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Detailed information for vg0212545067:

Variant ID: vg0212545067 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 12545067
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 116. )

Flanking Sequence (100 bp) in Reference Genome:

GTGCGTCCTTGAAGAAATTGTAGGAGGAGGGCACTCTCCCCAGTCATGGGACTATGGAGAGGGAACCGGGAGGTACTGAACCTGAACCCGTCCTGGGCCG[C/T]
ATGGTTGCGGTTGAGGACTACATTCTCTGTGGTTTTCTTCCTCCGCCTTCTGAGTTTTTCCTTCTTGTATTGAACTTCTACGGTCTTTCTCTGCTCCATC

Reverse complement sequence

GATGGAGCAGAGAAAGACCGTAGAAGTTCAATACAAGAAGGAAAAACTCAGAAGGCGGAGGAAGAAAACCACAGAGAATGTAGTCCTCAACCGCAACCAT[G/A]
CGGCCCAGGACGGGTTCAGGTTCAGTACCTCCCGGTTCCCTCTCCATAGTCCCATGACTGGGGAGAGTGCCCTCCTCCTACAATTTCTTCAAGGACGCAC

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	61.80%	37.90%	0.28%	0.00%	NA
All Indica	2759	96.30%	3.40%	0.25%	0.00%	NA
All Japonica	1512	1.70%	98.30%	0.07%	0.00%	NA
Aus	269	71.00%	28.60%	0.37%	0.00%	NA
Indica I	595	98.70%	1.20%	0.17%	0.00%	NA
Indica II	465	97.00%	2.60%	0.43%	0.00%	NA
Indica III	913	97.30%	2.60%	0.11%	0.00%	NA
Indica Intermediate	786	93.00%	6.60%	0.38%	0.00%	NA
Temperate Japonica	767	1.00%	99.00%	0.00%	0.00%	NA
Tropical Japonica	504	2.40%	97.60%	0.00%	0.00%	NA
Japonica Intermediate	241	2.10%	97.50%	0.41%	0.00%	NA
VI/Aromatic	96	8.30%	91.70%	0.00%	0.00%	NA
Intermediate	90	44.40%	51.10%	4.44%	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
vg0212545067	C -> T	LOC_Os02g21130.1	synonymous_variant ; p.Arg16Arg; LOW	synonymous_codon	Average:32.309; most accessible tissue: Zhenshan97 flag leaf, score: 49.845	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0212545067	1.63E-06	NA	mr1531	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
vg0212545067	8.20E-06	NA	mr1531	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
vg0212545067	NA	8.46E-06	mr1992_2	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