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Detailed information for vg0810065977:

Variant ID: vg0810065977 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 10065977
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.67, C: 0.32, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:

TGGCAACCAGAGAGAGAGAGGGGGTGGTATTAGGAAGCAATGGTACGTCGGGCTTGTTTGGTTTGAATCTAATTTTTGCCCTACCAAAATCTTGGTAGTG[T/C]
CAAAATCTTGACAAATTTTGGCACTACCAAATTGGACAGTATTGAATTTGAACTATTGTGACAAAAAATTGGTAGCAAACCAAACATGTATTTGCTTCTA

Reverse complement sequence

TAGAAGCAAATACATGTTTGGTTTGCTACCAATTTTTTGTCACAATAGTTCAAATTCAATACTGTCCAATTTGGTAGTGCCAAAATTTGTCAAGATTTTG[A/G]
CACTACCAAGATTTTGGTAGGGCAAAAATTAGATTCAAACCAAACAAGCCCGACGTACCATTGCTTCCTAATACCACCCCCTCTCTCTCTCTGGTTGCCA

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	35.20%	12.90%	0.47%	51.38%	NA
All Indica	2759	44.10%	3.20%	0.51%	52.23%	NA
All Japonica	1512	18.40%	33.30%	0.40%	47.88%	NA
Aus	269	51.70%	0.70%	0.00%	47.58%	NA
Indica I	595	44.90%	8.90%	0.67%	45.55%	NA
Indica II	465	44.30%	1.50%	0.43%	53.76%	NA
Indica III	913	48.60%	0.20%	0.22%	50.93%	NA
Indica Intermediate	786	38.20%	3.20%	0.76%	57.89%	NA
Temperate Japonica	767	30.00%	56.70%	0.52%	12.78%	NA
Tropical Japonica	504	1.20%	6.90%	0.40%	91.47%	NA
Japonica Intermediate	241	17.40%	14.10%	0.00%	68.46%	NA
VI/Aromatic	96	8.30%	0.00%	0.00%	91.67%	NA
Intermediate	90	24.40%	21.10%	2.22%	52.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0810065977	T -> C	LOC_Os08g16440.1	downstream_gene_variant ; 2292.0bp to feature; MODIFIER	silent_mutation	Average:66.572; most accessible tissue: Zhenshan97 flower, score: 84.018	N	N	N	N
vg0810065977	T -> C	LOC_Os08g16430-LOC_Os08g16440	intergenic_region ; MODIFIER	silent_mutation	Average:66.572; most accessible tissue: Zhenshan97 flower, score: 84.018	N	N	N	N
vg0810065977	T -> DEL	N	N	silent_mutation	Average:66.572; most accessible tissue: Zhenshan97 flower, score: 84.018	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0810065977	1.10E-06	NA	mr1057_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
vg0810065977	1.62E-06	9.76E-10	mr1057_2	Jap_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