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Detailed information for vg0218013275:

Variant ID: vg0218013275 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 18013275
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:


GTCATCTCACCACTTGGGAGGTGGAAGCTGTGTGTCTCAGACCTCCATCTGTCCACAAGTGCTGTCAACGCAGGAGCGTTGCACACTAGCATTCCGTTCA[C/T]
GACCAAGGTCACCCCGAGCAACCCGCCGCCCTTAGGTACGGGATGTACCTAACGTCGAACACTGGAGGGGGGCATGAGCTCTAACTCGGAGCGGTTGAAG

Reverse complement sequence

CTTCAACCGCTCCGAGTTAGAGCTCATGCCCCCCTCCAGTGTTCGACGTTAGGTACATCCCGTACCTAAGGGCGGCGGGTTGCTCGGGGTGACCTTGGTC[G/A]
TGAACGGAATGCTAGTGTGCAACGCTCCTGCGTTGACAGCACTTGTGGACAGATGGAGGTCTGAGACACACAGCTTCCACCTCCCAAGTGGTGAGATGAC

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 86.70% 13.30% 0.00% 0.00% NA
All Indica  2759 93.90% 6.10% 0.00% 0.00% NA
All Japonica  1512 70.40% 29.60% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 89.20% 10.80% 0.00% 0.00% NA
Indica III  913 90.40% 9.60% 0.00% 0.00% NA
Indica Intermediate  786 96.30% 3.70% 0.00% 0.00% NA
Temperate Japonica  767 98.20% 1.80% 0.00% 0.00% NA
Tropical Japonica  504 34.10% 65.90% 0.00% 0.00% NA
Japonica Intermediate  241 58.10% 41.90% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 86.70% 13.30% 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
vg0218013275 C -> T LOC_Os02g30290.1 missense_variant ; p.Val969Met; MODERATE nonsynonymous_codon ; V969M Average:64.006; most accessible tissue: Zhenshan97 young leaf, score: 78.044 unknown unknown TOLERATED 0.09

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0218013275 9.70E-06 NA mr1082 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
vg0218013275 NA 3.07E-06 mr1082 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
vg0218013275 NA 5.75E-11 mr1408 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
vg0218013275 NA 3.91E-10 mr1408_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
vg0218013275 NA 6.89E-06 mr1793_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