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Detailed information for vg1223881012:

Variant ID: vg1223881012 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 23881012
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, C: 0.00, others allele: 0.00, population size: 331. )

Flanking Sequence (100 bp) in Reference Genome:


TTAGCTGCATTTATTTGTTTTCTTACAACTGTATTATGTGCAGACAACTGTTGGTTTGCTATTATGAGCTTTAATGGATGATGATTCTTGATGGTCAAAA[A/C]
AATCGATTTGTGTGCAGGCTGTCCTGAAGGAGTGGAATGCTCGTCGGTGATTAGTAGGTCACCAGAATATCTTCTCTCCTAGCCTCCTGGGCTTGTTTAC

Reverse complement sequence

GTAAACAAGCCCAGGAGGCTAGGAGAGAAGATATTCTGGTGACCTACTAATCACCGACGAGCATTCCACTCCTTCAGGACAGCCTGCACACAAATCGATT[T/G]
TTTTGACCATCAAGAATCATCATCCATTAAAGCTCATAATAGCAAACCAACAGTTGTCTGCACATAATACAGTTGTAAGAAAACAAATAAATGCAGCTAA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.70% 1.30% 0.00% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 96.00% 4.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 93.40% 6.60% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 96.30% 3.70% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 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
vg1223881012 A -> C LOC_Os12g38860.1 downstream_gene_variant ; 4335.0bp to feature; MODIFIER silent_mutation Average:70.842; most accessible tissue: Callus, score: 89.564 N N N N
vg1223881012 A -> C LOC_Os12g38850.1 intron_variant ; MODIFIER silent_mutation Average:70.842; most accessible tissue: Callus, score: 89.564 N N N N
vg1223881012 A -> C LOC_Os12g38850.2 intron_variant ; MODIFIER silent_mutation Average:70.842; most accessible tissue: Callus, score: 89.564 N N N N
vg1223881012 A -> C LOC_Os12g38850.3 intron_variant ; MODIFIER silent_mutation Average:70.842; most accessible tissue: Callus, score: 89.564 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1223881012 NA 3.79E-06 mr1045 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
vg1223881012 6.43E-06 1.03E-06 mr1222 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
vg1223881012 1.63E-06 1.63E-06 mr1881 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