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Detailed information for vg0812796308:

Variant ID: vg0812796308 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 12796308
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: 115. )

Flanking Sequence (100 bp) in Reference Genome:

CAATTGAGAAGATGGTCTCAAATATGGGTTGGAGCGAGGAACGACTCCAAACCCGTCAATGCGGCATGTACACCGTCAAGAGGACGGAGATGCTCGCCGC[C/T]
CAGTTGGATCTCCTTATGAAGAGACTAGACAACAATGAGAAGGATAACAAGCAGGGTACCGTTAAAGCCCTGGACTTCCACACGACATGTGAGGTCTATG

Reverse complement sequence

CATAGACCTCACATGTCGTGTGGAAGTCCAGGGCTTTAACGGTACCCTGCTTGTTATCCTTCTCATTGTTGTCTAGTCTCTTCATAAGGAGATCCAACTG[G/A]
GCGGCGAGCATCTCCGTCCTCTTGACGGTGTACATGCCGCATTGACGGGTTTGGAGTCGTTCCTCGCTCCAACCCATATTTGAGACCATCTTCTCAATTG

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	63.60%	16.30%	3.83%	16.25%	NA
All Indica	2759	51.00%	19.80%	6.05%	23.20%	NA
All Japonica	1512	94.50%	0.30%	0.26%	4.89%	NA
Aus	269	4.50%	79.90%	2.97%	12.64%	NA
Indica I	595	36.80%	13.40%	5.88%	43.87%	NA
Indica II	465	83.20%	6.00%	1.72%	9.03%	NA
Indica III	913	46.40%	27.60%	8.21%	17.74%	NA
Indica Intermediate	786	48.00%	23.50%	6.23%	22.26%	NA
Temperate Japonica	767	96.10%	0.30%	0.26%	3.39%	NA
Tropical Japonica	504	94.20%	0.00%	0.40%	5.36%	NA
Japonica Intermediate	241	90.00%	1.20%	0.00%	8.71%	NA
VI/Aromatic	96	95.80%	3.10%	1.04%	0.00%	NA
Intermediate	90	73.30%	3.30%	1.11%	22.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0812796308	C -> T	LOC_Os08g21470.1	synonymous_variant ; p.Ala110Ala; LOW	synonymous_codon	Average:30.336; most accessible tissue: Minghui63 panicle, score: 64.459	N	N	N	N
vg0812796308	C -> DEL	LOC_Os08g21470.1	N	frameshift_variant	Average:30.336; most accessible tissue: Minghui63 panicle, score: 64.459	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0812796308	NA	6.76E-06	mr1543	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