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Detailed information for vg0822460634:

Variant ID: vg0822460634 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 22460634
Reference Allele: GAlternative Allele: T
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.73, T: 0.27, others allele: 0.00, population size: 173. )

Flanking Sequence (100 bp) in Reference Genome:


AATGAATTAGGATACATTGATTTTATTGGTTAGTTTTCTTTTCAAAATTTGATAGCAAATCAGTAGAGTTTGAAGCAAAAGGAGTTGTTCTTAGGTGAGC[G/T]
TCAAAATGACTGGTGTTGAGGTATGGTGTCGGCGCTAGTTGTTTGGTGCCGAGAGATAGATCCATATCTGAAATAAGTTTTTTAGTGGTCTGTTTGTAAA

Reverse complement sequence

TTTACAAACAGACCACTAAAAAACTTATTTCAGATATGGATCTATCTCTCGGCACCAAACAACTAGCGCCGACACCATACCTCAACACCAGTCATTTTGA[C/A]
GCTCACCTAAGAACAACTCCTTTTGCTTCAAACTCTACTGATTTGCTATCAAATTTTGAAAAGAAAACTAACCAATAAAATCAATGTATCCTAATTCATT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 65.00% 34.60% 0.11% 0.25% NA
All Indica  2759 97.70% 1.70% 0.14% 0.40% NA
All Japonica  1512 1.40% 98.50% 0.00% 0.07% NA
Aus  269 79.20% 20.80% 0.00% 0.00% NA
Indica I  595 99.00% 0.00% 0.50% 0.50% NA
Indica II  465 97.80% 1.50% 0.00% 0.65% NA
Indica III  913 98.80% 1.10% 0.00% 0.11% NA
Indica Intermediate  786 95.40% 3.90% 0.13% 0.51% NA
Temperate Japonica  767 1.40% 98.40% 0.00% 0.13% NA
Tropical Japonica  504 0.80% 99.20% 0.00% 0.00% NA
Japonica Intermediate  241 2.50% 97.50% 0.00% 0.00% NA
VI/Aromatic  96 91.70% 8.30% 0.00% 0.00% NA
Intermediate  90 60.00% 38.90% 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
vg0822460634 G -> T LOC_Os08g35630.1 upstream_gene_variant ; 1760.0bp to feature; MODIFIER silent_mutation Average:52.83; most accessible tissue: Minghui63 root, score: 77.009 N N N N
vg0822460634 G -> T LOC_Os08g35620-LOC_Os08g35630 intergenic_region ; MODIFIER silent_mutation Average:52.83; most accessible tissue: Minghui63 root, score: 77.009 N N N N
vg0822460634 G -> DEL N N silent_mutation Average:52.83; most accessible tissue: Minghui63 root, score: 77.009 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0822460634 2.21E-06 NA mr1123 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
vg0822460634 3.45E-07 NA mr1495 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
vg0822460634 NA 1.10E-24 mr1537 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
vg0822460634 NA 2.37E-46 mr1591 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
vg0822460634 NA 6.31E-51 mr1599 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
vg0822460634 NA 3.41E-19 mr1627 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
vg0822460634 NA 1.62E-34 mr1828 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
vg0822460634 NA 2.67E-39 mr1890 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
vg0822460634 NA 5.61E-07 mr1915 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
vg0822460634 NA 5.18E-35 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
vg0822460634 NA 6.08E-16 mr1578_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
vg0822460634 NA 1.14E-30 mr1913_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