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Detailed information for vg0401360082:

Variant ID: vg0401360082 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 1360082
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 291. )

Flanking Sequence (100 bp) in Reference Genome:

TTGGGCCATGGATCCAATCCTCAAGGCTTCCATTTGTCATAAACTCGTACACCAATGCACGGAATTCATTTCCACTGAAGTCTATACTTGAGCATAGTGT[C/T]
ACCAGCTTTACTAGGTTCCGATGTCGTATAGTGCTTAGAATCTCGCACTCTGCAACCCAGCTATTGGTTGCACCAATCTTGTTAAGATCTAGCACTTTGA

Reverse complement sequence

TCAAAGTGCTAGATCTTAACAAGATTGGTGCAACCAATAGCTGGGTTGCAGAGTGCGAGATTCTAAGCACTATACGACATCGGAACCTAGTAAAGCTGGT[G/A]
ACACTATGCTCAAGTATAGACTTCAGTGGAAATGAATTCCGTGCATTGGTGTACGAGTTTATGACAAATGGAAGCCTTGAGGATTGGATCCATGGCCCAA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	92.80%	7.00%	0.23%	0.00%	NA
All Indica	2759	88.00%	11.70%	0.33%	0.00%	NA
All Japonica	1512	99.70%	0.20%	0.13%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	91.30%	8.40%	0.34%	0.00%	NA
Indica II	465	81.50%	18.30%	0.22%	0.00%	NA
Indica III	913	85.30%	14.30%	0.33%	0.00%	NA
Indica Intermediate	786	92.40%	7.30%	0.38%	0.00%	NA
Temperate Japonica	767	99.70%	0.00%	0.26%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	4.40%	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
vg0401360082	C -> T	LOC_Os04g03210.1	synonymous_variant ; p.Val714Val; LOW	synonymous_codon	Average:58.25; most accessible tissue: Zhenshan97 young leaf, score: 81.841	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0401360082	3.52E-07	3.37E-06	mr1563_2	Ind_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