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Detailed information for vg0113519142:

Variant ID: vg0113519142 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 13519142
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 124. )

Flanking Sequence (100 bp) in Reference Genome:


GTTATTACTCCTGAAGAGATATGGACAAAATTAGAAGTAGTACGTAGATATATACTCCCTCCGTTTCAAAATGTTTGACACCGTTGACTTTTTAGCACAT[G/A]
TTTGACCGTTCGTCTTATTCAAAATAATTTGTGAAATATGTAAAACTATATGTGTACATGAAAGTATATTTAACAATGAATCAAATGATATGAAAATAAT

Reverse complement sequence

ATTATTTTCATATCATTTGATTCATTGTTAAATATACTTTCATGTACACATATAGTTTTACATATTTCACAAATTATTTTGAATAAGACGAACGGTCAAA[C/T]
ATGTGCTAAAAAGTCAACGGTGTCAAACATTTTGAAACGGAGGGAGTATATATCTACGTACTACTTCTAATTTTGTCCATATCTCTTCAGGAGTAATAAC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 74.90% 24.80% 0.23% 0.00% NA
All Indica  2759 67.00% 32.70% 0.25% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 9.30% 90.30% 0.37% 0.00% NA
Indica I  595 63.70% 35.60% 0.67% 0.00% NA
Indica II  465 73.10% 26.90% 0.00% 0.00% NA
Indica III  913 66.20% 33.70% 0.11% 0.00% NA
Indica Intermediate  786 66.90% 32.80% 0.25% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 72.20% 24.40% 3.33% 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
vg0113519142 G -> A LOC_Os01g24020.1 downstream_gene_variant ; 4330.0bp to feature; MODIFIER silent_mutation Average:32.975; most accessible tissue: Zhenshan97 root, score: 47.644 N N N N
vg0113519142 G -> A LOC_Os01g24010.1 intron_variant ; MODIFIER silent_mutation Average:32.975; most accessible tissue: Zhenshan97 root, score: 47.644 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0113519142 NA 7.97E-11 mr1553 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
vg0113519142 NA 2.52E-07 mr1654 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
vg0113519142 NA 4.66E-11 mr1193_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
vg0113519142 NA 2.46E-10 mr1378_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
vg0113519142 NA 7.07E-14 mr1654_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
vg0113519142 NA 1.27E-09 mr1654_2 Ind_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