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Detailed information for vg0501165891:

Variant ID: vg0501165891 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 1165891
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TATTCATTAAAAATACACGCATGATTCGTACGTACACACATAAATAAGTACTACCTCCGTTTTTTAATAAATGACGCCGTTGACTTTTTATCACATGTTT[G/A]
ATCATTCGTCTTATTCAAAAAATTTACGTAATTATATTTTTTTATTGTGAGTTATTTTATCACTCAAAGTACTTTAAGCATAATTTATATCTATACATTT

Reverse complement sequence

AAATGTATAGATATAAATTATGCTTAAAGTACTTTGAGTGATAAAATAACTCACAATAAAAAAATATAATTACGTAAATTTTTTGAATAAGACGAATGAT[C/T]
AAACATGTGATAAAAAGTCAACGGCGTCATTTATTAAAAAACGGAGGTAGTACTTATTTATGTGTGTACGTACGAATCATGCGTGTATTTTTAATGAATA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 63.20% 36.80% 0.04% 0.00% NA
All Indica  2759 97.30% 2.60% 0.07% 0.00% NA
All Japonica  1512 2.50% 97.50% 0.00% 0.00% NA
Aus  269 75.50% 24.50% 0.00% 0.00% NA
Indica I  595 99.30% 0.70% 0.00% 0.00% NA
Indica II  465 94.60% 5.20% 0.22% 0.00% NA
Indica III  913 98.60% 1.40% 0.00% 0.00% NA
Indica Intermediate  786 95.90% 3.90% 0.13% 0.00% NA
Temperate Japonica  767 3.00% 97.00% 0.00% 0.00% NA
Tropical Japonica  504 1.20% 98.80% 0.00% 0.00% NA
Japonica Intermediate  241 3.70% 96.30% 0.00% 0.00% NA
VI/Aromatic  96 28.10% 71.90% 0.00% 0.00% NA
Intermediate  90 37.80% 62.20% 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
vg0501165891 G -> A LOC_Os05g03040-LOC_Os05g03050 intergenic_region ; MODIFIER silent_mutation Average:41.364; most accessible tissue: Zhenshan97 root, score: 86.14 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0501165891 NA 8.09E-08 mr1666 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
vg0501165891 NA 3.36E-28 mr1793 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
vg0501165891 NA 2.70E-25 mr1588_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
vg0501165891 NA 9.28E-16 mr1666_2 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
vg0501165891 NA 6.92E-17 mr1712_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
vg0501165891 NA 9.06E-13 mr1717_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
vg0501165891 NA 1.78E-47 mr1721_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
vg0501165891 NA 5.55E-12 mr1761_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
vg0501165891 NA 1.48E-12 mr1770_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