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Detailed information for vg0200562862:

Variant ID: vg0200562862 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 562862
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, C: 0.00, others allele: 0.00, population size: 336. )

Flanking Sequence (100 bp) in Reference Genome:

CAGCTGGCTCATTCTTCTTCAGGAAGCTATCAACAAGCAGTGCATGCGATTCAGGGTCAGTACGGACACCACGGCGTGTCATAATGGCAAGAATCTCCTG[T/C]
GCTGCTTCTGGCACACCTTCCTTTGCATGCCCACGGATAAGACTGTTAAAAGCAGCCTTGTCATCAACGCCTTTCTTCATCAGCTGCCTGAAGAAAGTCT

Reverse complement sequence

AGACTTTCTTCAGGCAGCTGATGAAGAAAGGCGTTGATGACAAGGCTGCTTTTAACAGTCTTATCCGTGGGCATGCAAAGGAAGGTGTGCCAGAAGCAGC[A/G]
CAGGAGATTCTTGCCATTATGACACGCCGTGGTGTCCGTACTGACCCTGAATCGCATGCACTGCTTGTTGATAGCTTCCTGAAGAAGAATGAGCCAGCTG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	89.00%	11.00%	0.08%	0.00%	NA
All Indica	2759	81.40%	18.40%	0.14%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	74.60%	25.00%	0.34%	0.00%	NA
Indica II	465	67.10%	32.70%	0.22%	0.00%	NA
Indica III	913	89.50%	10.50%	0.00%	0.00%	NA
Indica Intermediate	786	85.80%	14.10%	0.13%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	90.00%	10.00%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0200562862	T -> C	LOC_Os02g02020.1	synonymous_variant ; p.Ala515Ala; LOW	synonymous_codon	Average:69.677; most accessible tissue: Zhenshan97 young leaf, score: 79.783	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0200562862	NA	2.28E-09	mr1352	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