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Detailed information for vg0233749871:

Variant ID: vg0233749871 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 33749871
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, G: 0.01, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:


CAACTAATTAATTCAAGTTTAATTCGAACTCAATATTTTTTTATTCGCGGTGACGACAAACTCGATACTCTCTCGGTCGTCTCAATATGTAGTACTCCCT[A/G]
TGTTTTGGACAAGGTTGAGGTCAAAGTTTTATAACTTTGACCATCACTAACTTTAAAAATATTTAGTTTAAAGAAACTAGAACAACATATATAAATTTGT

Reverse complement sequence

ACAAATTTATATATGTTGTTCTAGTTTCTTTAAACTAAATATTTTTAAAGTTAGTGATGGTCAAAGTTATAAAACTTTGACCTCAACCTTGTCCAAAACA[T/C]
AGGGAGTACTACATATTGAGACGACCGAGAGAGTATCGAGTTTGTCGTCACCGCGAATAAAAAAATATTGAGTTCGAATTAAACTTGAATTAATTAGTTG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 75.70% 22.20% 2.07% 0.00% NA
All Indica  2759 62.50% 33.90% 3.55% 0.00% NA
All Japonica  1512 98.90% 1.10% 0.00% 0.00% NA
Aus  269 75.10% 24.90% 0.00% 0.00% NA
Indica I  595 69.90% 28.20% 1.85% 0.00% NA
Indica II  465 69.90% 30.10% 0.00% 0.00% NA
Indica III  913 59.00% 37.20% 3.72% 0.00% NA
Indica Intermediate  786 56.60% 36.60% 6.74% 0.00% NA
Temperate Japonica  767 98.60% 1.40% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 1.70% 0.00% 0.00% NA
VI/Aromatic  96 87.50% 12.50% 0.00% 0.00% NA
Intermediate  90 77.80% 22.20% 0.00% 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
vg0233749871 A -> G LOC_Os02g55110.1 upstream_gene_variant ; 1991.0bp to feature; MODIFIER silent_mutation Average:53.587; most accessible tissue: Minghui63 root, score: 75.155 N N N N
vg0233749871 A -> G LOC_Os02g55100.1 downstream_gene_variant ; 2978.0bp to feature; MODIFIER silent_mutation Average:53.587; most accessible tissue: Minghui63 root, score: 75.155 N N N N
vg0233749871 A -> G LOC_Os02g55100-LOC_Os02g55110 intergenic_region ; MODIFIER silent_mutation Average:53.587; most accessible tissue: Minghui63 root, score: 75.155 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0233749871 NA 3.20E-06 mr1892 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
vg0233749871 NA 5.77E-06 mr1561_2 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
vg0233749871 NA 5.85E-07 mr1875_2 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
vg0233749871 NA 1.35E-06 mr1908_2 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