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Detailed information for vg0200660296:

Variant ID: vg0200660296 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 660296
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.63, C: 0.37, others allele: 0.00, population size: 51. )

Flanking Sequence (100 bp) in Reference Genome:


GGAGAGGGAGGAGGGGGGCTGACTGGGCGCCGGCTTGACTCGGTCAAGCGGGCCCAGGGCTGAGGTGGCGTCCACGTGGAAGCCACGTCGGATGGGGAGG[T/C]
AGAGGAGGCCGGGCAGGCTGATCCGATGGCCGGCGACGAGCGACGCAAACCGGCGAACGGCGGCGAGGTGGATTGGGGGGTTAGCACCGGAAGAGAGAGG

Reverse complement sequence

CCTCTCTCTTCCGGTGCTAACCCCCCAATCCACCTCGCCGCCGTTCGCCGGTTTGCGTCGCTCGTCGCCGGCCATCGGATCAGCCTGCCCGGCCTCCTCT[A/G]
CCTCCCCATCCGACGTGGCTTCCACGTGGACGCCACCTCAGCCCTGGGCCCGCTTGACCGAGTCAAGCCGGCGCCCAGTCAGCCCCCCTCCTCCCTCTCC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 91.30% 6.90% 0.25% 1.59% NA
All Indica  2759 91.10% 8.80% 0.04% 0.00% NA
All Japonica  1512 99.00% 0.50% 0.00% 0.53% NA
Aus  269 74.30% 8.20% 3.35% 14.13% NA
Indica I  595 93.40% 6.60% 0.00% 0.00% NA
Indica II  465 80.00% 20.00% 0.00% 0.00% NA
Indica III  913 98.70% 1.30% 0.00% 0.00% NA
Indica Intermediate  786 87.20% 12.70% 0.13% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 99.00% 0.40% 0.00% 0.60% NA
Japonica Intermediate  241 96.70% 1.20% 0.00% 2.07% NA
VI/Aromatic  96 30.20% 43.80% 0.00% 26.04% NA
Intermediate  90 82.20% 11.10% 2.22% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0200660296 T -> DEL N N silent_mutation Average:63.753; most accessible tissue: Zhenshan97 panicle, score: 75.67 N N N N
vg0200660296 T -> C LOC_Os02g02170.1 downstream_gene_variant ; 3051.0bp to feature; MODIFIER silent_mutation Average:63.753; most accessible tissue: Zhenshan97 panicle, score: 75.67 N N N N
vg0200660296 T -> C LOC_Os02g02180.1 intron_variant ; MODIFIER silent_mutation Average:63.753; most accessible tissue: Zhenshan97 panicle, score: 75.67 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0200660296 NA 2.68E-06 mr1049 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
vg0200660296 3.47E-06 3.47E-06 mr1452 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
vg0200660296 NA 1.64E-06 mr1513 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
vg0200660296 NA 2.00E-06 mr1590 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
vg0200660296 NA 6.42E-07 mr1704 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
vg0200660296 3.32E-06 2.11E-07 mr1964 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