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Detailed information for vg0121586545:

Variant ID: vg0121586545 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 21586545
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCCATGCAGCAGGTGAGGGCAGCAGCGGTGAAGAACGCACCAATGGTGGACACCCTAACAGCGCCTTTGGCAACGGTCCGCCACCGCTCCCAGAAAACCC[A/G]
ACGCTCGCACAAGTGATGGCCCATCAGACTCAGATGATTGCGGCCATGATGCAACAGATGCAGCAGCAGCACCATCAGATGCACCAGAGGATTCAGCAGC

Reverse complement sequence

GCTGCTGAATCCTCTGGTGCATCTGATGGTGCTGCTGCTGCATCTGTTGCATCATGGCCGCAATCATCTGAGTCTGATGGGCCATCACTTGTGCGAGCGT[T/C]
GGGTTTTCTGGGAGCGGTGGCGGACCGTTGCCAAAGGCGCTGTTAGGGTGTCCACCATTGGTGCGTTCTTCACCGCTGCTGCCCTCACCTGCTGCATGGC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 35.60% 12.30% 21.22% 30.89% NA
All Indica  2759 3.80% 20.50% 32.22% 43.46% NA
All Japonica  1512 96.20% 0.30% 0.53% 2.98% NA
Aus  269 3.70% 1.50% 33.09% 61.71% NA
Indica I  595 3.50% 6.70% 11.43% 78.32% NA
Indica II  465 4.30% 22.40% 22.58% 50.75% NA
Indica III  913 2.10% 31.80% 48.30% 17.85% NA
Indica Intermediate  786 5.70% 16.80% 34.99% 42.49% NA
Temperate Japonica  767 96.50% 0.00% 0.13% 3.39% NA
Tropical Japonica  504 97.60% 0.80% 1.19% 0.40% NA
Japonica Intermediate  241 92.50% 0.00% 0.41% 7.05% NA
VI/Aromatic  96 66.70% 1.00% 4.17% 28.12% NA
Intermediate  90 55.60% 4.40% 14.44% 25.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0121586545 A -> G LOC_Os01g38410.1 synonymous_variant ; p.Pro294Pro; LOW synonymous_codon Average:28.588; most accessible tissue: Callus, score: 51.085 N N N N
vg0121586545 A -> DEL LOC_Os01g38410.1 N frameshift_variant Average:28.588; most accessible tissue: Callus, score: 51.085 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0121586545 NA 9.87E-09 mr1047 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
vg0121586545 NA 7.76E-06 mr1189 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
vg0121586545 NA 1.32E-06 mr1781 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
vg0121586545 NA 1.38E-06 mr1796 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
vg0121586545 NA 8.40E-07 mr1990 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
vg0121586545 NA 6.64E-14 mr1326_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
vg0121586545 NA 9.01E-06 mr1329_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
vg0121586545 NA 7.41E-06 mr1524_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
vg0121586545 5.53E-07 NA mr1593_2 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
vg0121586545 NA 4.93E-08 mr1690_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
vg0121586545 NA 5.51E-16 mr1744_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