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Detailed information for vg0421433477:

Variant ID: vg0421433477 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 21433477
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.85, T: 0.15, others allele: 0.00, population size: 101. )

Flanking Sequence (100 bp) in Reference Genome:


ACCACGGCGGCAGCGCCTCTGGTGCCACAAAAAGAACTATTCCTGGAATAAGTTTTTCCAAGGGTCTCTTTGTAAAATAAGTTTTAGAAAAGGACCAAAT[C/T]
GTAAAAAATCTAGAAGGGTGGTTGGGGGTAAAATTAGTTGAAAATTAAATGAGGTGGTTGGTAAGAGAAGTATAGTACTCTATACATTGTTATATTCAAG

Reverse complement sequence

CTTGAATATAACAATGTATAGAGTACTATACTTCTCTTACCAACCACCTCATTTAATTTTCAACTAATTTTACCCCCAACCACCCTTCTAGATTTTTTAC[G/A]
ATTTGGTCCTTTTCTAAAACTTATTTTACAAAGAGACCCTTGGAAAAACTTATTCCAGGAATAGTTCTTTTTGTGGCACCAGAGGCGCTGCCGCCGTGGT

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 85.60% 14.40% 0.02% 0.00% NA
All Indica  2759 76.70% 23.20% 0.04% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 89.20% 10.80% 0.00% 0.00% NA
Indica I  595 76.30% 23.70% 0.00% 0.00% NA
Indica II  465 90.50% 9.50% 0.00% 0.00% NA
Indica III  913 69.20% 30.80% 0.00% 0.00% NA
Indica Intermediate  786 77.60% 22.30% 0.13% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 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 93.30% 6.70% 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
vg0421433477 C -> T LOC_Os04g35260.1 intron_variant ; MODIFIER silent_mutation Average:63.326; most accessible tissue: Callus, score: 87.556 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0421433477 4.80E-06 4.80E-06 mr1468 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
vg0421433477 NA 2.24E-06 mr1380_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
vg0421433477 NA 1.89E-07 mr1561_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
vg0421433477 NA 1.86E-06 mr1561_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
vg0421433477 NA 2.38E-07 mr1875_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
vg0421433477 NA 5.67E-06 mr1875_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
vg0421433477 NA 8.49E-08 mr1908_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
vg0421433477 NA 7.79E-07 mr1908_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