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Detailed information for vg1105847289:

Variant ID: vg1105847289 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 5847289
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGATCTTTTGAGATACATTTGACCATCCGTCTTATTAAAAAAAATTATGTAATCATTTATTTTGCTTGACTTGATTTATTATCAAATGTTCTTTAAGCAT[G/T]
ATATAATTATTTTTATATTTACATAAAAATTTTGAATAAGATAAATAATCAAACGTTGGTCAACAAGTCAACAGCGCATACATTAGAAAACAGGAGGAGT

Reverse complement sequence

ACTCCTCCTGTTTTCTAATGTATGCGCTGTTGACTTGTTGACCAACGTTTGATTATTTATCTTATTCAAAATTTTTATGTAAATATAAAAATAATTATAT[C/A]
ATGCTTAAAGAACATTTGATAATAAATCAAGTCAAGCAAAATAAATGATTACATAATTTTTTTTAATAAGACGGATGGTCAAATGTATCTCAAAAGATCA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	86.50%	13.40%	0.19%	0.00%	NA
All Indica	2759	85.00%	14.80%	0.22%	0.00%	NA
All Japonica	1512	93.30%	6.70%	0.00%	0.00%	NA
Aus	269	59.10%	40.10%	0.74%	0.00%	NA
Indica I	595	91.40%	8.20%	0.34%	0.00%	NA
Indica II	465	93.80%	6.00%	0.22%	0.00%	NA
Indica III	913	81.30%	18.70%	0.00%	0.00%	NA
Indica Intermediate	786	79.30%	20.40%	0.38%	0.00%	NA
Temperate Japonica	767	98.40%	1.60%	0.00%	0.00%	NA
Tropical Japonica	504	87.10%	12.90%	0.00%	0.00%	NA
Japonica Intermediate	241	90.00%	10.00%	0.00%	0.00%	NA
VI/Aromatic	96	94.80%	5.20%	0.00%	0.00%	NA
Intermediate	90	88.90%	10.00%	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
vg1105847289	G -> T	LOC_Os11g10650.1	downstream_gene_variant ; 4491.0bp to feature; MODIFIER	silent_mutation	Average:37.445; most accessible tissue: Callus, score: 89.317	N	N	N	N
vg1105847289	G -> T	LOC_Os11g10670.1	downstream_gene_variant ; 4764.0bp to feature; MODIFIER	silent_mutation	Average:37.445; most accessible tissue: Callus, score: 89.317	N	N	N	N
vg1105847289	G -> T	LOC_Os11g10650-LOC_Os11g10670	intergenic_region ; MODIFIER	silent_mutation	Average:37.445; most accessible tissue: Callus, score: 89.317	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1105847289	2.24E-06	2.24E-06	mr1918	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