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Detailed information for vg0208620450:

Variant ID: vg0208620450 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 8620450
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.58, G: 0.42, others allele: 0.00, population size: 50. )

Flanking Sequence (100 bp) in Reference Genome:

CTTCAAAGCCCATGAGCCTGGCCCGCTCTTTGCATCCTAATGGTTGTTACATTATGATTTAGAGATCACTTGCACTGCGGCTGAGGCTATATGAACCAGC[C/G]
CAAAGCGAAGATGATGAGAGAGTGAAGGGGATTAGAGACGATTACCAAAACATGTTGAAATTTGAGAGAACGATACAGTGTGAATCAGAAACCAAAAGAA

Reverse complement sequence

TTCTTTTGGTTTCTGATTCACACTGTATCGTTCTCTCAAATTTCAACATGTTTTGGTAATCGTCTCTAATCCCCTTCACTCTCTCATCATCTTCGCTTTG[G/C]
GCTGGTTCATATAGCCTCAGCCGCAGTGCAAGTGATCTCTAAATCATAATGTAACAACCATTAGGATGCAAAGAGCGGGCCAGGCTCATGGGCTTTGAAG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	23.40%	21.10%	0.28%	55.16%	NA
All Indica	2759	8.10%	26.90%	0.40%	64.66%	NA
All Japonica	1512	56.50%	1.10%	0.07%	42.26%	NA
Aus	269	2.20%	70.30%	0.37%	27.14%	NA
Indica I	595	13.30%	16.80%	0.50%	69.41%	NA
Indica II	465	5.20%	37.20%	0.43%	57.20%	NA
Indica III	913	0.80%	31.20%	0.11%	67.91%	NA
Indica Intermediate	786	14.40%	23.30%	0.64%	61.70%	NA
Temperate Japonica	767	81.40%	0.30%	0.00%	18.38%	NA
Tropical Japonica	504	29.20%	2.00%	0.20%	68.65%	NA
Japonica Intermediate	241	34.90%	2.10%	0.00%	63.07%	NA
VI/Aromatic	96	1.00%	24.00%	0.00%	75.00%	NA
Intermediate	90	25.60%	31.10%	0.00%	43.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0208620450	C -> G	LOC_Os02g15410-LOC_Os02g15420	intergenic_region ; MODIFIER	silent_mutation	Average:12.416; most accessible tissue: Callus, score: 79.39	N	N	N	N
vg0208620450	C -> DEL	N	N	silent_mutation	Average:12.416; most accessible tissue: Callus, score: 79.39	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0208620450	7.65E-07	NA	mr1987	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