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Detailed information for vg0135259527:

Variant ID: vg0135259527 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 35259527
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 340. )

Flanking Sequence (100 bp) in Reference Genome:


ATATAGTGACATCTCCTTGGATATTATTTGCTTGAATGCATCAACTAATTGATTGGTTCTTACTATTCGAAAAATAAGTCAGCTTGATACTTACATAGTC[A/G]
CGTCATTGTCATTTCTCAACGTTCTAGCCTTGTTCACATAATTTGGCAATTGATCATTGTTCTGAAATAGGTTACACTGTACAAATACATGCACAGAACT

Reverse complement sequence

AGTTCTGTGCATGTATTTGTACAGTGTAACCTATTTCAGAACAATGATCAATTGCCAAATTATGTGAACAAGGCTAGAACGTTGAGAAATGACAATGACG[T/C]
GACTATGTAAGTATCAAGCTGACTTATTTTTCGAATAGTAAGAACCAATCAATTAGTTGATGCATTCAAGCAAATAATATCCAAGGAGATGTCACTATAT

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 92.60% 7.40% 0.04% 0.00% NA
All Indica  2759 98.60% 1.40% 0.00% 0.00% NA
All Japonica  1512 80.00% 19.90% 0.13% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 96.10% 3.90% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 98.00% 2.00% 0.00% 0.00% NA
Temperate Japonica  767 70.70% 29.30% 0.00% 0.00% NA
Tropical Japonica  504 95.60% 4.20% 0.20% 0.00% NA
Japonica Intermediate  241 76.80% 22.80% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 88.90% 11.10% 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
vg0135259527 A -> G LOC_Os01g60960.1 downstream_gene_variant ; 79.0bp to feature; MODIFIER silent_mutation Average:61.232; most accessible tissue: Zhenshan97 root, score: 87.373 N N N N
vg0135259527 A -> G LOC_Os01g60960-LOC_Os01g60970 intergenic_region ; MODIFIER silent_mutation Average:61.232; most accessible tissue: Zhenshan97 root, score: 87.373 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0135259527 4.91E-06 NA mr1007 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
vg0135259527 NA 7.51E-06 mr1164_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