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Detailed information for vg1125307514:

Variant ID: vg1125307514 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 25307514
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.02, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:

CACTTGTTAAACCGTTGGATGTGTTCGGGATCGTGCTAGCCGTTCGATACACCGTGATTTCTGAGAAAAAGAGAAAAGCAACGCACAAGGAGGGATCGAT[C/T]
CTGTGATCTCATCCTATTTATACAAGTTACAGTATATGCTAGGTACATATGTAATTATAATACAATTATACAATTATAGTGTAATTATGAAAATTATATT

Reverse complement sequence

AATATAATTTTCATAATTACACTATAATTGTATAATTGTATTATAATTACATATGTACCTAGCATATACTGTAACTTGTATAAATAGGATGAGATCACAG[G/A]
ATCGATCCCTCCTTGTGCGTTGCTTTTCTCTTTTTCTCAGAAATCACGGTGTATCGAACGGCTAGCACGATCCCGAACACATCCAACGGTTTAACAAGTG

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	36.90%	27.10%	0.28%	35.70%	NA
All Indica	2759	53.80%	20.80%	0.04%	25.41%	NA
All Japonica	1512	14.40%	35.40%	0.66%	49.54%	NA
Aus	269	3.70%	36.80%	0.37%	59.11%	NA
Indica I	595	42.90%	6.20%	0.00%	50.92%	NA
Indica II	465	24.70%	41.50%	0.00%	33.76%	NA
Indica III	913	70.40%	20.40%	0.11%	9.09%	NA
Indica Intermediate	786	59.90%	20.00%	0.00%	20.10%	NA
Temperate Japonica	767	3.00%	54.80%	0.39%	41.85%	NA
Tropical Japonica	504	31.30%	10.50%	0.00%	58.13%	NA
Japonica Intermediate	241	14.90%	26.10%	2.90%	56.02%	NA
VI/Aromatic	96	1.00%	53.10%	1.04%	44.79%	NA
Intermediate	90	34.40%	26.70%	0.00%	38.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1125307514	C -> T	LOC_Os11g42050-LOC_Os11g42060	intergenic_region ; MODIFIER	silent_mutation	Average:35.852; most accessible tissue: Callus, score: 68.14	N	N	N	N
vg1125307514	C -> DEL	N	N	silent_mutation	Average:35.852; most accessible tissue: Callus, score: 68.14	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1125307514	4.70E-06	NA	mr1130	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