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Detailed information for vg0119929841:

Variant ID: vg0119929841 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 19929841
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.64, A: 0.36, others allele: 0.00, population size: 81. )

Flanking Sequence (100 bp) in Reference Genome:

AACCTTTCGATGAGCCACTCAGTTCAAAATTGGATTCCTGGAGCTCAGCAATTCGATTCCTCAGATCATGCTCATTTTTCCTGGCAAGCTCTTTTGTCTC[G/A]
TGCAGCAGACTCCTGGTGGTTTCAAGGGTCCCGAGATGAGGGACTAGCCTCTCTAAGGTTGCCGTTTTAGCTTCGTTCCTAAGATGAATCCTCTGCAAGA

Reverse complement sequence

TCTTGCAGAGGATTCATCTTAGGAACGAAGCTAAAACGGCAACCTTAGAGAGGCTAGTCCCTCATCTCGGGACCCTTGAAACCACCAGGAGTCTGCTGCA[C/T]
GAGACAAAAGAGCTTGCCAGGAAAAATGAGCATGATCTGAGGAATCGAATTGCTGAGCTCCAGGAATCCAATTTTGAACTGAGTGGCTCATCGAAAGGTT

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	77.50%	12.20%	10.26%	0.00%	NA
All Indica	2759	62.60%	20.70%	16.78%	0.00%	NA
All Japonica	1512	99.50%	0.10%	0.40%	0.00%	NA
Aus	269	95.20%	0.70%	4.09%	0.00%	NA
Indica I	595	64.40%	2.90%	32.77%	0.00%	NA
Indica II	465	95.30%	2.60%	2.15%	0.00%	NA
Indica III	913	38.60%	44.20%	17.20%	0.00%	NA
Indica Intermediate	786	69.70%	17.40%	12.85%	0.00%	NA
Temperate Japonica	767	99.10%	0.10%	0.78%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	91.10%	3.30%	5.56%	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
vg0119929841	G -> A	LOC_Os01g36020.1	synonymous_variant ; p.His464His; LOW	synonymous_codon	Average:42.575; most accessible tissue: Minghui63 flag leaf, score: 62.47	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0119929841	3.89E-06	NA	mr1911_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
vg0119929841	4.01E-06	NA	mr1911_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
vg0119929841	3.18E-07	NA	mr1918_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
vg0119929841	1.52E-06	NA	mr1918_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