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Detailed information for vg1213231314:

Variant ID: vg1213231314 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 13231314
Reference Allele: AAlternative Allele: C
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.87, A: 0.13, others allele: 0.00, population size: 32. )

Flanking Sequence (100 bp) in Reference Genome:


GCTGAATCCCACGCTCTTTGCAGGCGCGAATTTCAGCGCGGACATTGAGGAAAACCCAGCAGGCTTGCAAAGTGTGTTTCTTGGTTTTGTGGATAGGACA[A/C]
CAGGACCTTGTGGCTTCGGAAGTCATCTTTGTCGGCTCGCGGTTTATGTCGGAAGGACAAGGTTTGGCCACATCAGAATCCTTCTCGAGCTCGGATGTCG

Reverse complement sequence

CGACATCCGAGCTCGAGAAGGATTCTGATGTGGCCAAACCTTGTCCTTCCGACATAAACCGCGAGCCGACAAAGATGACTTCCGAAGCCACAAGGTCCTG[T/G]
TGTCCTATCCACAAAACCAAGAAACACACTTTGCAAGCCTGCTGGGTTTTCCTCAATGTCCGCGCTGAAATTCGCGCCTGCAAAGAGCGTGGGATTCAGC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 47.70% 17.40% 18.62% 16.27% NA
All Indica  2759 69.20% 4.60% 22.94% 3.30% NA
All Japonica  1512 6.50% 44.00% 7.28% 42.20% NA
Aus  269 60.60% 1.90% 28.62% 8.92% NA
Indica I  595 58.00% 7.60% 30.76% 3.70% NA
Indica II  465 67.30% 5.80% 18.28% 8.60% NA
Indica III  913 76.90% 2.00% 21.14% 0.00% NA
Indica Intermediate  786 69.80% 4.60% 21.88% 3.69% NA
Temperate Japonica  767 1.40% 78.50% 1.83% 18.25% NA
Tropical Japonica  504 14.30% 1.00% 11.71% 73.02% NA
Japonica Intermediate  241 6.60% 24.10% 15.35% 53.94% NA
VI/Aromatic  96 51.00% 0.00% 47.92% 1.04% NA
Intermediate  90 40.00% 27.80% 15.56% 16.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1213231314 A -> C LOC_Os12g23390.1 missense_variant ; p.Cys110Trp; MODERATE stop_gained Average:13.419; most accessible tissue: Callus, score: 36.349 N N N N
vg1213231314 A -> C LOC_Os12g23390.1 missense_variant ; p.Cys110Trp; MODERATE nonsynonymous_codon ; C110W Average:13.419; most accessible tissue: Callus, score: 36.349 unknown unknown TOLERATED 1.00
vg1213231314 A -> DEL LOC_Os12g23390.1 N frameshift_variant Average:13.419; most accessible tissue: Callus, score: 36.349 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1213231314 NA 2.00E-08 mr1022 Jap_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
vg1213231314 NA 1.25E-13 mr1079 Jap_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
vg1213231314 NA 1.40E-11 mr1178 Jap_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
vg1213231314 NA 1.74E-07 mr1657 Jap_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
vg1213231314 NA 1.37E-13 mr1079_2 Jap_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
vg1213231314 NA 7.46E-08 mr1156_2 Jap_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
vg1213231314 NA 3.14E-08 mr1607_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