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Detailed information for vg0210199468:

Variant ID: vg0210199468 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 10199468
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:


AATGCAATGTGAAATCTCTTATGTATATGATATATATGTCCAAAATAGCAAATGATTAATTCTCACATCTAGGATTAACATATTCCTTTAAAATAGTATA[C/A]
ATTCATATGATGCAAACACATTTAAATTCTTACTCCCTCCAGTTCCTTATTACTTGATGCTTTAGACAAGAATATATATACCAATAAGTAATTAATTAGG

Reverse complement sequence

CCTAATTAATTACTTATTGGTATATATATTCTTGTCTAAAGCATCAAGTAATAAGGAACTGGAGGGAGTAAGAATTTAAATGTGTTTGCATCATATGAAT[G/T]
TATACTATTTTAAAGGAATATGTTAATCCTAGATGTGAGAATTAATCATTTGCTATTTTGGACATATATATCATATACATAAGAGATTTCACATTGCATT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 89.80% 9.50% 0.78% 0.00% NA
All Indica  2759 83.10% 15.60% 1.23% 0.00% NA
All Japonica  1512 99.30% 0.70% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 97.60% 1.20% 1.18% 0.00% NA
Indica II  465 74.60% 23.00% 2.37% 0.00% NA
Indica III  913 73.40% 26.20% 0.44% 0.00% NA
Indica Intermediate  786 88.50% 9.90% 1.53% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 97.80% 2.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 92.20% 4.40% 3.33% 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
vg0210199468 C -> A LOC_Os02g17690.1 intron_variant ; MODIFIER silent_mutation Average:56.486; most accessible tissue: Callus, score: 89.208 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0210199468 8.41E-06 NA mr1225 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
vg0210199468 5.53E-06 5.53E-06 mr1473 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
vg0210199468 NA 1.27E-09 mr1319_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
vg0210199468 NA 4.30E-06 mr1332_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
vg0210199468 3.26E-06 3.26E-06 mr1848_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