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Detailed information for vg0824181264:

Variant ID: vg0824181264 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 24181264
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 345. )

Flanking Sequence (100 bp) in Reference Genome:

TATACTAGATTCATTTCTCTTATGCTGTTTGGTTGGCTAGGTAGATAAGCTCATACAGCATAAGAGAATTTGGTTGGCAACAGAGAATTGATTAATTTCT[T/C]
CAGAGGTCAGCTGATACACAGCTGCCACCCAATGCAACTAGAGCTCCAAAGCTCTAATGCCAATATGCCATTTCAAACTTGGCGTCCAATTTTACAATTT

Reverse complement sequence

AAATTGTAAAATTGGACGCCAAGTTTGAAATGGCATATTGGCATTAGAGCTTTGGAGCTCTAGTTGCATTGGGTGGCAGCTGTGTATCAGCTGACCTCTG[A/G]
AGAAATTAATCAATTCTCTGTTGCCAACCAAATTCTCTTATGCTGTATGAGCTTATCTACCTAGCCAACCAAACAGCATAAGAGAAATGAATCTAGTATA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	98.70%	1.10%	0.17%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	96.00%	3.40%	0.53%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	92.30%	6.60%	1.04%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	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
vg0824181264	T -> C	LOC_Os08g38160-LOC_Os08g38170	intergenic_region ; MODIFIER	silent_mutation	Average:63.147; most accessible tissue: Callus, score: 90.485	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0824181264	NA	2.66E-06	mr1648	Jap_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
vg0824181264	8.99E-08	1.02E-09	mr1697	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