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Detailed information for vg0401113415:

Variant ID: vg0401113415 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 1113415
Reference Allele: G	Alternative Allele: T,A
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.94, T: 0.06, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:

AATTAATGATGAATTATATATAGCATCTAATACACATGGTTAAGAACAAAAATGATATACTCATTCACATAAGGTGTTCTTGTAACTCGATTAATTTACA[G/T,A]
CAAATGTTCAGTTCATTTGTTGCCACTGGAGAGACGGGGAAGAGAGAAGAGTGGGGAGGATGGATGAAGATGGAAACGTGGGGATTGGAGGCAAATGTAT

Reverse complement sequence

ATACATTTGCCTCCAATCCCCACGTTTCCATCTTCATCCATCCTCCCCACTCTTCTCTCTTCCCCGTCTCTCCAGTGGCAACAAATGAACTGAACATTTG[C/A,T]
TGTAAATTAATCGAGTTACAAGAACACCTTATGTGAATGAGTATATCATTTTTGTTCTTAACCATGTGTATTAGATGCTATATATAATTCATCATTAATT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	85.00%	14.80%	0.15%	0.00%	A: 0.06%
All Indica	2759	83.00%	16.80%	0.25%	0.00%	NA
All Japonica	1512	97.60%	2.40%	0.00%	0.00%	A: 0.07%
Aus	269	32.30%	67.70%	0.00%	0.00%	NA
Indica I	595	97.30%	2.50%	0.17%	0.00%	NA
Indica II	465	80.90%	18.70%	0.43%	0.00%	NA
Indica III	913	77.50%	22.20%	0.22%	0.00%	NA
Indica Intermediate	786	79.60%	20.10%	0.25%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	94.60%	5.20%	0.00%	0.00%	A: 0.20%
Japonica Intermediate	241	96.30%	3.70%	0.00%	0.00%	NA
VI/Aromatic	96	93.80%	6.20%	0.00%	0.00%	NA
Intermediate	90	82.20%	15.60%	0.00%	0.00%	A: 2.22%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0401113415	G -> A	LOC_Os04g02860.1	upstream_gene_variant ; 60.0bp to feature; MODIFIER	silent_mutation	Average:76.224; most accessible tissue: Zhenshan97 panicle, score: 86.432	N	N	N	N
vg0401113415	G -> A	LOC_Os04g02850.1	downstream_gene_variant ; 119.0bp to feature; MODIFIER	silent_mutation	Average:76.224; most accessible tissue: Zhenshan97 panicle, score: 86.432	N	N	N	N
vg0401113415	G -> A	LOC_Os04g02850-LOC_Os04g02860	intergenic_region ; MODIFIER	silent_mutation	Average:76.224; most accessible tissue: Zhenshan97 panicle, score: 86.432	N	N	N	N
vg0401113415	G -> T	LOC_Os04g02860.1	upstream_gene_variant ; 60.0bp to feature; MODIFIER	silent_mutation	Average:76.224; most accessible tissue: Zhenshan97 panicle, score: 86.432	N	N	N	N
vg0401113415	G -> T	LOC_Os04g02850.1	downstream_gene_variant ; 119.0bp to feature; MODIFIER	silent_mutation	Average:76.224; most accessible tissue: Zhenshan97 panicle, score: 86.432	N	N	N	N
vg0401113415	G -> T	LOC_Os04g02850-LOC_Os04g02860	intergenic_region ; MODIFIER	silent_mutation	Average:76.224; most accessible tissue: Zhenshan97 panicle, score: 86.432	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0401113415	1.46E-06	NA	mr1261	All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0401113415	NA	3.91E-07	mr1841	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0401113415	NA	1.54E-06	mr1841_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251