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Detailed information for vg0433086358:

Variant ID: vg0433086358 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 33086358
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 359. )

Flanking Sequence (100 bp) in Reference Genome:


GGCACTTGAGCTGTGTCGTTTTGATCACGTTGGTAGTAAGAACTAAGAACAGTGCAATGTATATGTAACATGCGGTATGTATTAGCGTGATTTGCAATGT[T/C]
TCCGCAACCATTACACTGTTGCTTGAGCTTATGAATCTATCTCTGCTTTGGTTTACCGTGCAAGTGAACAGAAAACTCTAATTCTAGTTATGATAGATCT

Reverse complement sequence

AGATCTATCATAACTAGAATTAGAGTTTTCTGTTCACTTGCACGGTAAACCAAAGCAGAGATAGATTCATAAGCTCAAGCAACAGTGTAATGGTTGCGGA[A/G]
ACATTGCAAATCACGCTAATACATACCGCATGTTACATATACATTGCACTGTTCTTAGTTCTTACTACCAACGTGATCAAAACGACACAGCTCAAGTGCC

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 97.20% 2.60% 0.25% 0.00% NA
All Indica  2759 95.80% 3.80% 0.40% 0.00% NA
All Japonica  1512 98.80% 1.10% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 88.90% 9.70% 1.34% 0.00% NA
Indica II  465 99.80% 0.00% 0.22% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 94.10% 5.60% 0.25% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 96.80% 3.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0433086358 T -> C LOC_Os04g55570.1 3_prime_UTR_variant ; 199.0bp to feature; MODIFIER silent_mutation Average:68.834; most accessible tissue: Minghui63 panicle, score: 86.442 N N N N
vg0433086358 T -> C LOC_Os04g55580.1 upstream_gene_variant ; 2243.0bp to feature; MODIFIER silent_mutation Average:68.834; most accessible tissue: Minghui63 panicle, score: 86.442 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0433086358 NA 2.46E-07 mr1042 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
vg0433086358 NA 2.72E-07 mr1043 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
vg0433086358 NA 1.25E-07 mr1608 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
vg0433086358 NA 8.91E-06 mr1975 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