Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923).

Detailed information for vg1113239034:

Variant ID: vg1113239034 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 13239034
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 111. )

Flanking Sequence (100 bp) in Reference Genome:


ACTCGGTGAAGCCCGAATACGAGCTGTTCCCTCTGAAGTATCCACCGAACGACGAGGTCCTCTCACTAGGAAATGCCCGTGGTACCTTCATCCAATGGCC[T/C]
AAGGACCTCATTGAGATCAGGGTTATAGCGAGGCCAACCACTGCACCAGGCGGTCCTCCACCAAAGAGACCCGCCACTGCTCCTTCAGCCCCTCATGCTC

Reverse complement sequence

GAGCATGAGGGGCTGAAGGAGCAGTGGCGGGTCTCTTTGGTGGAGGACCGCCTGGTGCAGTGGTTGGCCTCGCTATAACCCTGATCTCAATGAGGTCCTT[A/G]
GGCCATTGGATGAAGGTACCACGGGCATTTCCTAGTGAGAGGACCTCGTCGTTCGGTGGATACTTCAGAGGGAACAGCTCGTATTCGGGCTTCACCGAGT

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 34.80% 1.30% 19.97% 43.91% NA
All Indica  2759 3.30% 1.90% 25.05% 69.77% NA
All Japonica  1512 94.60% 0.40% 2.12% 2.84% NA
Aus  269 1.50% 0.00% 75.09% 23.42% NA
Indica I  595 4.00% 2.90% 16.97% 76.13% NA
Indica II  465 2.20% 1.50% 11.40% 84.95% NA
Indica III  913 2.20% 1.30% 38.23% 58.27% NA
Indica Intermediate  786 4.60% 2.20% 23.92% 69.34% NA
Temperate Japonica  767 96.00% 0.80% 1.69% 1.56% NA
Tropical Japonica  504 91.30% 0.00% 3.37% 5.36% NA
Japonica Intermediate  241 97.50% 0.00% 0.83% 1.66% NA
VI/Aromatic  96 86.50% 0.00% 12.50% 1.04% NA
Intermediate  90 40.00% 4.40% 7.78% 47.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1113239034 T -> DEL LOC_Os11g23020.1 N frameshift_variant Average:21.258; most accessible tissue: Zhenshan97 panicle, score: 39.652 N N N N
vg1113239034 T -> C LOC_Os11g23020.1 synonymous_variant ; p.Pro466Pro; LOW synonymous_codon Average:21.258; most accessible tissue: Zhenshan97 panicle, score: 39.652 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1113239034 NA 3.55E-11 mr1277 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
vg1113239034 NA 1.05E-07 mr1277 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
vg1113239034 1.84E-06 NA mr1758 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
vg1113239034 3.61E-07 1.89E-09 mr1758 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
vg1113239034 NA 2.79E-07 mr1829 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
vg1113239034 NA 1.70E-09 mr1829 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
vg1113239034 NA 1.26E-13 mr1902 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
vg1113239034 NA 1.34E-07 mr1902 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