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Detailed information for vg0128646920:

Variant ID: vg0128646920 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 28646920
Reference Allele: TAlternative Allele: A
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:


CAGGAACCGTTTGGAGCTTTTGTTATGTGCTGTTAATTTGAACCTCCTTTATCACTTTTGTTATGTGCAGTTCGACTTTGCAGCTGTTAATTTGATGTTA[T/A]
GGAAGTATTATTTGGGTTGTTTGTGTTGCATCGATGAACTTATTCACATATTTTGGCTACTTTCAATCATATATGTCTGAATTCAACCTGGCATCTGTTT

Reverse complement sequence

AAACAGATGCCAGGTTGAATTCAGACATATATGATTGAAAGTAGCCAAAATATGTGAATAAGTTCATCGATGCAACACAAACAACCCAAATAATACTTCC[A/T]
TAACATCAAATTAACAGCTGCAAAGTCGAACTGCACATAACAAAAGTGATAAAGGAGGTTCAAATTAACAGCACATAACAAAAGCTCCAAACGGTTCCTG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 41.30% 39.20% 2.33% 17.16% NA
All Indica  2759 67.30% 7.00% 3.23% 22.51% NA
All Japonica  1512 1.40% 87.70% 0.79% 10.12% NA
Aus  269 16.70% 82.50% 0.74% 0.00% NA
Indica I  595 80.70% 5.50% 2.35% 11.43% NA
Indica II  465 45.60% 5.60% 4.30% 44.52% NA
Indica III  913 70.30% 4.70% 2.63% 22.34% NA
Indica Intermediate  786 66.40% 11.60% 3.94% 18.07% NA
Temperate Japonica  767 0.30% 99.30% 0.13% 0.26% NA
Tropical Japonica  504 3.40% 67.10% 1.79% 27.78% NA
Japonica Intermediate  241 0.80% 93.80% 0.83% 4.56% NA
VI/Aromatic  96 5.20% 60.40% 3.12% 31.25% NA
Intermediate  90 30.00% 57.80% 4.44% 7.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0128646920 T -> A LOC_Os01g49880.1 upstream_gene_variant ; 3861.0bp to feature; MODIFIER silent_mutation Average:19.725; most accessible tissue: Callus, score: 43.031 N N N N
vg0128646920 T -> A LOC_Os01g49870.1 intron_variant ; MODIFIER silent_mutation Average:19.725; most accessible tissue: Callus, score: 43.031 N N N N
vg0128646920 T -> DEL N N silent_mutation Average:19.725; most accessible tissue: Callus, score: 43.031 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0128646920 NA 4.55E-13 mr1013 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
vg0128646920 NA 1.69E-10 mr1316 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
vg0128646920 NA 1.46E-06 mr1321 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
vg0128646920 NA 7.42E-42 mr1458 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
vg0128646920 NA 2.53E-07 mr1717 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
vg0128646920 NA 3.12E-08 mr1770 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
vg0128646920 NA 1.86E-10 mr1819 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
vg0128646920 NA 1.59E-09 mr1827 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
vg0128646920 NA 3.70E-13 mr1914 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
vg0128646920 NA 4.13E-09 mr1946 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
vg0128646920 NA 3.40E-08 mr1989 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
vg0128646920 NA 6.73E-47 mr1458_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