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Detailed information for vg0128471692:

Variant ID: vg0128471692 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 28471692
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTAAAAATTGGCATGTCTAAAATATTGGCTAAAAACCAGTAAGAGCCTATGCGTATAAAATATAATAACTTCAAAATCTACTGTGATAGGGTCTGTTTGG[T/A]
ACAGCTCCAACTCCTAAATTTAGCTTCAGAAGTTGGGTCTACAGTAGAGTTGTGGAGCTGTCTAAACCCAGCTCCACTACTTACTACGAATTTAGGCACG

Reverse complement sequence

CGTGCCTAAATTCGTAGTAAGTAGTGGAGCTGGGTTTAGACAGCTCCACAACTCTACTGTAGACCCAACTTCTGAAGCTAAATTTAGGAGTTGGAGCTGT[A/T]
CCAAACAGACCCTATCACAGTAGATTTTGAAGTTATTATATTTTATACGCATAGGCTCTTACTGGTTTTTAGCCAATATTTTAGACATGCCAATTTTTAA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.30% 1.20% 0.53% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 94.70% 3.60% 1.65% 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 93.20% 3.80% 3.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 88.40% 10.80% 0.83% 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
vg0128471692 T -> A LOC_Os01g49490.1 upstream_gene_variant ; 520.0bp to feature; MODIFIER silent_mutation Average:74.174; most accessible tissue: Callus, score: 83.078 N N N N
vg0128471692 T -> A LOC_Os01g49490-LOC_Os01g49500 intergenic_region ; MODIFIER silent_mutation Average:74.174; most accessible tissue: Callus, score: 83.078 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0128471692 NA 3.37E-06 mr1006 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
vg0128471692 5.53E-06 5.53E-06 mr1015 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
vg0128471692 NA 6.37E-06 mr1298 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
vg0128471692 7.45E-06 7.45E-06 mr1480 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
vg0128471692 1.02E-07 2.10E-07 mr1731 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
vg0128471692 8.38E-07 8.38E-07 mr1935 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
vg0128471692 1.51E-06 1.51E-06 mr1987 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