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Detailed information for vg0127557410:

Variant ID: vg0127557410 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 27557410
Reference Allele: TAlternative Allele: G
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTGTTTAGTTATTTTTTGCGTCCTTTCCATCATAAGAAAAATACTTGCTCGGTGTTTCAATACATATTCTCTCTGTTCCAAAAATAAATTTATTTTACAC[T/G]
CATCCCATATGTACCAATATAAAACAAAAAGACATACCCTCACTTTATCAAATCTTAATGCAATTATTCCTCATTTTACCTACATTCCAGTGCATCTATT

Reverse complement sequence

AATAGATGCACTGGAATGTAGGTAAAATGAGGAATAATTGCATTAAGATTTGATAAAGTGAGGGTATGTCTTTTTGTTTTATATTGGTACATATGGGATG[A/C]
GTGTAAAATAAATTTATTTTTGGAACAGAGAGAATATGTATTGAAACACCGAGCAAGTATTTTTCTTATGATGGAAAGGACGCAAAAAATAACTAAACAA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.90% 0.90% 0.28% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 96.40% 2.70% 0.86% 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  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 93.00% 5.30% 1.69% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 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
vg0127557410 T -> G LOC_Os01g48130.2 intron_variant ; MODIFIER silent_mutation Average:68.238; most accessible tissue: Callus, score: 88.049 N N N N
vg0127557410 T -> G LOC_Os01g48130.1 intron_variant ; MODIFIER silent_mutation Average:68.238; most accessible tissue: Callus, score: 88.049 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0127557410 5.03E-07 4.56E-11 mr1062 Jap_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
vg0127557410 NA 9.03E-06 mr1210 Jap_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
vg0127557410 NA 9.87E-06 mr1305 Jap_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
vg0127557410 NA 1.75E-06 mr1358 Jap_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
vg0127557410 5.63E-06 5.63E-06 mr1525 Jap_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
vg0127557410 NA 3.03E-07 mr1585 Jap_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