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Detailed information for vg0826865048:

Variant ID: vg0826865048 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 26865048
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TAGGACAATTATATCAAAGGTCCGTTGTATGTTGTCTAATGCAGGTTTGCCCAAACAGTTTTGGGCGGAAGCCATTTCCATTGCTTGTTATCTTATCAAT[T/C]
GGTCACCCAGTTATGCCATTGATAAGAAGACTCCAATTGAGGTATGGTCTGGTTCCCCAGCAAATTATTCAGATTTAAGAGTATTTGGTTATACTACTTA

Reverse complement sequence

TAAGTAGTATAACCAAATACTCTTAAATCTGAATAATTTGCTGGGGAACCAGACCATACCTCAATTGGAGTCTTCTTATCAATGGCATAACTGGGTGACC[A/G]
ATTGATAAGATAACAAGCAATGGAAATGGCTTCCGCCCAAAACTGTTTGGGCAAACCTGCATTAGACAACATACAACGGACCTTTGATATAATTGTCCTA

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 72.80% 27.20% 0.02% 0.00% NA
All Indica  2759 98.60% 1.40% 0.00% 0.00% NA
All Japonica  1512 35.00% 64.90% 0.07% 0.00% NA
Aus  269 43.50% 56.50% 0.00% 0.00% NA
Indica I  595 98.80% 1.20% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 98.80% 1.20% 0.00% 0.00% NA
Indica Intermediate  786 97.50% 2.50% 0.00% 0.00% NA
Temperate Japonica  767 12.00% 88.00% 0.00% 0.00% NA
Tropical Japonica  504 61.90% 37.90% 0.20% 0.00% NA
Japonica Intermediate  241 51.90% 48.10% 0.00% 0.00% NA
VI/Aromatic  96 8.30% 91.70% 0.00% 0.00% NA
Intermediate  90 71.10% 28.90% 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
vg0826865048 T -> C LOC_Os08g42500.1 missense_variant ; p.Trp373Arg; MODERATE nonsynonymous_codon ; W373R Average:21.055; most accessible tissue: Callus, score: 44.88 unknown unknown TOLERATED 1.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0826865048 6.41E-06 1.29E-09 mr1364 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
vg0826865048 3.64E-06 1.72E-09 mr1443 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