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Detailed information for vg0813651729:

Variant ID: vg0813651729 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 13651729
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: 113. )

Flanking Sequence (100 bp) in Reference Genome:

TTTACCCACAAGACAGAAAACTTGACTTCATGTCAGCAATGCATCGCGATACCTCAAAGGTACCCGAAAAGTCAAGATCGTGACAAGACTATCCACCTAG[C/T]
TCAACCCAAAACAGAAGGACCCGCTAAGGTTTCGCCGCTCGCTGGTCCCCGACAAGGTAAAGGTTGCCGGATCCCCCGGGACGAGACAGGCCCTCTCTTG

Reverse complement sequence

CAAGAGAGGGCCTGTCTCGTCCCGGGGGATCCGGCAACCTTTACCTTGTCGGGGACCAGCGAGCGGCGAAACCTTAGCGGGTCCTTCTGTTTTGGGTTGA[G/A]
CTAGGTGGATAGTCTTGTCACGATCTTGACTTTTCGGGTACCTTTGAGGTATCGCGATGCATTGCTGACATGAAGTCAAGTTTTCTGTCTTGTGGGTAAA

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	79.50%	0.30%	3.47%	16.74%	NA
All Indica	2759	79.60%	0.40%	5.58%	14.39%	NA
All Japonica	1512	75.30%	0.10%	0.26%	24.40%	NA
Aus	269	98.10%	0.00%	0.74%	1.12%	NA
Indica I	595	74.50%	0.20%	8.74%	16.64%	NA
Indica II	465	79.40%	0.90%	6.24%	13.55%	NA
Indica III	913	81.50%	0.80%	3.29%	14.46%	NA
Indica Intermediate	786	81.40%	0.00%	5.47%	13.10%	NA
Temperate Japonica	767	97.00%	0.00%	0.26%	2.74%	NA
Tropical Japonica	504	55.00%	0.00%	0.20%	44.84%	NA
Japonica Intermediate	241	48.50%	0.40%	0.41%	50.62%	NA
VI/Aromatic	96	92.70%	0.00%	0.00%	7.29%	NA
Intermediate	90	77.80%	1.10%	4.44%	16.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0813651729	C -> T	LOC_Os08g22690.1	upstream_gene_variant ; 2514.0bp to feature; MODIFIER	silent_mutation	Average:28.783; most accessible tissue: Zhenshan97 flag leaf, score: 50.663	N	N	N	N
vg0813651729	C -> T	LOC_Os08g22700.1	upstream_gene_variant ; 1218.0bp to feature; MODIFIER	silent_mutation	Average:28.783; most accessible tissue: Zhenshan97 flag leaf, score: 50.663	N	N	N	N
vg0813651729	C -> T	LOC_Os08g22710.1	upstream_gene_variant ; 3193.0bp to feature; MODIFIER	silent_mutation	Average:28.783; most accessible tissue: Zhenshan97 flag leaf, score: 50.663	N	N	N	N
vg0813651729	C -> T	LOC_Os08g22690-LOC_Os08g22700	intergenic_region ; MODIFIER	silent_mutation	Average:28.783; most accessible tissue: Zhenshan97 flag leaf, score: 50.663	N	N	N	N
vg0813651729	C -> DEL	N	N	silent_mutation	Average:28.783; most accessible tissue: Zhenshan97 flag leaf, score: 50.663	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0813651729	1.48E-06	NA	mr1350_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
vg0813651729	2.79E-06	NA	mr1350_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