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Detailed information for vg0812591477:

Variant ID: vg0812591477 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 12591477
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.77, C: 0.23, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:


GTTCTGAGATAACACAAGTGCTCTTAGTGGTGTCCAAGTGTTGAAATATTTTTAGGAGCTGTTTTTGAAAATGGCTCTACTCGGGACAGAGAGTCCCACC[T/C]
GGAGGTTCTGTCCGGAACTTCCTGGCACCAAGGTGAGGTTGAAAAATTTCATAAGTGCTGCCCAGAAGTTCCTGGCACTTTTACCCGGAAGCTCCTGGCA

Reverse complement sequence

TGCCAGGAGCTTCCGGGTAAAAGTGCCAGGAACTTCTGGGCAGCACTTATGAAATTTTTCAACCTCACCTTGGTGCCAGGAAGTTCCGGACAGAACCTCC[A/G]
GGTGGGACTCTCTGTCCCGAGTAGAGCCATTTTCAAAAACAGCTCCTAAAAATATTTCAACACTTGGACACCACTAAGAGCACTTGTGTTATCTCAGAAC

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 55.20% 29.30% 2.90% 12.63% NA
All Indica  2759 76.70% 11.30% 4.42% 7.50% NA
All Japonica  1512 12.30% 66.90% 0.66% 20.17% NA
Aus  269 63.20% 10.80% 0.00% 26.02% NA
Indica I  595 86.60% 3.00% 6.72% 3.70% NA
Indica II  465 78.30% 8.80% 7.31% 5.59% NA
Indica III  913 72.00% 18.10% 2.08% 7.89% NA
Indica Intermediate  786 73.90% 11.30% 3.69% 11.07% NA
Temperate Japonica  767 3.40% 93.40% 0.00% 3.26% NA
Tropical Japonica  504 12.70% 39.10% 1.19% 47.02% NA
Japonica Intermediate  241 39.80% 40.70% 1.66% 17.84% NA
VI/Aromatic  96 89.60% 4.20% 2.08% 4.17% NA
Intermediate  90 53.30% 31.10% 3.33% 12.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0812591477 T -> C LOC_Os08g21060.1 missense_variant ; p.Leu43Pro; MODERATE nonsynonymous_codon ; L43S Average:17.275; most accessible tissue: Callus, score: 26.397 unknown unknown TOLERATED 0.65
vg0812591477 T -> C LOC_Os08g21060.1 missense_variant ; p.Leu43Pro; MODERATE nonsynonymous_codon ; L43P Average:17.275; most accessible tissue: Callus, score: 26.397 unknown unknown TOLERATED 1.00
vg0812591477 T -> DEL LOC_Os08g21060.1 N frameshift_variant Average:17.275; most accessible tissue: Callus, score: 26.397 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0812591477 NA 1.09E-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
vg0812591477 7.68E-06 9.69E-08 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
vg0812591477 NA 7.83E-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
vg0812591477 5.13E-08 5.13E-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
vg0812591477 NA 2.43E-06 mr1064_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
vg0812591477 3.79E-07 NA mr1238_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
vg0812591477 NA 9.00E-08 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
vg0812591477 NA 3.43E-06 mr1250_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
vg0812591477 3.78E-07 NA mr1484_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
vg0812591477 NA 7.16E-07 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
vg0812591477 1.48E-06 NA mr1841_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
vg0812591477 NA 7.53E-09 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
vg0812591477 4.60E-08 1.13E-21 mr1900_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
vg0812591477 NA 3.66E-07 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
vg0812591477 7.49E-06 NA mr1945_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