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Detailed information for vg0301474140:

Variant ID: vg0301474140 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 1474140
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:

TGAAACTATTCTTAATGCCGAGAACAACGAGAGAATCATTCAGAGTTCAGACATCTTTTCGACAGTCATATGCTAGCTCCTGCTATTAGAGCAAATTTAA[T/C]
AGTATAGTCCACTGCAAGCTTAAAATCATCTATAGTCAATCTAATAGTCAATTCATACAATGGTTATCTAGAAATGTATACTACACTATTAATATTTGGT

Reverse complement sequence

ACCAAATATTAATAGTGTAGTATACATTTCTAGATAACCATTGTATGAATTGACTATTAGATTGACTATAGATGATTTTAAGCTTGCAGTGGACTATACT[A/G]
TTAAATTTGCTCTAATAGCAGGAGCTAGCATATGACTGTCGAAAAGATGTCTGAACTCTGAATGATTCTCTCGTTGTTCTCGGCATTAAGAATAGTTTCA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	91.80%	7.80%	0.38%	0.00%	NA
All Indica	2759	99.70%	0.30%	0.00%	0.00%	NA
All Japonica	1512	78.00%	20.80%	1.12%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.40%	0.60%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.40%	0.60%	0.00%	0.00%	NA
Temperate Japonica	767	78.60%	19.80%	1.56%	0.00%	NA
Tropical Japonica	504	75.40%	24.00%	0.60%	0.00%	NA
Japonica Intermediate	241	81.70%	17.40%	0.83%	0.00%	NA
VI/Aromatic	96	60.40%	39.60%	0.00%	0.00%	NA
Intermediate	90	91.10%	7.80%	1.11%	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
vg0301474140	T -> C	LOC_Os03g03430.1	upstream_gene_variant ; 2195.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0301474140	T -> C	LOC_Os03g03420-LOC_Os03g03430	intergenic_region ; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0301474140	3.63E-07	NA	mr1062_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