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Detailed information for vg1221477991:

Variant ID: vg1221477991 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 21477991
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.02, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:


GTTCTTACAGCTTAAAAACAATGCTGGACAACAATTAATGTATGATGAAAAAACAAACAAAATCAACTGTAAAATTAAGATTTAAAATTTTGGTTGCGTC[C/T]
AATAAGCTACTCCCTCTGTCCTATAATATAAGGGATTTTGAGTTTTTGTTTGTATTATTTGACCACTCGTCTTATTCAAAAAATTTGTGCAAATATAAAA

Reverse complement sequence

TTTTATATTTGCACAAATTTTTTGAATAAGACGAGTGGTCAAATAATACAAACAAAAACTCAAAATCCCTTATATTATAGGACAGAGGGAGTAGCTTATT[G/A]
GACGCAACCAAAATTTTAAATCTTAATTTTACAGTTGATTTTGTTTGTTTTTTCATCATACATTAATTGTTGTCCAGCATTGTTTTTAAGCTGTAAGAAC

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 88.20% 11.70% 0.04% 0.00% NA
All Indica  2759 80.40% 19.50% 0.07% 0.00% NA
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 71.30% 28.60% 0.17% 0.00% NA
Indica II  465 96.30% 3.70% 0.00% 0.00% NA
Indica III  913 78.80% 21.20% 0.00% 0.00% NA
Indica Intermediate  786 79.90% 20.00% 0.13% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 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 86.70% 13.30% 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
vg1221477991 C -> T LOC_Os12g35340.1 upstream_gene_variant ; 2121.0bp to feature; MODIFIER silent_mutation Average:30.252; most accessible tissue: Callus, score: 62.067 N N N N
vg1221477991 C -> T LOC_Os12g35330-LOC_Os12g35340 intergenic_region ; MODIFIER silent_mutation Average:30.252; most accessible tissue: Callus, score: 62.067 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1221477991 NA 6.70E-06 mr1042 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
vg1221477991 5.77E-06 9.30E-11 mr1399 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
vg1221477991 3.42E-06 2.00E-09 mr1399 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