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Detailed information for vg0825213870:

Variant ID: vg0825213870 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 25213870
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.03, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:


AGCAGTTCATATGGTTATCATATCACAGCCACAGGTAGTAGGAATTCAACCTCTGTTGCTGGCCATGGAAATCAGCTCATGGGAGATCCTTTCGACAGTG[G/A]
TACTGCTGATAAGTTCAATGGGAATTCGTTTGATGGATTGCCTTTTGACTTCATTGGTAGTAGTCCAATCCCTGACATCGGTGTATTGCTAGATGATGAT

Reverse complement sequence

ATCATCATCTAGCAATACACCGATGTCAGGGATTGGACTACTACCAATGAAGTCAAAAGGCAATCCATCAAACGAATTCCCATTGAACTTATCAGCAGTA[C/T]
CACTGTCGAAAGGATCTCCCATGAGCTGATTTCCATGGCCAGCAACAGAGGTTGAATTCCTACTACCTGTGGCTGTGATATGATAACCATATGAACTGCT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 92.80% 7.10% 0.04% 0.00% NA
All Indica  2759 90.40% 9.50% 0.04% 0.00% NA
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 74.70% 24.90% 0.37% 0.00% NA
Indica I  595 97.80% 2.20% 0.00% 0.00% NA
Indica II  465 97.60% 2.20% 0.22% 0.00% NA
Indica III  913 85.00% 15.00% 0.00% 0.00% NA
Indica Intermediate  786 86.90% 13.10% 0.00% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg0825213870 G -> A LOC_Os08g39830.1 missense_variant ; p.Gly578Asp; MODERATE nonsynonymous_codon ; G578D Average:49.724; most accessible tissue: Minghui63 panicle, score: 66.554 unknown unknown TOLERATED 0.69
vg0825213870 G -> A LOC_Os08g39830.2 missense_variant ; p.Gly578Asp; MODERATE nonsynonymous_codon ; G578D Average:49.724; most accessible tissue: Minghui63 panicle, score: 66.554 unknown unknown TOLERATED 0.69

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0825213870 5.38E-06 NA mr1874 Ind_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
vg0825213870 NA 4.05E-06 mr1115_2 Ind_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
vg0825213870 NA 7.16E-06 mr1477_2 Ind_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
vg0825213870 4.35E-06 NA mr1874_2 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
vg0825213870 4.30E-07 3.62E-08 mr1874_2 Ind_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