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Detailed information for vg0529112100:

Variant ID: vg0529112100 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 29112100
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 120. )

Flanking Sequence (100 bp) in Reference Genome:

TAAGCCTAATTAATCCATGATTAGCCTATGTGATGCTACAGCAAACATATGTTAATTATGGATTAATTAGGCTTAAAAAATTATCACATAAATTAGCTCT[C/T]
ATTTATATAATTAGTTTTATAAGTAGTCTATATTTAATACTTTAAATTAGTATCAAATATCTGATGTGATAGGGACTAAAGAGTACCTGAATTCAAACAC

Reverse complement sequence

GTGTTTGAATTCAGGTACTCTTTAGTCCCTATCACATCAGATATTTGATACTAATTTAAAGTATTAAATATAGACTACTTATAAAACTAATTATATAAAT[G/A]
AGAGCTAATTTATGTGATAATTTTTTAAGCCTAATTAATCCATAATTAACATATGTTTGCTGTAGCATCACATAGGCTAATCATGGATTAATTAGGCTTA

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	89.70%	10.10%	0.13%	0.00%	NA
All Indica	2759	83.10%	16.70%	0.18%	0.00%	NA
All Japonica	1512	99.60%	0.40%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	54.80%	44.70%	0.50%	0.00%	NA
Indica II	465	76.80%	23.20%	0.00%	0.00%	NA
Indica III	913	99.70%	0.30%	0.00%	0.00%	NA
Indica Intermediate	786	89.10%	10.70%	0.25%	0.00%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	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	85.60%	13.30%	1.11%	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
vg0529112100	C -> T	LOC_Os05g50760-LOC_Os05g50770	intergenic_region ; MODIFIER	silent_mutation	Average:52.383; most accessible tissue: Minghui63 panicle, score: 79.811	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0529112100	NA	2.63E-07	mr1707	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
vg0529112100	2.58E-06	1.95E-09	mr1850	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
vg0529112100	6.79E-07	6.79E-07	mr1850	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