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Detailed information for vg0235815991:

Variant ID: vg0235815991 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 35815991
Reference Allele: TAlternative Allele: G
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 322. )

Flanking Sequence (100 bp) in Reference Genome:


CAGCGTGGCAATTACAATGCAGCATGATTCCATGCATAACTTTCACAGGTGATATCGACTGAGTGGGTTTTGGCACCAACTTAGGAGTTAGAAAAAACAA[T/G]
AACAGACCAAAAAAAATCTGGATTCTGAAAATAAAGGAATGAAGGCACAAAGCATACTTCAGGATAGATTCAACTGTCCTTTGCAAATAGTCTGGTCGAT

Reverse complement sequence

ATCGACCAGACTATTTGCAAAGGACAGTTGAATCTATCCTGAAGTATGCTTTGTGCCTTCATTCCTTTATTTTCAGAATCCAGATTTTTTTTGGTCTGTT[A/C]
TTGTTTTTTCTAACTCCTAAGTTGGTGCCAAAACCCACTCAGTCGATATCACCTGTGAAAGTTATGCATGGAATCATGCTGCATTGTAATTGCCACGCTG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.50% 1.80% 0.66% 0.00% NA
All Indica  2759 99.90% 0.00% 0.04% 0.00% NA
All Japonica  1512 92.50% 5.60% 1.92% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.70% 0.20% 0.17% 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  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 85.30% 11.00% 3.78% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 0.00% 1.11% 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
vg0235815991 T -> G LOC_Os02g58600.1 upstream_gene_variant ; 3117.0bp to feature; MODIFIER silent_mutation Average:49.323; most accessible tissue: Callus, score: 74.217 N N N N
vg0235815991 T -> G LOC_Os02g58580.1 downstream_gene_variant ; 3545.0bp to feature; MODIFIER silent_mutation Average:49.323; most accessible tissue: Callus, score: 74.217 N N N N
vg0235815991 T -> G LOC_Os02g58580.2 downstream_gene_variant ; 3545.0bp to feature; MODIFIER silent_mutation Average:49.323; most accessible tissue: Callus, score: 74.217 N N N N
vg0235815991 T -> G LOC_Os02g58580.4 downstream_gene_variant ; 3545.0bp to feature; MODIFIER silent_mutation Average:49.323; most accessible tissue: Callus, score: 74.217 N N N N
vg0235815991 T -> G LOC_Os02g58580.5 downstream_gene_variant ; 3545.0bp to feature; MODIFIER silent_mutation Average:49.323; most accessible tissue: Callus, score: 74.217 N N N N
vg0235815991 T -> G LOC_Os02g58590.1 intron_variant ; MODIFIER silent_mutation Average:49.323; most accessible tissue: Callus, score: 74.217 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0235815991 NA 9.98E-08 mr1210 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
vg0235815991 9.63E-06 6.69E-08 mr1305 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
vg0235815991 4.73E-06 4.73E-06 mr1409 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
vg0235815991 NA 1.91E-09 mr1585 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
vg0235815991 NA 1.51E-07 mr1586 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
vg0235815991 NA 8.46E-07 mr1765 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
vg0235815991 2.76E-08 1.98E-10 mr1305_2 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
vg0235815991 3.25E-06 3.75E-09 mr1585_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