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Detailed information for vg0226712993:

Variant ID: vg0226712993 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 26712993
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:

CAGTAAAACATGAACAGATCAAATACGCGCAACATGTCGAACATATACCGAGGTGGCGGAAAGACCGGTTGCTCGGCAGGAACTACTCACGGTTGCGAGC[G/A]
TCGACGAAGACACGAAGCACGCAAGCGGAGAGGAAGGCGGGCCGTCGCGGACGAATAGGGAGCAGTCGCGCGAAGCGCTTCCCAAAAACCTTATTGCCGC

Reverse complement sequence

GCGGCAATAAGGTTTTTGGGAAGCGCTTCGCGCGACTGCTCCCTATTCGTCCGCGACGGCCCGCCTTCCTCTCCGCTTGCGTGCTTCGTGTCTTCGTCGA[C/T]
GCTCGCAACCGTGAGTAGTTCCTGCCGAGCAACCGGTCTTTCCGCCACCTCGGTATATGTTCGACATGTTGCGCGTATTTGATCTGTTCATGTTTTACTG

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	74.90%	16.90%	8.25%	0.00%	NA
All Indica	2759	57.80%	28.50%	13.70%	0.00%	NA
All Japonica	1512	99.60%	0.20%	0.20%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	22.50%	44.40%	33.11%	0.00%	NA
Indica II	465	54.60%	35.50%	9.89%	0.00%	NA
Indica III	913	86.50%	11.10%	2.41%	0.00%	NA
Indica Intermediate	786	53.20%	32.40%	14.38%	0.00%	NA
Temperate Japonica	767	99.70%	0.00%	0.26%	0.00%	NA
Tropical Japonica	504	99.40%	0.40%	0.20%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	81.10%	8.90%	10.00%	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
vg0226712993	G -> A	LOC_Os02g44136.1	intron_variant ; MODIFIER	silent_mutation	Average:31.649; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0226712993	NA	2.60E-06	mr1227_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
vg0226712993	1.90E-06	1.63E-07	mr1270_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