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Detailed information for vg0210930737:

Variant ID: vg0210930737 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 10930737
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGGACCTATTGGAGCAGTCGCAGCCGGAGGAACAGGTTATGCTTTTAATGGTACTGTGGCGAATCTGGCACACACGGAATGAAATAGTGCATGGCAAACC[A/G]
GCCCCAGGAATACTAGTGTCCAAACGTTTCATTGAAAGCTATGTCCTCTCCCTTGCTGAGATCAAGCAACACCCCCAAGCAAGTCCTGAGAAGGGGAAAC

Reverse complement sequence

GTTTCCCCTTCTCAGGACTTGCTTGGGGGTGTTGCTTGATCTCAGCAAGGGAGAGGACATAGCTTTCAATGAAACGTTTGGACACTAGTATTCCTGGGGC[T/C]
GGTTTGCCATGCACTATTTCATTCCGTGTGTGCCAGATTCGCCACAGTACCATTAAAAGCATAACCTGTTCCTCCGGCTGCGACTGCTCCAATAGGTCCA

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 91.70% 0.10% 1.33% 6.81% NA
All Indica  2759 86.60% 0.20% 2.28% 10.98% NA
All Japonica  1512 99.90% 0.00% 0.00% 0.07% NA
Aus  269 95.50% 0.00% 0.00% 4.46% NA
Indica I  595 75.50% 0.80% 4.37% 19.33% NA
Indica II  465 95.30% 0.00% 0.43% 4.30% NA
Indica III  913 92.70% 0.00% 0.66% 6.68% NA
Indica Intermediate  786 82.70% 0.00% 3.69% 13.61% 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  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 0.00% 0.00% 1.04% NA
Intermediate  90 94.40% 0.00% 0.00% 5.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0210930737 A -> G LOC_Os02g18740.1 synonymous_variant ; p.Pro570Pro; LOW synonymous_codon Average:51.346; most accessible tissue: Zhenshan97 flower, score: 65.596 N N N N
vg0210930737 A -> DEL LOC_Os02g18740.1 N frameshift_variant Average:51.346; most accessible tissue: Zhenshan97 flower, score: 65.596 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0210930737 8.32E-06 7.75E-07 mr1115 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