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Detailed information for vg0210574754:

Variant ID: vg0210574754 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 10574754
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.97, C: 0.02, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:


CTTTTCAGGATTTAGTTTCATCTTGAAAGCGCGGATGCTCGCAAAGGTTTCTTCTAGATCCGTAATCAAGTCATCCTTCTGCTTGGTCTTGACGACTACG[T/C]
CATCCACATAAGCTTCGACGTTGCGGCCGATCTGAGTCGAAAAAGCGTTGGTAAGTTGCTCCTGCATTCTTCAATCCAAAAGGCATAGTGATATAGCAGT

Reverse complement sequence

ACTGCTATATCACTATGCCTTTTGGATTGAAGAATGCAGGAGCAACTTACCAACGCTTTTTCGACTCAGATCGGCCGCAACGTCGAAGCTTATGTGGATG[A/G]
CGTAGTCGTCAAGACCAAGCAGAAGGATGACTTGATTACGGATCTAGAAGAAACCTTTGCGAGCATCCGCGCTTTCAAGATGAAACTAAATCCTGAAAAG

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 87.70% 0.90% 5.12% 6.31% NA
All Indica  2759 79.70% 1.40% 8.30% 10.62% NA
All Japonica  1512 99.50% 0.10% 0.40% 0.07% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 80.70% 1.70% 11.60% 6.05% NA
Indica II  465 69.70% 2.20% 14.62% 13.55% NA
Indica III  913 86.30% 0.30% 3.18% 10.19% NA
Indica Intermediate  786 77.10% 2.00% 8.02% 12.85% NA
Temperate Japonica  767 99.10% 0.10% 0.65% 0.13% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 85.60% 2.20% 7.78% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0210574754 T -> DEL LOC_Os02g18210.1 N frameshift_variant Average:23.068; most accessible tissue: Zhenshan97 flag leaf, score: 64.225 N N N N
vg0210574754 T -> C LOC_Os02g18210.1 missense_variant ; p.Asp534Gly; MODERATE nonsynonymous_codon ; D534G Average:23.068; most accessible tissue: Zhenshan97 flag leaf, score: 64.225 benign 0.36 DELETERIOUS 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0210574754 3.19E-06 NA mr1216_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