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Detailed information for vg1111258215:

Variant ID: vg1111258215 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 11258215
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 300. )

Flanking Sequence (100 bp) in Reference Genome:


CACTTAAATAAGTAAATCAGTACATGCTCTTTTTTTTAAGCACTAAAAGGAGTAATCAGCATGGCAAATTCACAACTAACATAATCAATTGACAAACAAA[T/C]
CATTCTTCAAGATCAGGATGCACATCAGTCTTGCCATCTGCAGGAAGAGGGAAAGCAGAAGAGCCAGGCATGGCTTGTGACTGTGGAGAAGCAAGCCAAG

Reverse complement sequence

CTTGGCTTGCTTCTCCACAGTCACAAGCCATGCCTGGCTCTTCTGCTTTCCCTCTTCCTGCAGATGGCAAGACTGATGTGCATCCTGATCTTGAAGAATG[A/G]
TTTGTTTGTCAATTGATTATGTTAGTTGTGAATTTGCCATGCTGATTACTCCTTTTAGTGCTTAAAAAAAAGAGCATGTACTGATTTACTTATTTAAGTG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 55.90% 33.50% 0.44% 10.07% NA
All Indica  2759 81.40% 1.40% 0.72% 16.46% NA
All Japonica  1512 4.50% 94.60% 0.07% 0.79% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 74.10% 2.20% 0.84% 22.86% NA
Indica II  465 99.10% 0.20% 0.22% 0.43% NA
Indica III  913 74.20% 0.50% 0.77% 24.53% NA
Indica Intermediate  786 84.90% 2.50% 0.89% 11.70% NA
Temperate Japonica  767 3.30% 96.00% 0.00% 0.78% NA
Tropical Japonica  504 7.90% 91.10% 0.20% 0.79% NA
Japonica Intermediate  241 1.20% 97.90% 0.00% 0.83% NA
VI/Aromatic  96 14.60% 85.40% 0.00% 0.00% NA
Intermediate  90 53.30% 35.60% 0.00% 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
vg1111258215 T -> DEL LOC_Os11g19530.1 N frameshift_variant Average:70.724; most accessible tissue: Zhenshan97 panicle, score: 86.432 N N N N
vg1111258215 T -> C LOC_Os11g19530.1 stop_lost&splice_region_variant ; p.Ter79Trpext*?; HIGH stop_lost Average:70.724; most accessible tissue: Zhenshan97 panicle, score: 86.432 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1111258215 NA 5.10E-10 mr1128 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
vg1111258215 NA 1.57E-09 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
vg1111258215 NA 7.99E-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
vg1111258215 NA 3.63E-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
vg1111258215 NA 7.87E-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
vg1111258215 NA 2.32E-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
vg1111258215 NA 3.08E-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
vg1111258215 NA 7.87E-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
vg1111258215 NA 4.01E-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
vg1111258215 NA 2.02E-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
vg1111258215 NA 1.20E-07 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
vg1111258215 NA 5.66E-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
vg1111258215 NA 1.85E-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
vg1111258215 NA 6.49E-32 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
vg1111258215 NA 2.54E-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
vg1111258215 NA 3.45E-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
vg1111258215 NA 6.18E-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
vg1111258215 NA 2.66E-08 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
vg1111258215 NA 3.28E-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
vg1111258215 NA 2.28E-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
vg1111258215 NA 3.20E-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
vg1111258215 NA 2.14E-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
vg1111258215 NA 1.63E-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
vg1111258215 NA 1.23E-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