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Detailed information for vg0218499482:

Variant ID: vg0218499482 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 18499482
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTTACTTTTTACGTTTGAATCACCATTCTACATACTATTTAAATTTAAATTATCATAAACCATATTAATTTACTTAATCTGATATTATATAGCTATCTTA[C/T]
ACGTTATTTTTTTTATTATTATCATACTAAATTCCCGCAGCAATGCGCGGGGTTTAACCTATCTAGTATCTTTCGTGTACACCATGATTTACACTGTAAT

Reverse complement sequence

ATTACAGTGTAAATCATGGTGTACACGAAAGATACTAGATAGGTTAAACCCCGCGCATTGCTGCGGGAATTTAGTATGATAATAATAAAAAAAATAACGT[G/A]
TAAGATAGCTATATAATATCAGATTAAGTAAATTAATATGGTTTATGATAATTTAAATTTAAATAGTATGTAGAATGGTGATTCAAACGTAAAAAGTAAG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 88.50% 10.90% 0.55% 0.00% NA
All Indica  2759 91.80% 8.00% 0.14% 0.00% NA
All Japonica  1512 81.90% 16.70% 1.39% 0.00% NA
Aus  269 95.90% 4.10% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 79.80% 20.00% 0.22% 0.00% NA
Indica III  913 90.90% 9.00% 0.11% 0.00% NA
Indica Intermediate  786 93.80% 6.00% 0.25% 0.00% NA
Temperate Japonica  767 77.30% 20.10% 2.61% 0.00% NA
Tropical Japonica  504 90.10% 9.90% 0.00% 0.00% NA
Japonica Intermediate  241 79.30% 20.30% 0.41% 0.00% NA
VI/Aromatic  96 75.00% 25.00% 0.00% 0.00% NA
Intermediate  90 92.20% 6.70% 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
vg0218499482 C -> T LOC_Os02g30955.1 upstream_gene_variant ; 4339.0bp to feature; MODIFIER silent_mutation Average:37.421; most accessible tissue: Zhenshan97 panicle, score: 68.538 N N N N
vg0218499482 C -> T LOC_Os02g30960.1 upstream_gene_variant ; 1386.0bp to feature; MODIFIER silent_mutation Average:37.421; most accessible tissue: Zhenshan97 panicle, score: 68.538 N N N N
vg0218499482 C -> T LOC_Os02g30974.1 downstream_gene_variant ; 1721.0bp to feature; MODIFIER silent_mutation Average:37.421; most accessible tissue: Zhenshan97 panicle, score: 68.538 N N N N
vg0218499482 C -> T LOC_Os02g30960-LOC_Os02g30974 intergenic_region ; MODIFIER silent_mutation Average:37.421; most accessible tissue: Zhenshan97 panicle, score: 68.538 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0218499482 1.06E-07 NA mr1897 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
vg0218499482 NA 3.49E-06 mr1897 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
vg0218499482 7.07E-08 NA mr1317_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
vg0218499482 6.74E-06 NA mr1818_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
vg0218499482 2.04E-07 NA mr1897_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
vg0218499482 8.36E-08 NA mr1914_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