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Detailed information for vg0134264091:

Variant ID: vg0134264091 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 34264091
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GAAGTCGTTTAGGACAATGTTTAAGTCAAACCTTAGGATTATAAATCGTGAATAATTCTCAAATTATTGAGTTTGAAAATGTAAAAATTATATGAATAGA[T/A]
TTGTCTTGAAAAATACTTTCATAAAAGTATACATATATACCACTTTTCAATAAATATTTTTATAGAAACACGAAGTCAAAGTTGTGTTTTGGAGACCGTG

Reverse complement sequence

CACGGTCTCCAAAACACAACTTTGACTTCGTGTTTCTATAAAAATATTTATTGAAAAGTGGTATATATGTATACTTTTATGAAAGTATTTTTCAAGACAA[A/T]
TCTATTCATATAATTTTTACATTTTCAAACTCAATAATTTGAGAATTATTCACGATTTATAATCCTAAGGTTTGACTTAAACATTGTCCTAAACGACTTC

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 86.30% 13.60% 0.02% 0.00% NA
All Indica  2759 99.70% 0.30% 0.00% 0.00% NA
All Japonica  1512 65.10% 34.80% 0.07% 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 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.70% 0.30% 0.00% 0.00% NA
Indica Intermediate  786 99.50% 0.50% 0.00% 0.00% NA
Temperate Japonica  767 92.70% 7.30% 0.00% 0.00% NA
Tropical Japonica  504 35.30% 64.70% 0.00% 0.00% NA
Japonica Intermediate  241 39.80% 59.80% 0.41% 0.00% NA
VI/Aromatic  96 11.50% 88.50% 0.00% 0.00% NA
Intermediate  90 71.10% 28.90% 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
vg0134264091 T -> A LOC_Os01g59280.1 upstream_gene_variant ; 4593.0bp to feature; MODIFIER silent_mutation Average:45.905; most accessible tissue: Zhenshan97 root, score: 71.174 N N N N
vg0134264091 T -> A LOC_Os01g59265.1 downstream_gene_variant ; 4301.0bp to feature; MODIFIER silent_mutation Average:45.905; most accessible tissue: Zhenshan97 root, score: 71.174 N N N N
vg0134264091 T -> A LOC_Os01g59265-LOC_Os01g59280 intergenic_region ; MODIFIER silent_mutation Average:45.905; most accessible tissue: Zhenshan97 root, score: 71.174 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0134264091 NA 7.32E-06 mr1503 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
vg0134264091 7.84E-06 NA mr1679 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
vg0134264091 2.51E-06 NA mr1720 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
vg0134264091 1.35E-06 NA mr1758 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
vg0134264091 NA 7.21E-08 mr1084_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
vg0134264091 NA 3.50E-07 mr1180_2 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