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Detailed information for vg0105279447:

Variant ID: vg0105279447 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 5279447
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTTTTCTTATTACACGAAAGATGTGAACACATGTGGGAGTTGGTTTCATTCCTTTCCCAATCAACCTCACTCGTTTTCATGCGTACGCATTTTTAAACTG[C/T]
TAAACGGTATGTTAAATTTTATTTACAAAAATTGCTTTTAAAAATTATATTAATATTTTTTTTAAAAAATATAACACTTAATTAGTCATGCACTAAACAT

Reverse complement sequence

ATGTTTAGTGCATGACTAATTAAGTGTTATATTTTTTAAAAAAAATATTAATATAATTTTTAAAAGCAATTTTTGTAAATAAAATTTAACATACCGTTTA[G/A]
CAGTTTAAAAATGCGTACGCATGAAAACGAGTGAGGTTGATTGGGAAAGGAATGAAACCAACTCCCACATGTGTTCACATCTTTCGTGTAATAAGAAAAA

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 76.30% 22.80% 0.87% 0.00% NA
All Indica  2759 99.30% 0.70% 0.04% 0.00% NA
All Japonica  1512 33.50% 64.00% 2.51% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.00% 0.90% 0.11% 0.00% NA
Indica Intermediate  786 98.70% 1.30% 0.00% 0.00% NA
Temperate Japonica  767 56.30% 39.20% 4.43% 0.00% NA
Tropical Japonica  504 5.20% 94.40% 0.40% 0.00% NA
Japonica Intermediate  241 20.30% 78.80% 0.83% 0.00% NA
VI/Aromatic  96 29.20% 70.80% 0.00% 0.00% NA
Intermediate  90 71.10% 26.70% 2.22% 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
vg0105279447 C -> T LOC_Os01g10110.1 upstream_gene_variant ; 3769.0bp to feature; MODIFIER silent_mutation Average:37.783; most accessible tissue: Callus, score: 84.441 N N N N
vg0105279447 C -> T LOC_Os01g10120.1 upstream_gene_variant ; 1735.0bp to feature; MODIFIER silent_mutation Average:37.783; most accessible tissue: Callus, score: 84.441 N N N N
vg0105279447 C -> T LOC_Os01g10110-LOC_Os01g10120 intergenic_region ; MODIFIER silent_mutation Average:37.783; most accessible tissue: Callus, score: 84.441 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0105279447 NA 4.23E-06 mr1187 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
vg0105279447 7.86E-07 NA mr1482 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
vg0105279447 NA 5.58E-10 mr1510 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
vg0105279447 NA 5.32E-10 mr1578 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
vg0105279447 NA 1.02E-08 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
vg0105279447 NA 6.39E-07 mr1785 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
vg0105279447 6.66E-06 NA mr1788 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
vg0105279447 6.02E-06 NA mr1891 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
vg0105279447 NA 5.34E-10 mr1379_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
vg0105279447 NA 2.05E-06 mr1691_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
vg0105279447 NA 1.32E-08 mr1905_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