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Detailed information for vg1212722858:

Variant ID: vg1212722858 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 12722858
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.76, C: 0.25, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:


TATAGAGGGGGTGATTATGATCCAGGAATGGTGCACTATGGTGAGTTGTGTTGTGCAGGGGGTACTGTCACAGCCTCTATTCGGGTACTTTCCAGTATCG[C/T]
GACGCATGGTAGACATGATGTTGAGGCTGTGTCTTGTGTGTACAGTGGTACACCTCTGGCCAGAGTAAAACTATTCGAATAGCCGTGCCCACGGTTATGG

Reverse complement sequence

CCATAACCGTGGGCACGGCTATTCGAATAGTTTTACTCTGGCCAGAGGTGTACCACTGTACACACAAGACACAGCCTCAACATCATGTCTACCATGCGTC[G/A]
CGATACTGGAAAGTACCCGAATAGAGGCTGTGACAGTACCCCCTGCACAACACAACTCACCATAGTGCACCATTCCTGGATCATAATCACCCCCTCTATA

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 83.60% 16.30% 0.15% 0.00% NA
All Indica  2759 96.40% 3.40% 0.14% 0.00% NA
All Japonica  1512 56.90% 43.10% 0.00% 0.00% NA
Aus  269 98.90% 0.70% 0.37% 0.00% NA
Indica I  595 99.20% 0.80% 0.00% 0.00% NA
Indica II  465 97.00% 3.00% 0.00% 0.00% NA
Indica III  913 96.30% 3.70% 0.00% 0.00% NA
Indica Intermediate  786 94.30% 5.20% 0.51% 0.00% NA
Temperate Japonica  767 23.20% 76.80% 0.00% 0.00% NA
Tropical Japonica  504 98.60% 1.40% 0.00% 0.00% NA
Japonica Intermediate  241 77.20% 22.80% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 74.40% 23.30% 2.22% 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
vg1212722858 C -> T LOC_Os12g22530.1 downstream_gene_variant ; 4404.0bp to feature; MODIFIER silent_mutation Average:53.413; most accessible tissue: Minghui63 young leaf, score: 75.479 N N N N
vg1212722858 C -> T LOC_Os12g22540.1 intron_variant ; MODIFIER silent_mutation Average:53.413; most accessible tissue: Minghui63 young leaf, score: 75.479 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1212722858 NA 2.98E-06 mr1606 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
vg1212722858 NA 8.56E-06 mr1657 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
vg1212722858 NA 1.16E-07 mr1031_2 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
vg1212722858 NA 1.73E-08 mr1189_2 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
vg1212722858 NA 8.31E-09 mr1338_2 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
vg1212722858 NA 1.29E-08 mr1471_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
vg1212722858 NA 1.16E-07 mr1606_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
vg1212722858 NA 8.18E-12 mr1879_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