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Detailed information for vg0212583199:

Variant ID: vg0212583199 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 12583199
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:


GGTGATTTAATTTTTCCTTGGTCTTGGTGTTAAAAGTAATATGTGTAACTTTTGTGGATGGAAGGAGTAGCCGAGATACATAATATGTCCTCGCTTGACA[C/T]
GACTCTTATCTCTAACAAACTCTAAGATACACATAAGTCTTTACGGCAGACCTTTGCCCAAAACATATCTCTAAGGAAATTACATAAAATATCCTAATTA

Reverse complement sequence

TAATTAGGATATTTTATGTAATTTCCTTAGAGATATGTTTTGGGCAAAGGTCTGCCGTAAAGACTTATGTGTATCTTAGAGTTTGTTAGAGATAAGAGTC[G/A]
TGTCAAGCGAGGACATATTATGTATCTCGGCTACTCCTTCCATCCACAAAAGTTACACATATTACTTTTAACACCAAGACCAAGGAAAAATTAAATCACC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 92.30% 7.30% 0.42% 0.00% NA
All Indica  2759 99.80% 0.20% 0.00% 0.00% NA
All Japonica  1512 82.30% 16.50% 1.19% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.50% 0.50% 0.00% 0.00% NA
Temperate Japonica  767 96.50% 2.90% 0.65% 0.00% NA
Tropical Japonica  504 74.60% 24.60% 0.79% 0.00% NA
Japonica Intermediate  241 53.50% 42.70% 3.73% 0.00% NA
VI/Aromatic  96 14.60% 84.40% 1.04% 0.00% NA
Intermediate  90 88.90% 10.00% 1.11% 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
vg0212583199 C -> T LOC_Os02g21190.1 intron_variant ; MODIFIER silent_mutation Average:50.539; most accessible tissue: Minghui63 panicle, score: 78.92 N N N N
vg0212583199 C -> T LOC_Os02g21190.2 intron_variant ; MODIFIER silent_mutation Average:50.539; most accessible tissue: Minghui63 panicle, score: 78.92 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0212583199 NA 5.88E-06 mr1438 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
vg0212583199 NA 2.66E-08 mr1570 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
vg0212583199 4.89E-06 NA mr1542_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
vg0212583199 NA 8.61E-09 mr1829_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