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Detailed information for vg0903405991:

Variant ID: vg0903405991 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 3405991
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.80, A: 0.21, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:

TTTGCAGGATATATTACCAAATAAAAACGTAGATACAATTTGCTCACCACCCAGTATCAGTGCGCTGCTCTTCTGGAATATCAGTTGATACAGGATAACC[G/A]
ATCAGCCTGCAAACCCAAAAAGGATCTCCTGCGGTTGTACCTTCAAAAGCATCAACTGGCGCACCCAACGCCAAGGCTATACCTCGCATGATCTTTCTTG

Reverse complement sequence

CAAGAAAGATCATGCGAGGTATAGCCTTGGCGTTGGGTGCGCCAGTTGATGCTTTTGAAGGTACAACCGCAGGAGATCCTTTTTGGGTTTGCAGGCTGAT[C/T]
GGTTATCCTGTATCAACTGATATTCCAGAAGAGCAGCGCACTGATACTGGGTGGTGAGCAAATTGTATCTACGTTTTTATTTGGTAATATATCCTGCAAA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	63.00%	37.00%	0.02%	0.00%	NA
All Indica	2759	96.00%	4.00%	0.00%	0.00%	NA
All Japonica	1512	1.10%	98.90%	0.00%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	95.10%	4.90%	0.00%	0.00%	NA
Indica II	465	91.60%	8.40%	0.00%	0.00%	NA
Indica III	913	99.00%	1.00%	0.00%	0.00%	NA
Indica Intermediate	786	95.70%	4.30%	0.00%	0.00%	NA
Temperate Japonica	767	0.80%	99.20%	0.00%	0.00%	NA
Tropical Japonica	504	1.00%	99.00%	0.00%	0.00%	NA
Japonica Intermediate	241	2.10%	97.90%	0.00%	0.00%	NA
VI/Aromatic	96	7.30%	92.70%	0.00%	0.00%	NA
Intermediate	90	42.20%	56.70%	1.11%	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
vg0903405991	G -> A	LOC_Os09g07020.1	synonymous_variant ; p.Ile296Ile; LOW	synonymous_codon	Average:52.962; most accessible tissue: Zhenshan97 young leaf, score: 75.751	N	N	N	N
vg0903405991	G -> A	LOC_Os09g07020.2	synonymous_variant ; p.Ile295Ile; LOW	synonymous_codon	Average:52.962; most accessible tissue: Zhenshan97 young leaf, score: 75.751	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0903405991	NA	2.17E-07	mr1190	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