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Detailed information for vg1114878427:

Variant ID: vg1114878427 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 14878427
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: 304. )

Flanking Sequence (100 bp) in Reference Genome:


TTATTAGTTGAGTTCTCTCTACATGATCTTCCCACGGGATAAAATAAATACGATACCCTTGGAATACTCTCGGGTGAAATGCTACAATGGTATATCCGTG[C/T]
GCTTGCGGATGAACTCTGTAACCATAATATACTAGTAGTATTTATGCGTCATTGTTGGGAATTATATTTCTAGTAATGTCGTTAAAAATACCAACAGCAG

Reverse complement sequence

CTGCTGTTGGTATTTTTAACGACATTACTAGAAATATAATTCCCAACAATGACGCATAAATACTACTAGTATATTATGGTTACAGAGTTCATCCGCAAGC[G/A]
CACGGATATACCATTGTAGCATTTCACCCGAGAGTATTCCAAGGGTATCGTATTTATTTTATCCCGTGGGAAGATCATGTAGAGAGAACTCAACTAATAA

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 92.70% 7.30% 0.02% 0.00% NA
All Indica  2759 99.50% 0.50% 0.00% 0.00% NA
All Japonica  1512 78.30% 21.60% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.80% 1.20% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.00% 1.00% 0.00% 0.00% NA
Temperate Japonica  767 65.10% 34.90% 0.00% 0.00% NA
Tropical Japonica  504 99.20% 0.80% 0.00% 0.00% NA
Japonica Intermediate  241 76.80% 22.80% 0.41% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg1114878427 C -> T LOC_Os11g26020.1 upstream_gene_variant ; 2157.0bp to feature; MODIFIER silent_mutation Average:53.176; most accessible tissue: Minghui63 flag leaf, score: 74.563 N N N N
vg1114878427 C -> T LOC_Os11g26010.1 downstream_gene_variant ; 1022.0bp to feature; MODIFIER silent_mutation Average:53.176; most accessible tissue: Minghui63 flag leaf, score: 74.563 N N N N
vg1114878427 C -> T LOC_Os11g26010-LOC_Os11g26020 intergenic_region ; MODIFIER silent_mutation Average:53.176; most accessible tissue: Minghui63 flag leaf, score: 74.563 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1114878427 NA 1.98E-07 mr1190 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
vg1114878427 NA 1.41E-07 mr1382 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
vg1114878427 NA 3.14E-06 mr1382 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
vg1114878427 5.58E-07 2.04E-09 mr1424 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
vg1114878427 4.86E-07 4.86E-07 mr1424 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
vg1114878427 NA 1.06E-06 mr1445 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
vg1114878427 NA 9.84E-06 mr1509 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
vg1114878427 NA 2.34E-06 mr1884 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