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Detailed information for vg0121861493:

Variant ID: vg0121861493 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 21861493
Reference Allele: CAlternative Allele: G
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTTTTGTATACCTCCTCCTCCATTTATTTTCTCTTTTGAAATTTGGGAGAGTGCATGGCTATTTCTTTTTTTCTTTTCTTTTTTTCTTTTTGTTTCATCA[C/G]
CATGCTCCATACTTGTATGAGCACTTTTTTTCTTTCTTTTTGCATAGCCATGCCTCTCTCTCTTTTTTTTTCCTTTGAAAGAACTTTGGAGGAAGAGGCA

Reverse complement sequence

TGCCTCTTCCTCCAAAGTTCTTTCAAAGGAAAAAAAAAGAGAGAGAGGCATGGCTATGCAAAAAGAAAGAAAAAAAGTGCTCATACAAGTATGGAGCATG[G/C]
TGATGAAACAAAAAGAAAAAAAGAAAAGAAAAAAAGAAATAGCCATGCACTCTCCCAAATTTCAAAAGAGAAAATAAATGGAGGAGGAGGTATACAAAAG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 66.70% 0.10% 5.01% 28.18% NA
All Indica  2759 44.70% 0.10% 8.45% 46.68% NA
All Japonica  1512 99.70% 0.00% 0.00% 0.26% NA
Aus  269 90.00% 0.00% 0.74% 9.29% NA
Indica I  595 31.30% 0.20% 8.24% 60.34% NA
Indica II  465 36.80% 0.00% 6.45% 56.77% NA
Indica III  913 47.60% 0.20% 11.17% 40.96% NA
Indica Intermediate  786 56.20% 0.10% 6.62% 37.02% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.00% 0.20% NA
Japonica Intermediate  241 98.80% 0.00% 0.00% 1.24% NA
VI/Aromatic  96 96.90% 0.00% 1.04% 2.08% NA
Intermediate  90 84.40% 0.00% 1.11% 14.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0121861493 C -> G LOC_Os01g38920-LOC_Os01g38930 intergenic_region ; MODIFIER silent_mutation Average:13.639; most accessible tissue: Callus, score: 22.626 N N N N
vg0121861493 C -> DEL N N silent_mutation Average:13.639; most accessible tissue: Callus, score: 22.626 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0121861493 NA 3.74E-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
vg0121861493 NA 6.18E-07 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
vg0121861493 NA 4.19E-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
vg0121861493 4.78E-06 1.67E-06 mr1993 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
vg0121861493 NA 2.22E-07 mr1212_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