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Detailed information for vg0716044467:

Variant ID: vg0716044467 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 16044467
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:


TCTTTTTATACTTTGCGTTGCATCACCCCTAGTCGTGCTTAGAACCATAACCGCTAGCCTACTTTTTGATTGCCAACAAGGGTTTCATTGAGGTTTCAGC[C/T]
GATGAGTTATCTGGACGTTGCATCGGCTTATAAGGATTACATACAAGTTGGATTTAGCCGATCACAACAAAGGTTTCACTGTTTATTTAATCGTTTGGAT

Reverse complement sequence

ATCCAAACGATTAAATAAACAGTGAAACCTTTGTTGTGATCGGCTAAATCCAACTTGTATGTAATCCTTATAAGCCGATGCAACGTCCAGATAACTCATC[G/A]
GCTGAAACCTCAATGAAACCCTTGTTGGCAATCAAAAAGTAGGCTAGCGGTTATGGTTCTAAGCACGACTAGGGGTGATGCAACGCAAAGTATAAAAAGA

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 94.20% 5.80% 0.02% 0.00% NA
All Indica  2759 97.30% 2.70% 0.00% 0.00% NA
All Japonica  1512 88.30% 11.60% 0.07% 0.00% NA
Aus  269 94.10% 5.90% 0.00% 0.00% NA
Indica I  595 99.30% 0.70% 0.00% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 99.70% 0.30% 0.00% 0.00% NA
Indica Intermediate  786 91.90% 8.10% 0.00% 0.00% NA
Temperate Japonica  767 78.40% 21.50% 0.13% 0.00% NA
Tropical Japonica  504 98.60% 1.40% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 1.70% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg0716044467 C -> T LOC_Os07g27490-LOC_Os07g27500 intergenic_region ; MODIFIER silent_mutation Average:34.096; most accessible tissue: Minghui63 panicle, score: 56.842 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0716044467 NA 7.79E-06 mr1528 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
vg0716044467 6.04E-14 5.50E-13 mr1265_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
vg0716044467 1.17E-13 3.72E-14 mr1528_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