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Detailed information for vg0323673353:

Variant ID: vg0323673353 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 23673353
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:


CAGAAAGCCCATCACAAGAAGTCCAAACTAGTCCCTCAGCTTGGAGAACAACCAAACCAAGAGGTCGAGCCGTTGGTGACCGGCAAAGATTTTGGCATAA[C/T]
GGATTTCATTTCAGACACCGGTCTAACTGTGGATCAGCTAATTGGAGGCGCACCAATCCCGAAGGCGGAAGTGGCATACAAGTTTGAACTCGGTAAACCG

Reverse complement sequence

CGGTTTACCGAGTTCAAACTTGTATGCCACTTCCGCCTTCGGGATTGGTGCGCCTCCAATTAGCTGATCCACAGTTAGACCGGTGTCTGAAATGAAATCC[G/A]
TTATGCCAAAATCTTTGCCGGTCACCAACGGCTCGACCTCTTGGTTTGGTTGTTCTCCAAGCTGAGGGACTAGTTTGGACTTCTTGTGATGGGCTTTCTG

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 94.60% 5.10% 0.25% 0.00% NA
All Indica  2759 91.70% 7.90% 0.36% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 75.60% 23.40% 1.01% 0.00% NA
Indica II  465 97.80% 2.20% 0.00% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 90.80% 8.70% 0.51% 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 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 82.30% 16.70% 1.04% 0.00% NA
Intermediate  90 94.40% 4.40% 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
vg0323673353 C -> T LOC_Os03g42540.1 missense_variant ; p.Thr116Met; MODERATE nonsynonymous_codon ; T116M Average:36.335; most accessible tissue: Zhenshan97 flower, score: 55.587 probably damaging 2.764 DELETERIOUS 0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0323673353 NA 1.05E-07 mr1928 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
vg0323673353 4.45E-06 9.23E-09 mr1928 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