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Detailed information for vg0210830120:

Variant ID: vg0210830120 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 10830120
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 340. )

Flanking Sequence (100 bp) in Reference Genome:


TCCGATCGTGGTCGAACCCACTATTCGGAATATCAAGGTAGCGCGAGTCCTCATCGATGGCGGCAGTTCCATCAACTTTCTCTTCGCCAGCACCTTGGAC[G/A]
CAATGGGGATTCCTCGAAGCGAGTTGACACCAACCGATCAACCTTTTCATGGAATCACTCCCCAGTCTTCGTCCAAACCATTGGGCAAGATCACGCTTCC

Reverse complement sequence

GGAAGCGTGATCTTGCCCAATGGTTTGGACGAAGACTGGGGAGTGATTCCATGAAAAGGTTGATCGGTTGGTGTCAACTCGCTTCGAGGAATCCCCATTG[C/T]
GTCCAAGGTGCTGGCGAAGAGAAAGTTGATGGAACTGCCGCCATCGATGAGGACTCGCGCTACCTTGATATTCCGAATAGTGGGTTCGACCACGATCGGA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 91.90% 8.10% 0.00% 0.00% NA
All Indica  2759 86.40% 13.60% 0.00% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 97.80% 2.20% 0.00% 0.00% NA
Indica II  465 77.80% 22.20% 0.00% 0.00% NA
Indica III  913 79.70% 20.30% 0.00% 0.00% NA
Indica Intermediate  786 90.50% 9.50% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.20% 0.80% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0210830120 G -> A LOC_Os02g18560.1 missense_variant ; p.Ala585Thr; MODERATE nonsynonymous_codon ; A585T Average:59.076; most accessible tissue: Zhenshan97 flag leaf, score: 79.71 benign 0.767 TOLERATED 0.08

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0210830120 4.71E-06 4.71E-06 mr1313 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
vg0210830120 8.61E-06 8.60E-06 mr1473 Ind_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