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Detailed information for vg0815133905:

Variant ID: vg0815133905 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 15133905
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.89, A: 0.11, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:


GTTGTGTGGGCTGTGTCACATGGGGTGCATCATCAGTTTGTGAAGTCCGAAGCTCATTGGGTACCGATGACAACCCTCCACTGAAGCTGGACATGTCGCC[G/A]
TACGATGCAGTGTAAGGTCTAAACCCTGACATTAGTTCAGGGCGAAATGACCCTACATAAGCAATGTAGATATCAATGAAATTATCAAAGCTGGAGCAAA

Reverse complement sequence

TTTGCTCCAGCTTTGATAATTTCATTGATATCTACATTGCTTATGTAGGGTCATTTCGCCCTGAACTAATGTCAGGGTTTAGACCTTACACTGCATCGTA[C/T]
GGCGACATGTCCAGCTTCAGTGGAGGGTTGTCATCGGTACCCAATGAGCTTCGGACTTCACAAACTGATGATGCACCCCATGTGACACAGCCCACACAAC

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 69.10% 30.70% 0.21% 0.00% NA
All Indica  2759 90.00% 9.60% 0.36% 0.00% NA
All Japonica  1512 31.70% 68.30% 0.00% 0.00% NA
Aus  269 55.80% 44.20% 0.00% 0.00% NA
Indica I  595 99.50% 0.50% 0.00% 0.00% NA
Indica II  465 92.30% 7.30% 0.43% 0.00% NA
Indica III  913 82.70% 16.60% 0.66% 0.00% NA
Indica Intermediate  786 90.10% 9.70% 0.25% 0.00% NA
Temperate Japonica  767 14.20% 85.80% 0.00% 0.00% NA
Tropical Japonica  504 61.10% 38.90% 0.00% 0.00% NA
Japonica Intermediate  241 26.10% 73.90% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 65.60% 34.40% 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
vg0815133905 G -> A LOC_Os08g24960.1 synonymous_variant ; p.Tyr57Tyr; LOW synonymous_codon Average:36.79; most accessible tissue: Minghui63 root, score: 52.955 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0815133905 NA 7.85E-07 mr1040 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
vg0815133905 NA 1.28E-11 mr1746 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
vg0815133905 NA 1.29E-07 mr1825 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
vg0815133905 NA 1.97E-08 mr1864 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
vg0815133905 7.37E-06 3.03E-15 mr1938 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