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Detailed information for vg0609018598:

Variant ID: vg0609018598 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 9018598
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.88, G: 0.10, others allele: 0.00, population size: 76. )

Flanking Sequence (100 bp) in Reference Genome:


AGAGGTGCAAGGGGTGTATGCAATTGAATTGGGTGCCAAGAGAGCCCCCTTGCAGCTGGTGGGGGAGTATTTATACTCCCACCCACCAAAACTAGCCGTT[A/G]
GGGGCGAAATCCCCAAACTTTGTGCTCTGCCGGTCTGACCGAAGGTATGTGGCCGGTCAGACCATGCTACTCTGCAACGGCTAGAAAACTAGCCGTTGAA

Reverse complement sequence

TTCAACGGCTAGTTTTCTAGCCGTTGCAGAGTAGCATGGTCTGACCGGCCACATACCTTCGGTCAGACCGGCAGAGCACAAAGTTTGGGGATTTCGCCCC[T/C]
AACGGCTAGTTTTGGTGGGTGGGAGTATAAATACTCCCCCACCAGCTGCAAGGGGGCTCTCTTGGCACCCAATTCAATTGCATACACCCCTTGCACCTCT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 48.60% 2.70% 5.69% 43.02% NA
All Indica  2759 58.40% 2.40% 3.59% 35.67% NA
All Japonica  1512 42.30% 3.40% 8.66% 45.63% NA
Aus  269 1.10% 2.20% 1.49% 95.17% NA
Indica I  595 57.10% 1.00% 1.01% 40.84% NA
Indica II  465 78.30% 1.10% 3.23% 17.42% NA
Indica III  913 43.30% 4.80% 5.48% 46.44% NA
Indica Intermediate  786 65.00% 1.40% 3.56% 30.03% NA
Temperate Japonica  767 73.40% 1.30% 2.35% 22.95% NA
Tropical Japonica  504 8.90% 6.20% 14.68% 70.24% NA
Japonica Intermediate  241 12.90% 4.60% 16.18% 66.39% NA
VI/Aromatic  96 2.10% 2.10% 28.12% 67.71% NA
Intermediate  90 46.70% 2.20% 8.89% 42.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0609018598 A -> G LOC_Os06g15880.1 missense_variant ; p.Arg97Gly; MODERATE nonsynonymous_codon ; R97G Average:39.322; most accessible tissue: Zhenshan97 flag leaf, score: 83.994 unknown unknown TOLERATED 0.40
vg0609018598 A -> DEL LOC_Os06g15880.1 N frameshift_variant Average:39.322; most accessible tissue: Zhenshan97 flag leaf, score: 83.994 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0609018598 NA 1.07E-06 mr1057 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
vg0609018598 NA 3.99E-06 mr1096 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
vg0609018598 NA 1.61E-08 mr1570 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
vg0609018598 NA 6.14E-06 mr1606 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
vg0609018598 NA 1.16E-07 mr1057_2 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
vg0609018598 NA 3.61E-13 mr1087_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
vg0609018598 NA 1.45E-07 mr1096_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
vg0609018598 NA 8.04E-08 mr1338_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
vg0609018598 NA 5.51E-06 mr1341_2 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
vg0609018598 NA 5.50E-10 mr1530_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
vg0609018598 1.42E-08 4.90E-16 mr1570_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
vg0609018598 NA 1.36E-07 mr1642_2 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