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Detailed information for vg0218100630:

Variant ID: vg0218100630 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 18100630
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.73, T: 0.27, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:


CGACTGATGCCACAAATTGCACCTCTGGTTCTGCCACTGTAATCTCCATGGGCACTTCCGGCACTGGAATCTCCATGGCTGCCTCCGGCACTGCAATCTC[C/T]
GGTGGCACTTCCGGCACTGGATTATCCTTTTGCATATCGGGTTCCTCCGCCTTATCAGTCACCTTCCTCTTAGGAGGTCTCGGAGGTTTTCCCAACCCCG

Reverse complement sequence

CGGGGTTGGGAAAACCTCCGAGACCTCCTAAGAGGAAGGTGACTGATAAGGCGGAGGAACCCGATATGCAAAAGGATAATCCAGTGCCGGAAGTGCCACC[G/A]
GAGATTGCAGTGCCGGAGGCAGCCATGGAGATTCCAGTGCCGGAAGTGCCCATGGAGATTACAGTGGCAGAACCAGAGGTGCAATTTGTGGCATCAGTCG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 74.70% 23.60% 1.65% 0.00% NA
All Indica  2759 94.90% 3.80% 1.23% 0.00% NA
All Japonica  1512 36.60% 63.20% 0.20% 0.00% NA
Aus  269 94.80% 4.50% 0.74% 0.00% NA
Indica I  595 96.10% 1.80% 2.02% 0.00% NA
Indica II  465 94.80% 3.90% 1.29% 0.00% NA
Indica III  913 93.40% 5.80% 0.77% 0.00% NA
Indica Intermediate  786 95.80% 3.10% 1.15% 0.00% NA
Temperate Japonica  767 5.50% 94.50% 0.00% 0.00% NA
Tropical Japonica  504 81.20% 18.70% 0.20% 0.00% NA
Japonica Intermediate  241 42.30% 56.80% 0.83% 0.00% NA
VI/Aromatic  96 41.70% 22.90% 35.42% 0.00% NA
Intermediate  90 71.10% 23.30% 5.56% 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
vg0218100630 C -> T LOC_Os02g30390.1 synonymous_variant ; p.Pro458Pro; LOW synonymous_codon Average:10.497; most accessible tissue: Callus, score: 19.404 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0218100630 2.95E-07 1.49E-09 mr1073 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
vg0218100630 2.30E-06 2.30E-06 mr1073 Ind_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
vg0218100630 NA 2.67E-13 mr1334 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
vg0218100630 NA 6.00E-07 mr1511 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
vg0218100630 NA 5.23E-10 mr1549 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
vg0218100630 NA 2.55E-07 mr1723 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
vg0218100630 NA 1.53E-07 mr1733 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
vg0218100630 NA 1.54E-08 mr1757 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
vg0218100630 NA 9.78E-07 mr1257_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
vg0218100630 NA 1.61E-06 mr1629_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
vg0218100630 NA 1.57E-07 mr1733_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