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Detailed information for vg0205541527:

Variant ID: vg0205541527 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 5541527
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.72, C: 0.28, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:


AGGCACATTCTAGTACAACGAATTTGTACAGAGGTATATATGTCTAGATTCGTTATAGTAGGATATGTCTTATCCAGTCCTAAGTTGTTATATTTTGGAA[C/T]
GAAGAGGGTATATATAGTTGCAGCCTATTTCATCTTGTGCTCAAACCAAACATGTCTACGATGCCGAGATAATCAACAAGGGGTGCTGCTACAGTAGAGA

Reverse complement sequence

TCTCTACTGTAGCAGCACCCCTTGTTGATTATCTCGGCATCGTAGACATGTTTGGTTTGAGCACAAGATGAAATAGGCTGCAACTATATATACCCTCTTC[G/A]
TTCCAAAATATAACAACTTAGGACTGGATAAGACATATCCTACTATAACGAATCTAGACATATATACCTCTGTACAAATTCGTTGTACTAGAATGTGCCT

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 51.00% 48.80% 0.19% 0.02% NA
All Indica  2759 19.70% 80.00% 0.25% 0.04% NA
All Japonica  1512 98.90% 1.10% 0.07% 0.00% NA
Aus  269 81.00% 19.00% 0.00% 0.00% NA
Indica I  595 8.20% 91.30% 0.50% 0.00% NA
Indica II  465 33.80% 66.00% 0.22% 0.00% NA
Indica III  913 18.20% 81.70% 0.11% 0.00% NA
Indica Intermediate  786 21.80% 77.90% 0.25% 0.13% NA
Temperate Japonica  767 98.70% 1.30% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 97.90% 1.70% 0.41% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 67.80% 31.10% 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
vg0205541527 C -> T LOC_Os02g10520.1 upstream_gene_variant ; 4586.0bp to feature; MODIFIER silent_mutation Average:69.443; most accessible tissue: Callus, score: 97.601 N N N N
vg0205541527 C -> T LOC_Os02g10520-LOC_Os02g10530 intergenic_region ; MODIFIER silent_mutation Average:69.443; most accessible tissue: Callus, score: 97.601 N N N N
vg0205541527 C -> DEL N N silent_mutation Average:69.443; most accessible tissue: Callus, score: 97.601 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0205541527 NA 6.67E-18 mr1032 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
vg0205541527 NA 2.96E-08 mr1032 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
vg0205541527 NA 4.90E-18 mr1165 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
vg0205541527 NA 1.02E-07 mr1165 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
vg0205541527 NA 1.16E-09 mr1170 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
vg0205541527 NA 1.33E-18 mr1478 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
vg0205541527 NA 1.37E-08 mr1478 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
vg0205541527 NA 5.25E-06 mr1553 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
vg0205541527 NA 4.76E-13 mr1744 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
vg0205541527 NA 1.53E-06 mr1798 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
vg0205541527 NA 1.98E-06 mr1879 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
vg0205541527 NA 8.45E-21 mr1165_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
vg0205541527 NA 1.41E-06 mr1165_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
vg0205541527 NA 3.08E-06 mr1170_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
vg0205541527 NA 8.22E-07 mr1321_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
vg0205541527 NA 1.16E-09 mr1478_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
vg0205541527 NA 6.06E-07 mr1619_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
vg0205541527 NA 2.31E-11 mr1781_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