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Detailed information for vg1211463415:

Variant ID: vg1211463415 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 11463415
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.02, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:


CTCGAAGTCTTGCCCGAATGGAACCACAATCAACCACAAAATTGTTTAAAGATGCCTCTAGCCGATGAGATATATCTTCAAGAGTTCTTTTGACATCTTC[G/A]
TCTAGAGGAGCTAGGGTCTTGCTTGTTGTTTCATCTTTTGCCTCTTGATCAAGATAATCCTTGATATCAAAGGAGAACATATCAGCTAATACCTGCAAAA

Reverse complement sequence

TTTTGCAGGTATTAGCTGATATGTTCTCCTTTGATATCAAGGATTATCTTGATCAAGAGGCAAAAGATGAAACAACAAGCAAGACCCTAGCTCCTCTAGA[C/T]
GAAGATGTCAAAAGAACTCTTGAAGATATATCTCATCGGCTAGAGGCATCTTTAAACAATTTTGTGGTTGATTGTGGTTCCATTCGGGCAAGACTTCGAG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 84.20% 14.10% 1.74% 0.00% NA
All Indica  2759 80.60% 18.90% 0.47% 0.00% NA
All Japonica  1512 86.60% 9.00% 4.37% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.20% 1.70% 0.17% 0.00% NA
Indica II  465 64.70% 33.50% 1.72% 0.00% NA
Indica III  913 79.10% 20.70% 0.22% 0.00% NA
Indica Intermediate  786 78.60% 21.10% 0.25% 0.00% NA
Temperate Japonica  767 97.00% 0.50% 2.48% 0.00% NA
Tropical Japonica  504 67.70% 25.20% 7.14% 0.00% NA
Japonica Intermediate  241 93.40% 2.10% 4.56% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 87.80% 8.90% 3.33% 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
vg1211463415 G -> A LOC_Os12g19670.1 synonymous_variant ; p.Asp292Asp; LOW synonymous_codon Average:46.938; most accessible tissue: Zhenshan97 young leaf, score: 76.099 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1211463415 NA 3.62E-06 mr1050 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
vg1211463415 1.81E-06 1.81E-06 mr1265 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
vg1211463415 NA 8.03E-06 mr1364 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
vg1211463415 2.20E-06 2.20E-06 mr1528 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
vg1211463415 NA 1.23E-06 mr1603 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
vg1211463415 NA 2.11E-07 mr1696 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