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Detailed information for vg1125261664:

Variant ID: vg1125261664 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 25261664
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:


CACTATTTCTTTTCTTGTATTTATCTTGCTGATCTTGGTATTCATACATTTTGCATCCCAACTATTTTGCTCTGGCCCATCCTCTCTCTAGTCTTCTCTT[G/T]
CCATTTTTGTTCAACCAAATATTCAATTGATTATTGATTGTTGTACATTATGAAAGATGTGCAGAAAAGCTTGCTTATAAGAGGCAAAAGGAGAAGGAAA

Reverse complement sequence

TTTCCTTCTCCTTTTGCCTCTTATAAGCAAGCTTTTCTGCACATCTTTCATAATGTACAACAATCAATAATCAATTGAATATTTGGTTGAACAAAAATGG[C/A]
AAGAGAAGACTAGAGAGAGGATGGGCCAGAGCAAAATAGTTGGGATGCAAAATGTATGAATACCAAGATCAGCAAGATAAATACAAGAAAAGAAATAGTG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 85.40% 14.60% 0.06% 0.00% NA
All Indica  2759 75.70% 24.20% 0.07% 0.00% NA
All Japonica  1512 99.00% 0.90% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 66.70% 33.30% 0.00% 0.00% NA
Indica II  465 96.80% 3.00% 0.22% 0.00% NA
Indica III  913 70.60% 29.20% 0.11% 0.00% NA
Indica Intermediate  786 75.80% 24.20% 0.00% 0.00% NA
Temperate Japonica  767 98.70% 1.30% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 1.20% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 0.00% 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
vg1125261664 G -> T LOC_Os11g42010.1 downstream_gene_variant ; 1592.0bp to feature; MODIFIER silent_mutation Average:52.024; most accessible tissue: Zhenshan97 root, score: 63.237 N N N N
vg1125261664 G -> T LOC_Os11g42000.1 intron_variant ; MODIFIER silent_mutation Average:52.024; most accessible tissue: Zhenshan97 root, score: 63.237 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1125261664 1.04E-06 NA mr1191 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
vg1125261664 1.57E-06 1.20E-07 mr1191 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
vg1125261664 2.38E-08 NA mr1644 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
vg1125261664 6.46E-08 1.73E-08 mr1644 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
vg1125261664 1.19E-09 NA mr1191_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
vg1125261664 3.44E-09 2.10E-09 mr1191_2 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