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Detailed information for vg0231332457:

Variant ID: vg0231332457 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 31332457
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, T: 0.01, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:


CAGAGTCGGCGAAGCATGAGGTGGCGGTGAGGCGGCCTGCAAAGGCGACACGTCCCCCACTGGGCAGTCTATCGCTGCCGTCGCCGCCAGCTCGAGCCGC[A/T]
ACAGCGCTTCTTCAACTTGTTGGCATGTGGTCGCCGCAGTCGGCGGTGGCAGGTTCGACTTGATGCGCGCGAAGACGCTCTCCACCGGGATCGGCTTCCA

Reverse complement sequence

TGGAAGCCGATCCCGGTGGAGAGCGTCTTCGCGCGCATCAAGTCGAACCTGCCACCGCCGACTGCGGCGACCACATGCCAACAAGTTGAAGAAGCGCTGT[T/A]
GCGGCTCGAGCTGGCGGCGACGGCAGCGATAGACTGCCCAGTGGGGGACGTGTCGCCTTTGCAGGCCGCCTCACCGCCACCTCATGCTTCGCCGACTCTG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 92.90% 6.00% 1.10% 0.00% NA
All Indica  2759 88.00% 10.10% 1.85% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 99.60% 0.00% 0.37% 0.00% NA
Indica I  595 99.00% 0.00% 1.01% 0.00% NA
Indica II  465 68.20% 27.50% 4.30% 0.00% NA
Indica III  913 93.40% 6.10% 0.44% 0.00% NA
Indica Intermediate  786 85.10% 12.20% 2.67% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 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
vg0231332457 A -> T LOC_Os02g51200.1 intron_variant ; MODIFIER silent_mutation Average:57.93; most accessible tissue: Zhenshan97 young leaf, score: 80.325 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0231332457 NA 1.40E-06 mr1428_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
vg0231332457 7.61E-07 7.59E-07 mr1473_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
vg0231332457 9.55E-06 9.54E-06 mr1473_2 Ind_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
vg0231332457 NA 3.97E-07 mr1497_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
vg0231332457 6.86E-07 6.84E-07 mr1630_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
vg0231332457 8.18E-07 8.16E-07 mr1848_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