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Detailed information for vg1111473925:

Variant ID: vg1111473925 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 11473925
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.04, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:


GGCTGGTGACACTTGGCGAGAAGTAAGTTGACGAGTTTGAGGTCGTTTGATTCATCGAATTCAGGCGGCTCGTCTTGATGGCCATTACGGGAATTTTTCA[T/C]
AGGGCGGTGTGGGCGAAGGCGGCACAAGACGGGTCTGGAGGGAACTCTAGTGCGTCTCCTGCAGTGGCCTTGACAGATGTCGTGGTCGTGCCCAGGAGCC

Reverse complement sequence

GGCTCCTGGGCACGACCACGACATCTGTCAAGGCCACTGCAGGAGACGCACTAGAGTTCCCTCCAGACCCGTCTTGTGCCGCCTTCGCCCACACCGCCCT[A/G]
TGAAAAATTCCCGTAATGGCCATCAAGACGAGCCGCCTGAATTCGATGAATCAAACGACCTCAAACTCGTCAACTTACTTCTCGCCAAGTGTCACCAGCC

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 61.40% 38.50% 0.15% 0.00% NA
All Indica  2759 90.00% 9.90% 0.18% 0.00% NA
All Japonica  1512 5.40% 94.60% 0.07% 0.00% NA
Aus  269 98.90% 1.10% 0.00% 0.00% NA
Indica I  595 90.60% 8.90% 0.50% 0.00% NA
Indica II  465 97.80% 2.20% 0.00% 0.00% NA
Indica III  913 85.80% 14.10% 0.11% 0.00% NA
Indica Intermediate  786 89.70% 10.20% 0.13% 0.00% NA
Temperate Japonica  767 3.70% 96.20% 0.13% 0.00% NA
Tropical Japonica  504 9.10% 90.90% 0.00% 0.00% NA
Japonica Intermediate  241 2.90% 97.10% 0.00% 0.00% NA
VI/Aromatic  96 14.60% 85.40% 0.00% 0.00% NA
Intermediate  90 64.40% 34.40% 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
vg1111473925 T -> C LOC_Os11g19930.1 synonymous_variant ; p.His209His; LOW synonymous_codon Average:62.955; most accessible tissue: Zhenshan97 young leaf, score: 84.624 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1111473925 NA 5.72E-22 mr1168 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
vg1111473925 NA 7.99E-24 mr1383 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
vg1111473925 NA 1.98E-93 mr1758 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
vg1111473925 NA 9.03E-11 mr1216_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
vg1111473925 NA 3.25E-08 mr1600_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
vg1111473925 2.36E-10 8.30E-138 mr1758_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
vg1111473925 2.68E-10 1.75E-09 mr1758_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