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Detailed information for vg1202831546:

Variant ID: vg1202831546 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 2831546
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, T: 0.09, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:


CAAATGTATATGCTGCCAGTGGAAACTGGGAGAATGTTGTTGTTGCAAGGAAGTATTTGAGGGATAGTGGTGCTAAAAAAGAGATGGGCAGGAGTTGGAT[T/C]
GAGGCGAAAGGCAAGATTCATGTTTTTGTTGCTGGAGAGAGAGAACACCCAGGAATAACTGATGTATACAATAAGTTGGAGGAAATTTACCATGAGATGA

Reverse complement sequence

TCATCTCATGGTAAATTTCCTCCAACTTATTGTATACATCAGTTATTCCTGGGTGTTCTCTCTCTCCAGCAACAAAAACATGAATCTTGCCTTTCGCCTC[A/G]
ATCCAACTCCTGCCCATCTCTTTTTTAGCACCACTATCCCTCAAATACTTCCTTGCAACAACAACATTCTCCCAGTTTCCACTGGCAGCATATACATTTG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 91.70% 8.20% 0.06% 0.00% NA
All Indica  2759 94.00% 6.00% 0.04% 0.00% NA
All Japonica  1512 98.90% 1.10% 0.00% 0.00% NA
Aus  269 24.20% 75.10% 0.74% 0.00% NA
Indica I  595 93.30% 6.70% 0.00% 0.00% NA
Indica II  465 98.10% 1.90% 0.00% 0.00% NA
Indica III  913 93.40% 6.60% 0.00% 0.00% NA
Indica Intermediate  786 92.70% 7.10% 0.13% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 98.80% 1.20% 0.00% 0.00% NA
Japonica Intermediate  241 95.90% 4.10% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 93.30% 6.70% 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
vg1202831546 T -> C LOC_Os12g06070.1 synonymous_variant ; p.Ile501Ile; LOW synonymous_codon Average:52.206; most accessible tissue: Callus, score: 81.666 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1202831546 NA 8.55E-40 mr1549 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
vg1202831546 NA 8.15E-38 mr1757 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
vg1202831546 NA 1.28E-33 mr1549_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
vg1202831546 NA 4.29E-32 mr1757_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
vg1202831546 NA 1.77E-06 mr1762_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