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Detailed information for vg0200812022:

Variant ID: vg0200812022 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 812022
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:

GGGCCATGTCTCAGTCCCAGTGTGGCTGATCATCCTCTCGGACCAGCTACTGATCATCGCCTTGGTAAGCTATTGCCTCACCAACTAGCTAATCAGACGC[G/T]
AGCCCCTCCTTGGGCGGATTTCTCCTTTTGCTCCTCAACCTACGGGGTATTACCAACCATTTCCAGTTGTTGTTCCCCTCCCAAAGGCAGGTTCTTACGC

Reverse complement sequence

GCGTAAGAACCTGCCTTTGGGAGGGGAACAACAACTGGAAATGGTTGGTAATACCCCGTAGGTTGAGGAGCAAAAGGAGAAATCCGCCCAAGGAGGGGCT[C/A]
GCGTCTGATTAGCTAGTTGGTGAGGCAATAGCTTACCAAGGCGATGATCAGTAGCTGGTCCGAGAGGATGATCAGCCACACTGGGACTGAGACATGGCCC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	89.20%	10.30%	0.49%	0.00%	NA
All Indica	2759	86.00%	13.20%	0.83%	0.00%	NA
All Japonica	1512	99.80%	0.20%	0.00%	0.00%	NA
Aus	269	56.50%	43.50%	0.00%	0.00%	NA
Indica I	595	93.40%	5.20%	1.34%	0.00%	NA
Indica II	465	72.30%	26.20%	1.51%	0.00%	NA
Indica III	913	91.50%	8.20%	0.33%	0.00%	NA
Indica Intermediate	786	82.20%	17.20%	0.64%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	5.60%	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
vg0200812022	G -> T	LOC_Os02g02380-LOC_Os02g02390	intergenic_region ; MODIFIER	silent_mutation	Average:33.687; most accessible tissue: Zhenshan97 root, score: 51.776	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0200812022	2.94E-07	2.94E-07	mr1259	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
vg0200812022	6.23E-06	6.23E-06	mr1299	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
vg0200812022	NA	2.87E-06	mr1669	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