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Detailed information for vg0228612339:

Variant ID: vg0228612339 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 28612339
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:

CGAGTTTCAATAAATCGCCAAATGCCTTGTCACTAACACCATTTTTTGCCTTCCATTGCAAGAACTCCAGAGTGGTATCCAACTTTTTGTGCCCCTGCTC[G/A]
CAACCTGAGTACAACGACGTTCTGTGGTCCTCTAACATCTTGTCCAATTGATGGGCCCCTTTTTCACTTTCGCAGTCCTCCTTGGCGTCCTGCAACATCT

Reverse complement sequence

AGATGTTGCAGGACGCCAAGGAGGACTGCGAAAGTGAAAAAGGGGCCCATCAATTGGACAAGATGTTAGAGGACCACAGAACGTCGTTGTACTCAGGTTG[C/T]
GAGCAGGGGCACAAAAAGTTGGATACCACTCTGGAGTTCTTGCAATGGAAGGCAAAAAATGGTGTTAGTGACAAGGCATTTGGCGATTTATTGAAACTCG

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	67.00%	32.10%	0.83%	0.00%	NA
All Indica	2759	87.50%	12.00%	0.51%	0.00%	NA
All Japonica	1512	45.50%	53.30%	1.19%	0.00%	NA
Aus	269	6.30%	93.30%	0.37%	0.00%	NA
Indica I	595	98.00%	1.70%	0.34%	0.00%	NA
Indica II	465	93.80%	5.60%	0.65%	0.00%	NA
Indica III	913	84.00%	15.80%	0.22%	0.00%	NA
Indica Intermediate	786	80.00%	19.10%	0.89%	0.00%	NA
Temperate Japonica	767	59.80%	38.50%	1.69%	0.00%	NA
Tropical Japonica	504	10.90%	88.50%	0.60%	0.00%	NA
Japonica Intermediate	241	72.20%	27.00%	0.83%	0.00%	NA
VI/Aromatic	96	1.00%	99.00%	0.00%	0.00%	NA
Intermediate	90	52.20%	41.10%	6.67%	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
vg0228612339	G -> A	LOC_Os02g46900.1	synonymous_variant ; p.Cys76Cys; LOW	synonymous_codon	Average:12.695; most accessible tissue: Minghui63 root, score: 19.68	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0228612339	NA	9.69E-06	mr1734	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
vg0228612339	NA	8.31E-07	mr1548_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
vg0228612339	8.66E-07	NA	mr1627_2	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
vg0228612339	9.23E-06	1.73E-07	mr1627_2	Jap_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