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Detailed information for vg0519166799:

Variant ID: vg0519166799 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 19166799
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.92, A: 0.08, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:


CTTGTCCAAGAACACATCCAATTAGAGTATGCAATTGACCAAGCATACCACCAACAATTAGACCTCGTATAATACTGAGAAATGCAGATGGGAAGAAGTC[G/A]
TCCTCAAGTGATTGGTAAAAACAGCAAAGAGCCACCAAGAACTTCTCTTCTCTACAGAGACAATCAATCACAAGACTGTAGGTGATGTCATTGGGAGCAA

Reverse complement sequence

TTGCTCCCAATGACATCACCTACAGTCTTGTGATTGATTGTCTCTGTAGAGAAGAGAAGTTCTTGGTGGCTCTTTGCTGTTTTTACCAATCACTTGAGGA[C/T]
GACTTCTTCCCATCTGCATTTCTCAGTATTATACGAGGTCTAATTGTTGGTGGTATGCTTGGTCAATTGCATACTCTAATTGGATGTGTTCTTGGACAAG

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 63.90% 35.40% 0.02% 0.68% NA
All Indica  2759 54.30% 44.70% 0.00% 1.01% NA
All Japonica  1512 87.60% 12.30% 0.00% 0.07% NA
Aus  269 14.90% 84.80% 0.37% 0.00% NA
Indica I  595 27.90% 71.30% 0.00% 0.84% NA
Indica II  465 58.50% 40.20% 0.00% 1.29% NA
Indica III  913 61.10% 38.00% 0.00% 0.88% NA
Indica Intermediate  786 63.90% 35.00% 0.00% 1.15% NA
Temperate Japonica  767 98.70% 1.30% 0.00% 0.00% NA
Tropical Japonica  504 71.20% 28.60% 0.00% 0.20% NA
Japonica Intermediate  241 86.70% 13.30% 0.00% 0.00% NA
VI/Aromatic  96 92.70% 7.30% 0.00% 0.00% NA
Intermediate  90 75.60% 21.10% 0.00% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0519166799 G -> DEL LOC_Os05g32730.1 N frameshift_variant Average:52.865; most accessible tissue: Callus, score: 81.399 N N N N
vg0519166799 G -> A LOC_Os05g32730.1 synonymous_variant ; p.Asp479Asp; LOW synonymous_codon Average:52.865; most accessible tissue: Callus, score: 81.399 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0519166799 NA 2.81E-06 mr1044 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
vg0519166799 NA 6.22E-06 mr1044 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
vg0519166799 NA 8.48E-06 mr1199 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
vg0519166799 NA 2.63E-14 mr1301 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
vg0519166799 NA 2.80E-11 mr1410 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
vg0519166799 NA 5.52E-06 mr1482 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
vg0519166799 NA 2.35E-06 mr1518 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
vg0519166799 NA 2.51E-09 mr1676 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
vg0519166799 NA 1.40E-13 mr1769 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
vg0519166799 NA 4.41E-07 mr1830 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
vg0519166799 NA 2.04E-08 mr1951 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
vg0519166799 NA 8.56E-07 mr1131_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
vg0519166799 NA 1.85E-07 mr1199_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
vg0519166799 NA 3.35E-06 mr1325_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
vg0519166799 NA 5.09E-06 mr1333_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
vg0519166799 NA 1.84E-11 mr1410_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
vg0519166799 NA 3.71E-09 mr1482_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
vg0519166799 NA 1.53E-06 mr1482_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
vg0519166799 NA 6.20E-07 mr1498_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
vg0519166799 NA 4.84E-09 mr1676_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
vg0519166799 NA 2.35E-06 mr1763_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
vg0519166799 NA 6.87E-15 mr1769_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
vg0519166799 NA 4.37E-07 mr1830_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
vg0519166799 NA 5.99E-08 mr1846_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