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Detailed information for vg0316912605:

Variant ID: vg0316912605 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 16912605
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 313. )

Flanking Sequence (100 bp) in Reference Genome:


TGTTAATTGATTCAACAAAAAGACAAGGTTATATTTTGTGAAAAGTTGAAATGTTTGATTACATACCGGTGGAGGAGGATTGAAAGCATTGAATGGCACG[A/G]
CTGGCAGCAAGTGCGAATAGCTGACGACGGTAGCATTCGAGAAGATCTTGTACATCCTCTCCTTCATAACCTTAAAGTTAAGAGAGTCTGGATCTTCACG

Reverse complement sequence

CGTGAAGATCCAGACTCTCTTAACTTTAAGGTTATGAAGGAGAGGATGTACAAGATCTTCTCGAATGCTACCGTCGTCAGCTATTCGCACTTGCTGCCAG[T/C]
CGTGCCATTCAATGCTTTCAATCCTCCTCCACCGGTATGTAATCAAACATTTCAACTTTTCACAAAATATAACCTTGTCTTTTTGTTGAATCAATTAACA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 84.00% 2.20% 12.70% 1.16% NA
All Indica  2759 72.90% 3.70% 21.42% 1.99% NA
All Japonica  1512 99.80% 0.00% 0.20% 0.00% NA
Aus  269 99.60% 0.00% 0.37% 0.00% NA
Indica I  595 66.40% 3.20% 29.58% 0.84% NA
Indica II  465 92.00% 1.30% 6.24% 0.43% NA
Indica III  913 67.00% 4.90% 24.10% 3.94% NA
Indica Intermediate  786 73.30% 4.10% 21.12% 1.53% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.00% 0.40% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 94.40% 0.00% 5.56% 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
vg0316912605 A -> DEL LOC_Os03g29660.1 N frameshift_variant Average:43.598; most accessible tissue: Minghui63 young leaf, score: 74.007 N N N N
vg0316912605 A -> G LOC_Os03g29660.1 missense_variant ; p.Val284Ala; MODERATE nonsynonymous_codon ; V284A Average:43.598; most accessible tissue: Minghui63 young leaf, score: 74.007 possibly damaging 1.537 DELETERIOUS 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0316912605 NA 1.00E-07 mr1925 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