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Detailed information for vg0409481337:

Variant ID: vg0409481337 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 9481337
Reference Allele: TAlternative Allele: G
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.88, T: 0.12, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:


TGCTTCTCCAAATCGGCCCAACTGTTGATTGATCCACATGGCAAAGAAGAACACCAAGTAAAAGCCGATCCAGACAAAGACAATGGAAACAACCTAACCC[T/G]
CAGAGCATCCACAGCCGATGCTTCACCACACTGAGCTAAGAATCGGCTAACGTGCTCATAGGTTGAAACGCTGTCCTGTCCTGAGAATTTTGAAAAATAT

Reverse complement sequence

ATATTTTTCAAAATTCTCAGGACAGGACAGCGTTTCAACCTATGAGCACGTTAGCCGATTCTTAGCTCAGTGTGGTGAAGCATCGGCTGTGGATGCTCTG[A/C]
GGGTTAGGTTGTTTCCATTGTCTTTGTCTGGATCGGCTTTTACTTGGTGTTCTTCTTTGCCATGTGGATCAATCAACAGTTGGGCCGATTTGGAGAAGCA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 62.70% 31.00% 2.24% 4.08% NA
All Indica  2759 94.10% 1.30% 1.05% 3.62% NA
All Japonica  1512 2.40% 87.20% 4.96% 5.42% NA
Aus  269 98.50% 0.70% 0.00% 0.74% NA
Indica I  595 92.60% 0.70% 1.51% 5.21% NA
Indica II  465 94.60% 2.40% 0.65% 2.37% NA
Indica III  913 94.70% 1.00% 0.66% 3.61% NA
Indica Intermediate  786 94.00% 1.40% 1.40% 3.18% NA
Temperate Japonica  767 0.50% 97.70% 0.52% 1.30% NA
Tropical Japonica  504 4.00% 71.80% 12.30% 11.90% NA
Japonica Intermediate  241 5.00% 86.30% 3.73% 4.98% NA
VI/Aromatic  96 17.70% 74.00% 1.04% 7.29% NA
Intermediate  90 56.70% 40.00% 1.11% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0409481337 T -> DEL LOC_Os04g17290.1 N frameshift_variant Average:50.911; most accessible tissue: Minghui63 young leaf, score: 78.443 N N N N
vg0409481337 T -> G LOC_Os04g17290.1 synonymous_variant ; p.Arg91Arg; LOW synonymous_codon Average:50.911; most accessible tissue: Minghui63 young leaf, score: 78.443 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0409481337 NA 9.72E-13 mr1010 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
vg0409481337 NA 6.19E-59 mr1019 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
vg0409481337 NA 2.58E-27 mr1072 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
vg0409481337 NA 1.40E-68 mr1132 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
vg0409481337 NA 9.78E-30 mr1202 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
vg0409481337 NA 1.65E-33 mr1350 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
vg0409481337 NA 1.91E-38 mr1719 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
vg0409481337 NA 3.33E-77 mr1778 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
vg0409481337 NA 1.10E-33 mr1932 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
vg0409481337 NA 1.06E-58 mr1962 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
vg0409481337 NA 3.60E-74 mr1019_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
vg0409481337 NA 1.00E-12 mr1035_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
vg0409481337 NA 7.46E-80 mr1132_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
vg0409481337 NA 2.48E-34 mr1448_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
vg0409481337 NA 4.87E-99 mr1619_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
vg0409481337 NA 1.04E-35 mr1689_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
vg0409481337 NA 1.09E-74 mr1778_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
vg0409481337 2.28E-06 NA mr1870_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
vg0409481337 NA 7.01E-121 mr1962_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