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Detailed information for vg0314910671:

Variant ID: vg0314910671 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 14910671
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.94, T: 0.06, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:


CAAACTCAGACAGTAATGGAGCTACTACTTCTGAAATGGACTGAGAATCTGCATTGTCAGTAGGTTCAAGCAAAACAGCATCCCAAATATCACAACCCTT[C/T]
TGCCATTTCAATATTTGAGGGTAAGAAATAGCACATAATTCAGTCTGGGAATCAGACTCTTGAACACCTTGCAGTGCAATCCACTGATCTTGGTAGAAAA

Reverse complement sequence

TTTTCTACCAAGATCAGTGGATTGCACTGCAAGGTGTTCAAGAGTCTGATTCCCAGACTGAATTATGTGCTATTTCTTACCCTCAAATATTGAAATGGCA[G/A]
AAGGGTTGTGATATTTGGGATGCTGTTTTGCTTGAACCTACTGACAATGCAGATTCTCAGTCCATTTCAGAAGTAGTAGCTCCATTACTGTCTGAGTTTG

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 49.90% 49.90% 0.23% 0.00% NA
All Indica  2759 64.00% 35.60% 0.40% 0.00% NA
All Japonica  1512 22.90% 77.10% 0.00% 0.00% NA
Aus  269 66.20% 33.80% 0.00% 0.00% NA
Indica I  595 40.70% 59.30% 0.00% 0.00% NA
Indica II  465 55.10% 44.50% 0.43% 0.00% NA
Indica III  913 80.70% 19.20% 0.11% 0.00% NA
Indica Intermediate  786 67.60% 31.40% 1.02% 0.00% NA
Temperate Japonica  767 3.50% 96.50% 0.00% 0.00% NA
Tropical Japonica  504 52.20% 47.80% 0.00% 0.00% NA
Japonica Intermediate  241 23.20% 76.80% 0.00% 0.00% NA
VI/Aromatic  96 34.40% 65.60% 0.00% 0.00% NA
Intermediate  90 40.00% 60.00% 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
vg0314910671 C -> T LOC_Os03g26020.1 synonymous_variant ; p.Gln483Gln; LOW synonymous_codon Average:25.844; most accessible tissue: Zhenshan97 panicle, score: 32.308 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0314910671 NA 7.14E-06 mr1376 Ind_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
vg0314910671 NA 7.14E-06 mr1431 Ind_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
vg0314910671 NA 8.79E-06 mr1500 Ind_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
vg0314910671 NA 5.37E-06 mr1505 Ind_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
vg0314910671 9.44E-08 NA mr1542 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
vg0314910671 4.71E-07 3.33E-08 mr1542 Ind_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
vg0314910671 NA 5.05E-06 mr1959 Ind_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
vg0314910671 1.31E-07 NA mr1542_2 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
vg0314910671 7.26E-07 7.19E-09 mr1542_2 Ind_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
vg0314910671 NA 4.95E-06 mr1671_2 Ind_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