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Detailed information for vg1209056273:

Variant ID: vg1209056273 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 9056273
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.86, C: 0.14, others allele: 0.00, population size: 58. )

Flanking Sequence (100 bp) in Reference Genome:


CACAAAAACCAAGTTACTCCGGGAAGAAGAATGAAGGAGATGAAAAAAAGATCACCAACCTAAGGAGGTCATCACCACGCCCGTTTCCACGGGTGAGTTT[T/C]
GTCCCATATCGTCCTGCGACACAGGCGTTTGGAGGGTAATCGCCGGGGCGACCACCGGTAACTTGGGCTGCCCACGCTGCTGGACATCCTCGACATCGAC

Reverse complement sequence

GTCGATGTCGAGGATGTCCAGCAGCGTGGGCAGCCCAAGTTACCGGTGGTCGCCCCGGCGATTACCCTCCAAACGCCTGTGTCGCAGGACGATATGGGAC[A/G]
AAACTCACCCGTGGAAACGGGCGTGGTGATGACCTCCTTAGGTTGGTGATCTTTTTTTCATCTCCTTCATTCTTCTTCCCGGAGTAACTTGGTTTTTGTG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 52.80% 34.80% 1.29% 11.15% NA
All Indica  2759 74.70% 5.00% 2.07% 18.30% NA
All Japonica  1512 4.60% 94.30% 0.07% 0.99% NA
Aus  269 95.90% 3.00% 0.74% 0.37% NA
Indica I  595 49.60% 6.70% 3.03% 40.67% NA
Indica II  465 66.00% 5.80% 3.01% 25.16% NA
Indica III  913 93.60% 1.80% 1.20% 3.40% NA
Indica Intermediate  786 76.70% 6.90% 1.78% 14.63% NA
Temperate Japonica  767 6.30% 92.60% 0.00% 1.17% NA
Tropical Japonica  504 3.60% 95.60% 0.20% 0.60% NA
Japonica Intermediate  241 1.70% 97.10% 0.00% 1.24% NA
VI/Aromatic  96 74.00% 22.90% 0.00% 3.12% NA
Intermediate  90 40.00% 55.60% 1.11% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1209056273 T -> C LOC_Os12g15910.1 synonymous_variant ; p.Thr646Thr; LOW synonymous_codon Average:15.755; most accessible tissue: Callus, score: 34.334 N N N N
vg1209056273 T -> DEL LOC_Os12g15910.1 N frameshift_variant Average:15.755; most accessible tissue: Callus, score: 34.334 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1209056273 NA 3.69E-07 mr1066 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
vg1209056273 NA 5.01E-18 mr1133 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
vg1209056273 NA 4.37E-06 mr1574 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
vg1209056273 NA 1.28E-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
vg1209056273 NA 3.21E-06 mr1020_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
vg1209056273 NA 5.33E-15 mr1133_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
vg1209056273 NA 8.71E-08 mr1582_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
vg1209056273 NA 1.57E-09 mr1582_2 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
vg1209056273 NA 2.95E-06 mr1882_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