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Detailed information for vg0203136151:

Variant ID: vg0203136151 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 3136151
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.00, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:

CGGAATTCTGCAAGAATGAATTTTTGATACATTTAGACTGCTTCGATTCACATCATCTTACATAGCTGTGTACTTATACATTACCAGAATTCCTGGATCA[C/T]
TCTTCACCCATGTATTCCTTCCAGTTTATTATCAAAAAAACGAGTTCCCTCCAATGTCCTTTTCTTTATTTTTGTATTTTCCGCCTTTCATAGGAAAACC

Reverse complement sequence

GGTTTTCCTATGAAAGGCGGAAAATACAAAAATAAAGAAAAGGACATTGGAGGGAACTCGTTTTTTTGATAATAAACTGGAAGGAATACATGGGTGAAGA[G/A]
TGATCCAGGAATTCTGGTAATGTATAAGTACACAGCTATGTAAGATGATGTGAATCGAAGCAGTCTAAATGTATCAAAAATTCATTCTTGCAGAATTCCG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	87.30%	10.30%	0.47%	1.95%	NA
All Indica	2759	79.90%	17.30%	0.29%	2.50%	NA
All Japonica	1512	99.70%	0.10%	0.07%	0.13%	NA
Aus	269	99.30%	0.40%	0.00%	0.37%	NA
Indica I	595	77.10%	22.40%	0.50%	0.00%	NA
Indica II	465	86.50%	13.30%	0.00%	0.22%	NA
Indica III	913	77.10%	18.70%	0.00%	4.16%	NA
Indica Intermediate	786	81.40%	14.10%	0.64%	3.82%	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	98.80%	0.00%	0.41%	0.83%	NA
VI/Aromatic	96	70.80%	1.00%	13.54%	14.58%	NA
Intermediate	90	85.60%	7.80%	0.00%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0203136151	C -> T	LOC_Os02g06270.1	upstream_gene_variant ; 1166.0bp to feature; MODIFIER	silent_mutation	Average:49.683; most accessible tissue: Minghui63 flag leaf, score: 68.16	N	N	N	N
vg0203136151	C -> T	LOC_Os02g06280.1	downstream_gene_variant ; 32.0bp to feature; MODIFIER	silent_mutation	Average:49.683; most accessible tissue: Minghui63 flag leaf, score: 68.16	N	N	N	N
vg0203136151	C -> T	LOC_Os02g06270-LOC_Os02g06280	intergenic_region ; MODIFIER	silent_mutation	Average:49.683; most accessible tissue: Minghui63 flag leaf, score: 68.16	N	N	N	N
vg0203136151	C -> DEL	N	N	silent_mutation	Average:49.683; most accessible tissue: Minghui63 flag leaf, score: 68.16	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0203136151	NA	1.63E-06	mr1337	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
vg0203136151	4.18E-06	4.18E-06	mr1337	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