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Detailed information for vg0200456993:

Variant ID: vg0200456993 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 456993
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.94, T: 0.07, others allele: 0.00, population size: 200. )

Flanking Sequence (100 bp) in Reference Genome:


CATACGCCTTATGCACATCCAATTTAATCGCACATAACCCCCTTTTCCCTTGTTTCCTCTTGATAGTATGAATACATTCATACGCAATCAGAATATTATC[T/C]
GTAATTAATCTACCTGGAACAAAAGCACTGATCACTTATAACCTCAGGAAGGATGCTCTTCATCCTGCGAGAGAGCATTTTTGAAATAACTTTATACACC

Reverse complement sequence

GGTGTATAAAGTTATTTCAAAAATGCTCTCTCGCAGGATGAAGAGCATCCTTCCTGAGGTTATAAGTGATCAGTGCTTTTGTTCCAGGTAGATTAATTAC[A/G]
GATAATATTCTGATTGCGTATGAATGTATTCATACTATCAAGAGGAAACAAGGGAAAAGGGGGTTATGTGCGATTAAATTGGATGTGCATAAGGCGTATG

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 53.10% 46.80% 0.06% 0.00% NA
All Indica  2759 79.70% 20.20% 0.11% 0.00% NA
All Japonica  1512 2.10% 97.90% 0.00% 0.00% NA
Aus  269 61.00% 39.00% 0.00% 0.00% NA
Indica I  595 61.70% 38.00% 0.34% 0.00% NA
Indica II  465 78.10% 21.90% 0.00% 0.00% NA
Indica III  913 88.60% 11.30% 0.11% 0.00% NA
Indica Intermediate  786 84.10% 15.90% 0.00% 0.00% NA
Temperate Japonica  767 0.50% 99.50% 0.00% 0.00% NA
Tropical Japonica  504 3.60% 96.40% 0.00% 0.00% NA
Japonica Intermediate  241 3.70% 96.30% 0.00% 0.00% NA
VI/Aromatic  96 76.00% 24.00% 0.00% 0.00% NA
Intermediate  90 46.70% 53.30% 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
vg0200456993 T -> C LOC_Os02g01820.1 upstream_gene_variant ; 2684.0bp to feature; MODIFIER silent_mutation Average:51.986; most accessible tissue: Callus, score: 86.607 N N N N
vg0200456993 T -> C LOC_Os02g01840.1 upstream_gene_variant ; 3873.0bp to feature; MODIFIER silent_mutation Average:51.986; most accessible tissue: Callus, score: 86.607 N N N N
vg0200456993 T -> C LOC_Os02g01830.1 downstream_gene_variant ; 1603.0bp to feature; MODIFIER silent_mutation Average:51.986; most accessible tissue: Callus, score: 86.607 N N N N
vg0200456993 T -> C LOC_Os02g01825.1 intron_variant ; MODIFIER silent_mutation Average:51.986; most accessible tissue: Callus, score: 86.607 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0200456993 NA 1.90E-07 mr1680 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
vg0200456993 NA 8.35E-06 mr1002_2 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
vg0200456993 NA 3.90E-06 mr1020_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
vg0200456993 NA 2.28E-14 mr1133_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
vg0200456993 2.69E-06 5.39E-15 mr1349_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
vg0200456993 NA 1.31E-07 mr1349_2 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
vg0200456993 NA 1.90E-11 mr1377_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
vg0200456993 NA 9.16E-06 mr1452_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
vg0200456993 NA 3.11E-08 mr1568_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
vg0200456993 NA 1.49E-09 mr1576_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
vg0200456993 NA 2.02E-14 mr1666_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
vg0200456993 NA 3.18E-17 mr1712_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
vg0200456993 NA 1.31E-12 mr1761_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