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Detailed information for vg1125439473:

Variant ID: vg1125439473 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 25439473
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 116. )

Flanking Sequence (100 bp) in Reference Genome:


AAAAAGTCCGATTCCCCATAAGAAAGTGGCGAAAATAAAAAAAACTACCGTATCCGATTCCCATCTAATTTTGTTCGTTTTCTTTTTTTTCTGTTTTTTT[C/T]
CGTTTTATTTTCTTTTCCTGTTTCTTTTTTTTCTTTCACCTTTTTTCCGGTTTTCTTTGTCCGTTTTCTTTTCCTCCTTTTTGCGTATTTTCTTTTCGCC

Reverse complement sequence

GGCGAAAAGAAAATACGCAAAAAGGAGGAAAAGAAAACGGACAAAGAAAACCGGAAAAAAGGTGAAAGAAAAAAAAGAAACAGGAAAAGAAAATAAAACG[G/A]
AAAAAAACAGAAAAAAAAGAAAACGAACAAAATTAGATGGGAATCGGATACGGTAGTTTTTTTTATTTTCGCCACTTTCTTATGGGGAATCGGACTTTTT

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 91.00% 7.60% 1.35% 0.00% NA
All Indica  2759 85.80% 12.60% 1.63% 0.00% NA
All Japonica  1512 99.70% 0.20% 0.07% 0.00% NA
Aus  269 94.80% 0.00% 5.20% 0.00% NA
Indica I  595 56.50% 40.20% 3.36% 0.00% NA
Indica II  465 82.40% 13.30% 4.30% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 93.50% 5.90% 0.64% 0.00% NA
Temperate Japonica  767 99.50% 0.40% 0.13% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 85.60% 10.00% 4.44% 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
vg1125439473 C -> T LOC_Os11g42230.1 upstream_gene_variant ; 2466.0bp to feature; MODIFIER silent_mutation Average:15.956; most accessible tissue: Minghui63 flag leaf, score: 22.563 N N N N
vg1125439473 C -> T LOC_Os11g42220.1 downstream_gene_variant ; 4680.0bp to feature; MODIFIER silent_mutation Average:15.956; most accessible tissue: Minghui63 flag leaf, score: 22.563 N N N N
vg1125439473 C -> T LOC_Os11g42240.1 downstream_gene_variant ; 1401.0bp to feature; MODIFIER silent_mutation Average:15.956; most accessible tissue: Minghui63 flag leaf, score: 22.563 N N N N
vg1125439473 C -> T LOC_Os11g42230-LOC_Os11g42240 intergenic_region ; MODIFIER silent_mutation Average:15.956; most accessible tissue: Minghui63 flag leaf, score: 22.563 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1125439473 NA 1.71E-08 mr1301 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
vg1125439473 8.56E-06 3.96E-08 mr1745 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
vg1125439473 1.47E-06 6.70E-07 mr1780 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
vg1125439473 NA 1.09E-07 mr1825 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