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Detailed information for vg0135984355:

Variant ID: vg0135984355 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 35984355
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.94, A: 0.07, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:


CTTGCTATCAAAACCGACCAATCATCGAAAGTAACCAAAATTCGCATTACAATTCTATCACCTGTTGGTATGTTTCATCTCATGTCAAGGTAAACAAAAA[G/A]
AGACAAAAGTAATCAAGCAAAGCGACCAGAATCACGCCGGCAAACTGCTGCCAATCCTGCTCACATACTGGCACAGCTGGTCCCTCAGCGCGGCCGCGCC

Reverse complement sequence

GGCGCGGCCGCGCTGAGGGACCAGCTGTGCCAGTATGTGAGCAGGATTGGCAGCAGTTTGCCGGCGTGATTCTGGTCGCTTTGCTTGATTACTTTTGTCT[C/T]
TTTTTGTTTACCTTGACATGAGATGAAACATACCAACAGGTGATAGAATTGTAATGCGAATTTTGGTTACTTTCGATGATTGGTCGGTTTTGATAGCAAG

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 63.90% 36.00% 0.04% 0.02% NA
All Indica  2759 98.20% 1.70% 0.07% 0.04% NA
All Japonica  1512 2.10% 97.90% 0.00% 0.00% NA
Aus  269 58.70% 41.30% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 99.30% 0.70% 0.00% 0.00% NA
Indica Intermediate  786 94.70% 5.00% 0.25% 0.13% NA
Temperate Japonica  767 1.20% 98.80% 0.00% 0.00% NA
Tropical Japonica  504 2.80% 97.20% 0.00% 0.00% NA
Japonica Intermediate  241 3.30% 96.70% 0.00% 0.00% NA
VI/Aromatic  96 82.30% 17.70% 0.00% 0.00% NA
Intermediate  90 48.90% 51.10% 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
vg0135984355 G -> A LOC_Os01g62160.1 3_prime_UTR_variant ; 32.0bp to feature; MODIFIER silent_mutation Average:73.095; most accessible tissue: Zhenshan97 flower, score: 86.268 N N N N
vg0135984355 G -> DEL N N silent_mutation Average:73.095; most accessible tissue: Zhenshan97 flower, score: 86.268 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0135984355 NA 5.78E-48 mr1125 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
vg0135984355 NA 5.55E-25 mr1251 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
vg0135984355 NA 2.28E-17 mr1253 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
vg0135984355 NA 4.93E-25 mr1411 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
vg0135984355 NA 3.73E-36 mr1435 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
vg0135984355 NA 6.01E-20 mr1541 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
vg0135984355 NA 1.63E-49 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
vg0135984355 NA 1.53E-63 mr1125_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
vg0135984355 NA 3.26E-36 mr1223_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
vg0135984355 NA 1.79E-24 mr1350_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
vg0135984355 NA 9.49E-21 mr1968_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
vg0135984355 NA 3.42E-12 mr1986_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