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Detailed information for vg0815322514:

Variant ID: vg0815322514 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 15322514
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:


CAACATGCCAAGTCTGCTTCAAGCGAGGCCACACTGCCACAGATTGCTGGTATAGGTATGATGAAGACTATGTTCCTGATAACAAACATGTTGCAGCAGC[T/A]
GCGGCGGCGAGCTCCTCCCATGGCATCGACACCAACTGGTACATCGACACCGGCGCTACAGATCACATCACCGGTGAGTTGGAAAAACTCACGGTGAAAG

Reverse complement sequence

CTTTCACCGTGAGTTTTTCCAACTCACCGGTGATGTGATCTGTAGCGCCGGTGTCGATGTACCAGTTGGTGTCGATGCCATGGGAGGAGCTCGCCGCCGC[A/T]
GCTGCTGCAACATGTTTGTTATCAGGAACATAGTCTTCATCATACCTATACCAGCAATCTGTGGCAGTGTGGCCTCGCTTGAAGCAGACTTGGCATGTTG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.60% 2.10% 0.28% 0.00% NA
All Indica  2759 99.90% 0.00% 0.04% 0.00% NA
All Japonica  1512 92.80% 6.50% 0.73% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.00% 0.22% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 99.30% 0.00% 0.65% 0.00% NA
Tropical Japonica  504 81.30% 17.70% 0.99% 0.00% NA
Japonica Intermediate  241 95.90% 3.70% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 2.20% 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
vg0815322514 T -> A LOC_Os08g25220.1 synonymous_variant ; p.Ala281Ala; LOW synonymous_codon Average:67.541; most accessible tissue: Minghui63 flag leaf, score: 78.782 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0815322514 NA 5.20E-07 mr1073 Jap_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
vg0815322514 1.64E-07 3.55E-09 mr1218 Jap_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
vg0815322514 2.81E-06 3.18E-11 mr1583 Jap_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
vg0815322514 NA 3.69E-06 mr1794 Jap_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
vg0815322514 3.25E-06 3.76E-09 mr1218_2 Jap_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
vg0815322514 9.14E-06 2.36E-10 mr1850_2 Jap_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