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Detailed information for vg0825230903:

Variant ID: vg0825230903 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 25230903
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:

TGATCGTCAGATCTATAATACACCCGGTGAATTCAAATCCTCAAACAGGAGTAGGGTATTACCTCTCATCGATAGGGCCTAAACCTGTATAAATCCTTGT[C/T]
TTTGCATCCATCCACTTTTAGGTCTAGTGCGCTACCCCTTTTATATTGCTGAAATATTGTTTCGACAAGCTACATCACGAACTCCAAGACGACATACAAA

Reverse complement sequence

TTTGTATGTCGTCTTGGAGTTCGTGATGTAGCTTGTCGAAACAATATTTCAGCAATATAAAAGGGGTAGCGCACTAGACCTAAAAGTGGATGGATGCAAA[G/A]
ACAAGGATTTATACAGGTTTAGGCCCTATCGATGAGAGGTAATACCCTACTCCTGTTTGAGGATTTGAATTCACCGGGTGTATTATAGATCTGACGATCA

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	92.90%	7.10%	0.02%	0.00%	NA
All Indica	2759	94.90%	5.10%	0.00%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	31.60%	68.00%	0.37%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	95.90%	4.10%	0.00%	0.00%	NA
Indica III	913	94.20%	5.80%	0.00%	0.00%	NA
Indica Intermediate	786	91.10%	8.90%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	94.80%	5.20%	0.00%	0.00%	NA
Intermediate	90	93.30%	6.70%	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
vg0825230903	C -> T	LOC_Os08g39840-LOC_Os08g39850	intergenic_region ; MODIFIER	silent_mutation	Average:51.949; most accessible tissue: Zhenshan97 root, score: 70.636	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0825230903	4.20E-07	3.77E-18	mr1874	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
vg0825230903	3.78E-07	3.15E-22	mr1874_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
vg0825230903	NA	2.30E-12	mr1914_2	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