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Detailed information for vg1203199238:

Variant ID: vg1203199238 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 3199238
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, T: 0.01, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:

AGGGGCTACCACGTAATGTGATAGACAGTGCATCAAGAGAAATGGGCTTGATACCCACCTAAGGTTGCACAATAGTGGAAACCTATCCATTGTGATCGGA[G/T]
ATCCCGTGAATTTGGATGGCGAAACAAACTATTGTGTGGCTGAGAGAAGAGACCATTGAAAAGAGCTCATTTTCATGATGTACTTCTCTTCTATTCTGCA

Reverse complement sequence

TGCAGAATAGAAGAGAAGTACATCATGAAAATGAGCTCTTTTCAATGGTCTCTTCTCTCAGCCACACAATAGTTTGTTTCGCCATCCAAATTCACGGGAT[C/A]
TCCGATCACAATGGATAGGTTTCCACTATTGTGCAACCTTAGGTGGGTATCAAGCCCATTTCTCTTGATGCACTGTCTATCACATTACGTGGTAGCCCCT

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	80.00%	20.00%	0.02%	0.00%	NA
All Indica	2759	75.50%	24.50%	0.04%	0.00%	NA
All Japonica	1512	99.70%	0.30%	0.00%	0.00%	NA
Aus	269	6.30%	93.70%	0.00%	0.00%	NA
Indica I	595	83.00%	17.00%	0.00%	0.00%	NA
Indica II	465	83.00%	17.00%	0.00%	0.00%	NA
Indica III	913	66.20%	33.70%	0.11%	0.00%	NA
Indica Intermediate	786	76.10%	23.90%	0.00%	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	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	95.80%	4.20%	0.00%	0.00%	NA
Intermediate	90	90.00%	10.00%	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
vg1203199238	G -> T	LOC_Os12g06610.1	upstream_gene_variant ; 2377.0bp to feature; MODIFIER	silent_mutation	Average:35.952; most accessible tissue: Zhenshan97 flag leaf, score: 49.845	N	N	N	N
vg1203199238	G -> T	LOC_Os12g06590.1	downstream_gene_variant ; 2336.0bp to feature; MODIFIER	silent_mutation	Average:35.952; most accessible tissue: Zhenshan97 flag leaf, score: 49.845	N	N	N	N
vg1203199238	G -> T	LOC_Os12g06600.1	intron_variant ; MODIFIER	silent_mutation	Average:35.952; 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
vg1203199238	2.69E-06	NA	mr1095	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
vg1203199238	NA	8.90E-06	mr1095	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