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Detailed information for vg0510460804:

Variant ID: vg0510460804 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 10460804
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:


GTGCCAACCACAAGCCAGCGTGGGCAACGGCTTTATCTTTTGTATAGCATGATTCATTATGGTGTGCCAGACTGTGAAACGGCGAGAAGTCCGTGGAGGT[C/T]
GCTGGGGAGTCCATTGCCTCTGGTTTTGACGGGGAGATTATGATCTAGGAACGGTGCATTGTGGTGAGTTGTGTTGTGCGAGGGGTAATGTCACAGTTCC

Reverse complement sequence

GGAACTGTGACATTACCCCTCGCACAACACAACTCACCACAATGCACCGTTCCTAGATCATAATCTCCCCGTCAAAACCAGAGGCAATGGACTCCCCAGC[G/A]
ACCTCCACGGACTTCTCGCCGTTTCACAGTCTGGCACACCATAATGAATCATGCTATACAAAAGATAAAGCCGTTGCCCACGCTGGCTTGTGGTTGGCAC

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 91.60% 4.20% 3.34% 0.87% NA
All Indica  2759 85.60% 7.20% 5.69% 1.49% NA
All Japonica  1512 99.90% 0.00% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 77.60% 13.10% 9.24% 0.00% NA
Indica II  465 95.10% 4.30% 0.65% 0.00% NA
Indica III  913 83.10% 5.10% 7.23% 4.49% NA
Indica Intermediate  786 88.80% 7.00% 4.20% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 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  90 100.00% 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
vg0510460804 C -> T LOC_Os05g18190-LOC_Os05g18200 intergenic_region ; MODIFIER silent_mutation Average:50.798; most accessible tissue: Minghui63 young leaf, score: 76.82 N N N N
vg0510460804 C -> DEL N N silent_mutation Average:50.798; most accessible tissue: Minghui63 young leaf, score: 76.82 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0510460804 NA 9.06E-08 mr1125 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
vg0510460804 NA 1.95E-07 mr1593 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
vg0510460804 NA 3.63E-06 mr1123_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
vg0510460804 NA 2.01E-06 mr1242_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
vg0510460804 3.98E-06 NA mr1245_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
vg0510460804 4.63E-06 NA mr1371_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
vg0510460804 5.40E-06 NA mr1371_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
vg0510460804 8.93E-07 NA mr1373_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
vg0510460804 6.77E-06 NA mr1373_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
vg0510460804 5.53E-06 NA mr1652_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
vg0510460804 6.57E-06 NA mr1683_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