	3L_15618088_SNP [dm3] 3L_15624988_SNP [dm6]	G	A	4.197e^-6	0.081	DOWNSTREAM CG7372 INTRON comm3
2L	11289225	2L_11289225_SNP [dm3] 2L_11289225_SNP [dm6]	C	T	4.400e^-6	0.083	INTERGENIC
X	22251955	X_22251955_SNP [dm3] X_22850119_SNP [dm6]	A	T	4.456e^-6	0.083	INTRON fog & 1 other
3L	18583668	3L_18583668_SNP [dm3] 3L_18590568_SNP [dm6]	T	A	4.469e^-6	0.083	DOWNSTREAM CG7271 INTERGENIC
2L	12766800	2L_12766800_SNP [dm3] 2L_12766800_SNP [dm6]	A	T	4.473e^-6	0.083	INTERGENIC

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By genomic position
Variant impact
Gene name

Microbiota_OTU082 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results