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Detailed information for vg1113936658:

Variant ID: vg1113936658 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 13936658
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, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:

AATTCAATGGAACTTGAGTCTCTGTGAGAGGATGAAATTCTTGGTTCAAAAATAACGGAATATCCGATATGACATCGGACTACCCGATCGATCGGATTGT[C/T]
CGAAATTCTCCAGAATTTCATTCTCTATCTCTGGCCTGCTTGGGAGTCAAAAACATCGGACTATCCGATGTCACCTCGGACTTTCCGAGGTGGGATGAAA

Reverse complement sequence

TTTCATCCCACCTCGGAAAGTCCGAGGTGACATCGGATAGTCCGATGTTTTTGACTCCCAAGCAGGCCAGAGATAGAGAATGAAATTCTGGAGAATTTCG[G/A]
ACAATCCGATCGATCGGGTAGTCCGATGTCATATCGGATATTCCGTTATTTTTGAACCAAGAATTTCATCCTCTCACAGAGACTCAAGTTCCATTGAATT

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	61.60%	34.60%	3.75%	0.00%	NA
All Indica	2759	92.90%	2.00%	5.11%	0.00%	NA
All Japonica	1512	3.30%	96.60%	0.13%	0.00%	NA
Aus	269	88.10%	0.40%	11.52%	0.00%	NA
Indica I	595	96.10%	2.90%	1.01%	0.00%	NA
Indica II	465	97.60%	1.70%	0.65%	0.00%	NA
Indica III	913	88.20%	0.70%	11.17%	0.00%	NA
Indica Intermediate	786	93.30%	2.90%	3.82%	0.00%	NA
Temperate Japonica	767	3.90%	96.10%	0.00%	0.00%	NA
Tropical Japonica	504	3.00%	96.60%	0.40%	0.00%	NA
Japonica Intermediate	241	2.10%	97.90%	0.00%	0.00%	NA
VI/Aromatic	96	9.40%	90.60%	0.00%	0.00%	NA
Intermediate	90	58.90%	37.80%	3.33%	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
vg1113936658	C -> T	LOC_Os11g24440.1	upstream_gene_variant ; 3823.0bp to feature; MODIFIER	silent_mutation	Average:14.648; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg1113936658	C -> T	LOC_Os11g24450.1	upstream_gene_variant ; 4899.0bp to feature; MODIFIER	silent_mutation	Average:14.648; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg1113936658	C -> T	LOC_Os11g24440-LOC_Os11g24450	intergenic_region ; MODIFIER	silent_mutation	Average:14.648; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1113936658	NA	7.95E-23	mr1168	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
vg1113936658	NA	1.06E-15	mr1376	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
vg1113936658	NA	3.78E-25	mr1383	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
vg1113936658	NA	1.06E-15	mr1431	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
vg1113936658	NA	7.39E-08	mr1506	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
vg1113936658	NA	1.23E-07	mr1659	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
vg1113936658	NA	6.64E-11	mr1775	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
vg1113936658	NA	1.44E-06	mr1886	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