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Detailed information for vg0821112264:

Variant ID: vg0821112264 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 21112264
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTTATTTTTAATTGTATTTATATATAAACGTATCTTTCGATATTCTTTTTTTTATTTCACTTACTTCTAAATTGTATTTCTATATGAACTCTAGACTCTT[T/C]
TTTCAATATTTATTAATTTTTAATTTTATTTATTTCTATGTTGTATTTCTATATAGACTCTAAACGCTACTTTTAATCTTTTATTTTTATTCCGAATTTG

Reverse complement sequence

CAAATTCGGAATAAAAATAAAAGATTAAAAGTAGCGTTTAGAGTCTATATAGAAATACAACATAGAAATAAATAAAATTAAAAATTAATAAATATTGAAA[A/G]
AAGAGTCTAGAGTTCATATAGAAATACAATTTAGAAGTAAGTGAAATAAAAAAAAGAATATCGAAAGATACGTTTATATATAAATACAATTAAAAATAAC

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 68.30% 27.90% 2.31% 1.54% NA
All Indica  2759 92.60% 1.20% 3.59% 2.61% NA
All Japonica  1512 22.90% 76.90% 0.26% 0.00% NA
Aus  269 99.30% 0.40% 0.37% 0.00% NA
Indica I  595 89.90% 0.50% 6.89% 2.69% NA
Indica II  465 86.20% 0.90% 6.67% 6.24% NA
Indica III  913 98.50% 1.40% 0.00% 0.11% NA
Indica Intermediate  786 91.70% 1.50% 3.44% 3.31% NA
Temperate Japonica  767 3.90% 95.80% 0.26% 0.00% NA
Tropical Japonica  504 48.60% 51.40% 0.00% 0.00% NA
Japonica Intermediate  241 29.50% 69.70% 0.83% 0.00% NA
VI/Aromatic  96 12.50% 87.50% 0.00% 0.00% NA
Intermediate  90 51.10% 42.20% 5.56% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0821112264 T -> C LOC_Os08g33760.1 upstream_gene_variant ; 4100.0bp to feature; MODIFIER silent_mutation Average:16.189; most accessible tissue: Callus, score: 37.968 N N N N
vg0821112264 T -> C LOC_Os08g33750-LOC_Os08g33760 intergenic_region ; MODIFIER silent_mutation Average:16.189; most accessible tissue: Callus, score: 37.968 N N N N
vg0821112264 T -> DEL N N silent_mutation Average:16.189; most accessible tissue: Callus, score: 37.968 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0821112264 NA 1.49E-09 mr1277 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
vg0821112264 1.78E-07 NA mr1301 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
vg0821112264 1.83E-12 1.86E-18 mr1410 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
vg0821112264 NA 4.82E-16 mr1410 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
vg0821112264 NA 7.83E-08 mr1514 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
vg0821112264 NA 6.31E-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
vg0821112264 NA 2.58E-08 mr1691 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
vg0821112264 NA 5.20E-09 mr1693 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
vg0821112264 9.69E-07 NA mr1301_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
vg0821112264 1.28E-11 1.65E-17 mr1410_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
vg0821112264 NA 1.30E-16 mr1410_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
vg0821112264 NA 2.20E-08 mr1660_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
vg0821112264 NA 3.49E-06 mr1668_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
vg0821112264 NA 3.60E-21 mr1679_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
vg0821112264 NA 1.84E-08 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