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Detailed information for vg1214762481:

Variant ID: vg1214762481 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 14762481
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 123. )

Flanking Sequence (100 bp) in Reference Genome:

GCCCTCAAGTTGAGGTGAATTGCATGCTTGAATTGAGTGCAATAAATGCCTCTTCGGCCTCCTGTGTCCATACAAATTTGTCTTGCTTTTTCAGCAGAGC[G/A]
AAGAAAGGTTGTCCTCGCTCTCCCATCCTAGCGACGAACCTGCTTAGTGCTGCCATGCATCCGGTTAGCTTCTGTACTTCTTTGAGTCTTGTAGGCGACT

Reverse complement sequence

AGTCGCCTACAAGACTCAAAGAAGTACAGAAGCTAACCGGATGCATGGCAGCACTAAGCAGGTTCGTCGCTAGGATGGGAGAGCGAGGACAACCTTTCTT[C/T]
GCTCTGCTGAAAAAGCAAGACAAATTTGTATGGACACAGGAGGCCGAAGAGGCATTTATTGCACTCAATTCAAGCATGCAATTCACCTCAACTTGAGGGC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	92.20%	7.80%	0.00%	0.00%	NA
All Indica	2759	96.70%	3.30%	0.00%	0.00%	NA
All Japonica	1512	86.40%	13.60%	0.00%	0.00%	NA
Aus	269	82.50%	17.50%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	89.00%	11.00%	0.00%	0.00%	NA
Indica III	913	97.50%	2.50%	0.00%	0.00%	NA
Indica Intermediate	786	97.80%	2.20%	0.00%	0.00%	NA
Temperate Japonica	767	97.00%	3.00%	0.00%	0.00%	NA
Tropical Japonica	504	70.80%	29.20%	0.00%	0.00%	NA
Japonica Intermediate	241	85.50%	14.50%	0.00%	0.00%	NA
VI/Aromatic	96	80.20%	19.80%	0.00%	0.00%	NA
Intermediate	90	92.20%	7.80%	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
vg1214762481	G -> A	LOC_Os12g25510.1	synonymous_variant ; p.Phe1272Phe; LOW	synonymous_codon	Average:23.366; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1214762481	1.97E-07	1.97E-07	mr1877	Jap_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