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Detailed information for vg0821929781:

Variant ID: vg0821929781 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 21929781
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.00, others allele: 0.00, population size: 213. )

Flanking Sequence (100 bp) in Reference Genome:


TGTGAGCCTGAAATTTGACAACTAAGTCGACATTATGAGGAACCACAAATCTGTTGTCAATTTCTACCTCATTTCTTTTAAAAGTTATTCCATTGTTTGG[C/T]
CGTGCATACTGTGTAAAACCATTTTCTAATATAGTAGTTTCCTCACAGAATTCTTTGGGGTAGAATTTGGTGCATTTTCCTTCAGACATGCATACTGAGG

Reverse complement sequence

CCTCAGTATGCATGTCTGAAGGAAAATGCACCAAATTCTACCCCAAAGAATTCTGTGAGGAAACTACTATATTAGAAAATGGTTTTACACAGTATGCACG[G/A]
CCAAACAATGGAATAACTTTTAAAAGAAATGAGGTAGAAATTGACAACAGATTTGTGGTTCCTCATAATGTCGACTTAGTTGTCAAATTTCAGGCTCACA

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 87.80% 7.90% 1.67% 2.69% NA
All Indica  2759 95.80% 0.20% 1.67% 2.32% NA
All Japonica  1512 70.40% 23.70% 1.92% 4.03% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 95.10% 0.20% 1.68% 3.03% NA
Indica II  465 97.00% 0.20% 1.08% 1.72% NA
Indica III  913 95.60% 0.20% 1.64% 2.52% NA
Indica Intermediate  786 95.90% 0.10% 2.04% 1.91% NA
Temperate Japonica  767 97.90% 0.70% 0.91% 0.52% NA
Tropical Japonica  504 25.80% 61.90% 3.17% 9.13% NA
Japonica Intermediate  241 75.90% 17.00% 2.49% 4.56% NA
VI/Aromatic  96 96.90% 1.00% 2.08% 0.00% NA
Intermediate  90 87.80% 7.80% 2.22% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0821929781 C -> T LOC_Os08g34850.1 synonymous_variant ; p.Arg529Arg; LOW synonymous_codon Average:28.105; most accessible tissue: Zhenshan97 flag leaf, score: 36.135 N N N N
vg0821929781 C -> DEL LOC_Os08g34850.1 N frameshift_variant Average:28.105; most accessible tissue: Zhenshan97 flag leaf, score: 36.135 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0821929781 NA 9.19E-06 mr1277 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
vg0821929781 NA 9.49E-06 mr1543 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
vg0821929781 NA 1.27E-06 mr1543 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
vg0821929781 NA 7.83E-08 mr1039_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
vg0821929781 NA 3.77E-10 mr1304_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
vg0821929781 NA 1.82E-08 mr1401_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
vg0821929781 NA 7.42E-06 mr1408_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
vg0821929781 NA 2.15E-06 mr1422_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
vg0821929781 NA 2.86E-06 mr1510_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
vg0821929781 NA 1.04E-11 mr1533_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
vg0821929781 NA 1.06E-08 mr1551_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
vg0821929781 NA 1.72E-07 mr1606_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
vg0821929781 NA 8.70E-08 mr1632_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
vg0821929781 NA 2.61E-08 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
vg0821929781 NA 1.02E-08 mr1696_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
vg0821929781 NA 8.41E-11 mr1696_2 Jap_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
vg0821929781 NA 2.15E-06 mr1705_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
vg0821929781 NA 2.78E-09 mr1769_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
vg0821929781 NA 9.52E-08 mr1819_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
vg0821929781 NA 5.50E-07 mr1819_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
vg0821929781 NA 9.18E-06 mr1830_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
vg0821929781 NA 6.01E-06 mr1873_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
vg0821929781 NA 1.80E-11 mr1916_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