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Detailed information for vg0623329456:

Variant ID: vg0623329456 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 23329456
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:


CCGCTTGAGCTTTCCTTTTCCCATTTTTGCGATTTTTCTTCTTGCTTGACTCAGGTGCGTCCGTGGCTAGTTTCTTCTCTCCCCCGGTCTTCGGCTTATC[G/A]
TTCTTGCGTCTTAGCGCATCATCTGCGTGGGCGCATCGCTCAACAATTTCGAACAATCTCTGAGTAGTTGTGATGCGTCTTGTTGCCAACTCCTGAGTAG

Reverse complement sequence

CTACTCAGGAGTTGGCAACAAGACGCATCACAACTACTCAGAGATTGTTCGAAATTGTTGAGCGATGCGCCCACGCAGATGATGCGCTAAGACGCAAGAA[C/T]
GATAAGCCGAAGACCGGGGGAGAGAAGAAACTAGCCACGGACGCACCTGAGTCAAGCAAGAAGAAAAATCGCAAAAATGGGAAAAGGAAAGCTCAAGCGG

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 73.50% 26.30% 0.23% 0.00% NA
All Indica  2759 58.50% 41.10% 0.40% 0.00% NA
All Japonica  1512 99.60% 0.40% 0.00% 0.00% NA
Aus  269 67.30% 32.70% 0.00% 0.00% NA
Indica I  595 19.70% 80.00% 0.34% 0.00% NA
Indica II  465 93.30% 6.70% 0.00% 0.00% NA
Indica III  913 59.40% 40.10% 0.55% 0.00% NA
Indica Intermediate  786 66.30% 33.20% 0.51% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.20% 0.80% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 85.60% 14.40% 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
vg0623329456 G -> A LOC_Os06g39320.1 synonymous_variant ; p.Asn194Asn; LOW synonymous_codon Average:51.523; most accessible tissue: Zhenshan97 flag leaf, score: 72.012 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0623329456 1.51E-08 NA mr1659 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
vg0623329456 2.38E-08 1.74E-11 mr1659 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
vg0623329456 NA 7.01E-07 mr1715 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
vg0623329456 4.83E-06 3.04E-11 mr1659_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