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Detailed information for vg0235474703:

Variant ID: vg0235474703 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 35474703
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: 0.01, others allele: 0.00, population size: 213. )

Flanking Sequence (100 bp) in Reference Genome:

GGGTGCATGGTTTTGCTGGTCGCACCCATGGCATTTAAGGACCGGTTCGCGGGAAACACTGGAAGAACTTATCGTGCTTACCACAAGCCAGCGTGGGCAA[C/T]
GGCTGGGCTTGTAGTATAACTTTTCTCTAGCTGACGCATCCAGGCAAGGGTGGGCGTGATGGAGTTTGGATGGGCCCTGCGACGGCCTATGTGGCTTCCG

Reverse complement sequence

CGGAAGCCACATAGGCCGTCGCAGGGCCCATCCAAACTCCATCACGCCCACCCTTGCCTGGATGCGTCAGCTAGAGAAAAGTTATACTACAAGCCCAGCC[G/A]
TTGCCCACGCTGGCTTGTGGTAAGCACGATAAGTTCTTCCAGTGTTTCCCGCGAACCGGTCCTTAAATGCCATGGGTGCGACCAGCAAAACCATGCACCC

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	90.50%	3.20%	2.43%	3.85%	NA
All Indica	2759	88.50%	3.20%	3.70%	4.57%	NA
All Japonica	1512	97.50%	0.10%	0.20%	2.18%	NA
Aus	269	73.20%	18.60%	1.49%	6.69%	NA
Indica I	595	81.70%	8.70%	5.55%	4.03%	NA
Indica II	465	94.00%	1.50%	2.58%	1.94%	NA
Indica III	913	89.70%	0.30%	3.29%	6.68%	NA
Indica Intermediate	786	89.20%	3.30%	3.44%	4.07%	NA
Temperate Japonica	767	96.20%	0.00%	0.13%	3.65%	NA
Tropical Japonica	504	99.20%	0.20%	0.00%	0.60%	NA
Japonica Intermediate	241	97.90%	0.40%	0.83%	0.83%	NA
VI/Aromatic	96	85.40%	9.40%	4.17%	1.04%	NA
Intermediate	90	91.10%	2.20%	2.22%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0235474703	C -> T	LOC_Os02g57930.1	downstream_gene_variant ; 2630.0bp to feature; MODIFIER	silent_mutation	Average:29.803; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0235474703	C -> T	LOC_Os02g57930-LOC_Os02g57940	intergenic_region ; MODIFIER	silent_mutation	Average:29.803; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0235474703	C -> DEL	N	N	silent_mutation	Average:29.803; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0235474703	1.37E-07	1.37E-07	mr1335_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