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Detailed information for vg0812695428:

Variant ID: vg0812695428 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 12695428
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.72, C: 0.28, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:


TGTCGGCGACGTCAGACAGCTCATGGGAGGTGCGTGAGGAGGAGAGGAGGCGATGCATCGACGGAGGAGGAGAAGAGGCGATGCGTTCGTCCAGCCAGGG[C/T]
ACACAAACGACAATTGTTGACATACAGATCCACGTCTTACAAAAATATAAAAGATTACAAATGCAGCGGAAAAGAAAAAAACGAGATAAGCCTGAAGAAT

Reverse complement sequence

ATTCTTCAGGCTTATCTCGTTTTTTTCTTTTCCGCTGCATTTGTAATCTTTTATATTTTTGTAAGACGTGGATCTGTATGTCAACAATTGTCGTTTGTGT[G/A]
CCCTGGCTGGACGAACGCATCGCCTCTTCTCCTCCTCCGTCGATGCATCGCCTCCTCTCCTCCTCACGCACCTCCCATGAGCTGTCTGACGTCGCCGACA

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 24.00% 20.20% 0.30% 55.52% NA
All Indica  2759 11.30% 2.20% 0.43% 86.01% NA
All Japonica  1512 37.10% 56.30% 0.07% 6.55% NA
Aus  269 48.00% 7.80% 0.37% 43.87% NA
Indica I  595 3.00% 3.40% 0.50% 93.11% NA
Indica II  465 9.20% 3.40% 0.65% 86.67% NA
Indica III  913 18.00% 0.70% 0.11% 81.27% NA
Indica Intermediate  786 11.20% 2.40% 0.64% 85.75% NA
Temperate Japonica  767 10.20% 84.60% 0.13% 5.08% NA
Tropical Japonica  504 70.00% 24.00% 0.00% 5.95% NA
Japonica Intermediate  241 53.90% 33.60% 0.00% 12.45% NA
VI/Aromatic  96 97.90% 0.00% 0.00% 2.08% NA
Intermediate  90 41.10% 23.30% 0.00% 35.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0812695428 C -> T LOC_Os08g21260.1 synonymous_variant ; p.Gly34Gly; LOW synonymous_codon Average:12.173; most accessible tissue: Callus, score: 36.856 N N N N
vg0812695428 C -> DEL LOC_Os08g21260.1 N frameshift_variant Average:12.173; most accessible tissue: Callus, score: 36.856 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0812695428 NA 9.25E-09 mr1045 Jap_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
vg0812695428 NA 3.56E-06 mr1063 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
vg0812695428 NA 1.22E-06 mr1164 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
vg0812695428 NA 3.98E-06 mr1180 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
vg0812695428 NA 1.14E-07 mr1183 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
vg0812695428 NA 4.63E-07 mr1238 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
vg0812695428 NA 1.79E-07 mr1309 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
vg0812695428 NA 1.63E-07 mr1503 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
vg0812695428 NA 1.51E-07 mr1521 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
vg0812695428 NA 8.45E-07 mr1668 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
vg0812695428 NA 4.59E-09 mr1841 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
vg0812695428 NA 2.29E-08 mr1864 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
vg0812695428 5.09E-08 5.09E-08 mr1900 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
vg0812695428 NA 1.03E-06 mr1045_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
vg0812695428 NA 1.91E-07 mr1180_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
vg0812695428 NA 2.02E-07 mr1183_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
vg0812695428 NA 3.07E-07 mr1194_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
vg0812695428 NA 1.66E-06 mr1238_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
vg0812695428 NA 5.00E-06 mr1484_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
vg0812695428 NA 3.00E-08 mr1521_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
vg0812695428 NA 4.79E-10 mr1580_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
vg0812695428 NA 1.14E-07 mr1671_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
vg0812695428 NA 1.22E-09 mr1746_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
vg0812695428 NA 1.02E-09 mr1794_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
vg0812695428 NA 3.50E-08 mr1805_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
vg0812695428 NA 1.28E-07 mr1841_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
vg0812695428 NA 4.80E-06 mr1900_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