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Detailed information for vg1111258252:

Variant ID: vg1111258252 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 11258252
Reference Allele: TAlternative Allele: G
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 309. )

Flanking Sequence (100 bp) in Reference Genome:


AAGCACTAAAAGGAGTAATCAGCATGGCAAATTCACAACTAACATAATCAATTGACAAACAAATCATTCTTCAAGATCAGGATGCACATCAGTCTTGCCA[T/G]
CTGCAGGAAGAGGGAAAGCAGAAGAGCCAGGCATGGCTTGTGACTGTGGAGAAGCAAGCCAAGCAGTCGGTGGCAGTGAGAACCAGAGACCTCCATATGG

Reverse complement sequence

CCATATGGAGGTCTCTGGTTCTCACTGCCACCGACTGCTTGGCTTGCTTCTCCACAGTCACAAGCCATGCCTGGCTCTTCTGCTTTCCCTCTTCCTGCAG[A/C]
TGGCAAGACTGATGTGCATCCTGATCTTGAAGAATGATTTGTTTGTCAATTGATTATGTTAGTTGTGAATTTGCCATGCTGATTACTCCTTTTAGTGCTT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 56.00% 33.60% 0.38% 10.03% NA
All Indica  2759 81.50% 1.50% 0.62% 16.35% NA
All Japonica  1512 4.40% 94.70% 0.00% 0.86% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 74.30% 2.00% 0.67% 23.03% NA
Indica II  465 99.10% 0.40% 0.00% 0.43% NA
Indica III  913 74.30% 0.70% 1.10% 23.99% NA
Indica Intermediate  786 85.00% 2.80% 0.38% 11.83% NA
Temperate Japonica  767 3.00% 96.20% 0.00% 0.78% NA
Tropical Japonica  504 8.10% 91.10% 0.00% 0.79% NA
Japonica Intermediate  241 1.20% 97.50% 0.00% 1.24% NA
VI/Aromatic  96 14.60% 85.40% 0.00% 0.00% NA
Intermediate  90 52.20% 35.60% 1.11% 11.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1111258252 T -> DEL LOC_Os11g19530.1 N frameshift_variant Average:73.736; most accessible tissue: Zhenshan97 panicle, score: 88.35 N N N N
vg1111258252 T -> G LOC_Os11g19530.1 missense_variant ; p.Asp67Ala; MODERATE nonsynonymous_codon ; D67A Average:73.736; most accessible tissue: Zhenshan97 panicle, score: 88.35 unknown unknown TOLERATED 1.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1111258252 NA 9.32E-10 mr1302 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
vg1111258252 NA 5.69E-07 mr1315 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
vg1111258252 NA 1.88E-09 mr1336 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
vg1111258252 NA 4.75E-14 mr1376 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
vg1111258252 NA 3.91E-24 mr1383 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
vg1111258252 NA 5.60E-12 mr1386 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
vg1111258252 NA 1.77E-07 mr1392 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
vg1111258252 NA 4.75E-14 mr1431 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
vg1111258252 NA 2.41E-08 mr1488 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
vg1111258252 NA 2.37E-12 mr1521 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
vg1111258252 NA 8.51E-08 mr1604 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
vg1111258252 NA 5.28E-13 mr1636 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
vg1111258252 NA 2.22E-13 mr1641 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
vg1111258252 NA 1.52E-31 mr1647 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
vg1111258252 NA 1.99E-11 mr1683 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
vg1111258252 NA 3.04E-13 mr1701 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
vg1111258252 NA 6.75E-28 mr1723 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
vg1111258252 NA 4.26E-18 mr1767 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
vg1111258252 NA 5.54E-09 mr1776 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
vg1111258252 NA 1.69E-07 mr1779 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
vg1111258252 NA 1.50E-07 mr1810 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
vg1111258252 NA 4.33E-20 mr1838 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
vg1111258252 NA 1.89E-24 mr1839 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
vg1111258252 NA 1.15E-06 mr1886 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
vg1111258252 NA 1.02E-14 mr1909 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