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Detailed information for vg0324949511:

Variant ID: vg0324949511 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 24949511
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.57, C: 0.42, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:


GGTTGTTTTAGTTCCTAGGACAAAATTGTATGGTTAGTGTAGTGTATGTATTAATTCACAACGGTCAAAGTATGTCTCATTCAGTCCTAGTTTATTATAT[C/T]
TTGGGGCAAAGAGAGTATCTTAGAGATTGTATAACCTCTAAGATAACCACATAGCTATATTTTGAGATAGAGAGAGTTTCTGTTTAGAGATTGTACAACC

Reverse complement sequence

GGTTGTACAATCTCTAAACAGAAACTCTCTCTATCTCAAAATATAGCTATGTGGTTATCTTAGAGGTTATACAATCTCTAAGATACTCTCTTTGCCCCAA[G/A]
ATATAATAAACTAGGACTGAATGAGACATACTTTGACCGTTGTGAATTAATACATACACTACACTAACCATACAATTTTGTCCTAGGAACTAAAACAACC

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 53.00% 46.90% 0.17% 0.00% NA
All Indica  2759 80.20% 19.50% 0.29% 0.00% NA
All Japonica  1512 0.90% 99.10% 0.00% 0.00% NA
Aus  269 83.60% 16.40% 0.00% 0.00% NA
Indica I  595 71.80% 27.70% 0.50% 0.00% NA
Indica II  465 96.60% 3.40% 0.00% 0.00% NA
Indica III  913 84.10% 15.70% 0.22% 0.00% NA
Indica Intermediate  786 72.50% 27.10% 0.38% 0.00% NA
Temperate Japonica  767 0.70% 99.30% 0.00% 0.00% NA
Tropical Japonica  504 0.80% 99.20% 0.00% 0.00% NA
Japonica Intermediate  241 1.70% 98.30% 0.00% 0.00% NA
VI/Aromatic  96 9.40% 90.60% 0.00% 0.00% NA
Intermediate  90 46.70% 53.30% 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
vg0324949511 C -> T LOC_Os03g44370.1 upstream_gene_variant ; 895.0bp to feature; MODIFIER silent_mutation Average:47.783; most accessible tissue: Callus, score: 74.366 N N N N
vg0324949511 C -> T LOC_Os03g44370-LOC_Os03g44380 intergenic_region ; MODIFIER silent_mutation Average:47.783; most accessible tissue: Callus, score: 74.366 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0324949511 NA 8.81E-09 mr1637 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
vg0324949511 1.18E-07 NA mr1671 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
vg0324949511 NA 1.91E-09 mr1671 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
vg0324949511 NA 1.20E-33 mr1733 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
vg0324949511 NA 1.40E-06 mr1733 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
vg0324949511 NA 6.87E-06 mr1821 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
vg0324949511 NA 9.53E-08 mr1915 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
vg0324949511 1.58E-06 NA mr1031_2 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
vg0324949511 NA 2.95E-07 mr1212_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
vg0324949511 NA 5.11E-11 mr1216_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
vg0324949511 1.62E-06 NA mr1671_2 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
vg0324949511 NA 2.12E-06 mr1671_2 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