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Detailed information for vg0230509424:

Variant ID: vg0230509424 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 30509424
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, T: 0.03, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:

GGCGTAGCAGCTCAGCTCAGGCTTCGTCCTAACTCTGGATCCCAATCCCCCATGCGGCGTCTCTACCTCTATCAATCAGGTCAGGCTCCGATCCCCATTC[G/T]
CTCGTGCTCTCGTCGGCGTGGAGCAGCAAGTGCAAGAAGCTGGGCAGGCTAGCCAAGATGTCCAGCGCCGACGTGGAAGGGGCCGAGAAGGTGGAGGAAC

Reverse complement sequence

GTTCCTCCACCTTCTCGGCCCCTTCCACGTCGGCGCTGGACATCTTGGCTAGCCTGCCCAGCTTCTTGCACTTGCTGCTCCACGCCGACGAGAGCACGAG[C/A]
GAATGGGGATCGGAGCCTGACCTGATTGATAGAGGTAGAGACGCCGCATGGGGGATTGGGATCCAGAGTTAGGACGAAGCCTGAGCTGAGCTGCTACGCC

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	55.00%	43.40%	1.69%	0.00%	NA
All Indica	2759	26.20%	71.00%	2.83%	0.00%	NA
All Japonica	1512	99.80%	0.20%	0.00%	0.00%	NA
Aus	269	77.00%	23.00%	0.00%	0.00%	NA
Indica I	595	9.60%	88.20%	2.18%	0.00%	NA
Indica II	465	34.00%	62.80%	3.23%	0.00%	NA
Indica III	913	27.70%	70.30%	1.97%	0.00%	NA
Indica Intermediate	786	32.30%	63.60%	4.07%	0.00%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	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	71.10%	26.70%	2.22%	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
vg0230509424	G -> T	LOC_Os02g49930.1	downstream_gene_variant ; 1172.0bp to feature; MODIFIER	silent_mutation	Average:65.113; most accessible tissue: Minghui63 young leaf, score: 81.798	N	N	N	N
vg0230509424	G -> T	LOC_Os02g49940.1	downstream_gene_variant ; 4136.0bp to feature; MODIFIER	silent_mutation	Average:65.113; most accessible tissue: Minghui63 young leaf, score: 81.798	N	N	N	N
vg0230509424	G -> T	LOC_Os02g49930-LOC_Os02g49940	intergenic_region ; MODIFIER	silent_mutation	Average:65.113; most accessible tissue: Minghui63 young leaf, score: 81.798	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0230509424	NA	4.70E-14	mr1609	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