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Detailed information for vg0825997874:

Variant ID: vg0825997874 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 25997874
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, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:

CAGCCGTGCATCTCGGCGCAGCCCAGCGTCGTCGCCACCGTCTCCACTGACACGCTCTCCCACAGCTTCTGGGCGCACATCAGCTTCAGCCCGTCCAGCG[C/T]
GTACCTGTCCGCCGCCGCGAGCAAACGCTGATGATGAAGCAGATGATCGCTCGTGCTCGCCGTCGTCGACGACGATGAGCCCTCGATGATCTGCAGAACG

Reverse complement sequence

CGTTCTGCAGATCATCGAGGGCTCATCGTCGTCGACGACGGCGAGCACGAGCGATCATCTGCTTCATCATCAGCGTTTGCTCGCGGCGGCGGACAGGTAC[G/A]
CGCTGGACGGGCTGAAGCTGATGTGCGCCCAGAAGCTGTGGGAGAGCGTGTCAGTGGAGACGGTGGCGACGACGCTGGGCTGCGCCGAGATGCACGGCTG

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	91.50%	4.90%	3.62%	0.00%	NA
All Indica	2759	85.50%	8.30%	6.16%	0.00%	NA
All Japonica	1512	99.90%	0.00%	0.07%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	53.10%	28.40%	18.49%	0.00%	NA
Indica II	465	96.80%	1.10%	2.15%	0.00%	NA
Indica III	913	98.80%	1.10%	0.11%	0.00%	NA
Indica Intermediate	786	87.90%	5.90%	6.23%	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	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	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
vg0825997874	C -> T	LOC_Os08g41150.1	missense_variant ; p.Ala276Thr; MODERATE	nonsynonymous_codon ; A276T	Average:71.473; most accessible tissue: Zhenshan97 panicle, score: 84.824	unknown	unknown	DELETERIOUS	0.04

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0825997874	NA	3.61E-13	mr1709_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
vg0825997874	NA	2.33E-09	mr1709_2	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