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Detailed information for vg1115880748:

Variant ID: vg1115880748 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 15880748
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.03, others allele: 0.00, population size: 76. )

Flanking Sequence (100 bp) in Reference Genome:

TTTATGTGCTATATGTCTAGGTGTACACCATTTCTTCATTCCATATTCCTTGTCGAGATCCAGCAACCGTTCTCGAGCGATCGAGAAGGCGTAGAGTCTG[C/T]
GACGGAGCTTTGTCGACATTTGTCGTACTCGTCTTAGTCGATCTTGGTGTAGAACCATAGGGACATGGAGTCTTCCACAATGTTGAATAGAATTTTCCTG

Reverse complement sequence

CAGGAAAATTCTATTCAACATTGTGGAAGACTCCATGTCCCTATGGTTCTACACCAAGATCGACTAAGACGAGTACGACAAATGTCGACAAAGCTCCGTC[G/A]
CAGACTCTACGCCTTCTCGATCGCTCGAGAACGGTTGCTGGATCTCGACAAGGAATATGGAATGAAGAAATGGTGTACACCTAGACATATAGCACATAAA

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	88.10%	3.90%	8.00%	0.00%	NA
All Indica	2759	81.20%	6.00%	12.79%	0.00%	NA
All Japonica	1512	98.60%	0.70%	0.66%	0.00%	NA
Aus	269	97.80%	1.50%	0.74%	0.00%	NA
Indica I	595	92.30%	0.80%	6.89%	0.00%	NA
Indica II	465	54.20%	16.60%	29.25%	0.00%	NA
Indica III	913	88.90%	4.40%	6.68%	0.00%	NA
Indica Intermediate	786	79.90%	5.50%	14.63%	0.00%	NA
Temperate Japonica	767	97.80%	1.30%	0.91%	0.00%	NA
Tropical Japonica	504	99.40%	0.00%	0.60%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	96.90%	1.00%	2.08%	0.00%	NA
Intermediate	90	83.30%	4.40%	12.22%	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
vg1115880748	C -> T	LOC_Os11g27570.1	3_prime_UTR_variant ; 744.0bp to feature; MODIFIER	silent_mutation	Average:40.732; most accessible tissue: Callus, score: 65.857	N	N	N	N
vg1115880748	C -> T	LOC_Os11g27580.1	upstream_gene_variant ; 2307.0bp to feature; MODIFIER	silent_mutation	Average:40.732; most accessible tissue: Callus, score: 65.857	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1115880748	4.91E-06	4.91E-06	mr1500_2	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