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Detailed information for vg0219418052:

Variant ID: vg0219418052 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 19418052
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.01, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:


TGGATACTTCTTTTAATATTGCTTATTTTTAATTCCGAATTTCAGCTATTTTTGAATTGTATTTCTACTTGGACTCTCCTTTTCTTTTTCTCCGATTAAT[G/T]
TGAGAATTTCTAGCCCCCACAGCGAACGTGGTGCCTCTTTTCAAAGCTGTCTTAATAATATAATTAGCATGGTGGCCCGCGAAGATTACGCGGCTAGCAT

Reverse complement sequence

ATGCTAGCCGCGTAATCTTCGCGGGCCACCATGCTAATTATATTATTAAGACAGCTTTGAAAAGAGGCACCACGTTCGCTGTGGGGGCTAGAAATTCTCA[C/A]
ATTAATCGGAGAAAAAGAAAAGGAGAGTCCAAGTAGAAATACAATTCAAAAATAGCTGAAATTCGGAATTAAAAATAAGCAATATTAAAAGAAGTATCCA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 87.60% 7.60% 4.78% 0.00% NA
All Indica  2759 80.00% 12.20% 7.87% 0.00% NA
All Japonica  1512 98.70% 1.10% 0.20% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 84.50% 10.80% 4.71% 0.00% NA
Indica II  465 56.30% 30.50% 13.12% 0.00% NA
Indica III  913 93.60% 3.80% 2.52% 0.00% NA
Indica Intermediate  786 74.60% 12.10% 13.36% 0.00% NA
Temperate Japonica  767 98.30% 1.40% 0.26% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 97.90% 1.70% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 85.60% 7.80% 6.67% 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
vg0219418052 G -> T LOC_Os02g32690.1 intron_variant ; MODIFIER silent_mutation Average:25.837; most accessible tissue: Minghui63 panicle, score: 46.754 N N N N
vg0219418052 G -> T LOC_Os02g32690.2 intron_variant ; MODIFIER silent_mutation Average:25.837; most accessible tissue: Minghui63 panicle, score: 46.754 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0219418052 NA 2.04E-07 mr1236_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
vg0219418052 NA 1.53E-06 mr1236_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
vg0219418052 NA 2.42E-06 mr1763_2 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
vg0219418052 NA 3.42E-06 mr1876_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