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Detailed information for vg0814303967:

Variant ID: vg0814303967 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 14303967
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.97, C: 0.03, others allele: 0.00, population size: 159. )

Flanking Sequence (100 bp) in Reference Genome:


TGGCTAGGGAGGATGAGGAAAAAACTGCATTCATTACCCCCATAGGAACTTATTGTTATACGACAATGCCTTTCGGGTTAAAGAACGCAGGTCCTACTTT[T/C]
CAACGTACTACTCGAATTTCTTTGGGTAGCCAGATAGGACGCAATGTTGAGGCCTATGTTGATGACTTGGTTGTAAAGACGCGCAACCAAGAGACCTTAC

Reverse complement sequence

GTAAGGTCTCTTGGTTGCGCGTCTTTACAACCAAGTCATCAACATAGGCCTCAACATTGCGTCCTATCTGGCTACCCAAAGAAATTCGAGTAGTACGTTG[A/G]
AAAGTAGGACCTGCGTTCTTTAACCCGAAAGGCATTGTCGTATAACAATAAGTTCCTATGGGGGTAATGAATGCAGTTTTTTCCTCATCCTCCCTAGCCA

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 58.80% 22.50% 12.89% 5.73% NA
All Indica  2759 92.20% 6.10% 1.59% 0.07% NA
All Japonica  1512 2.50% 56.70% 24.27% 16.47% NA
Aus  269 58.40% 3.00% 38.66% 0.00% NA
Indica I  595 96.60% 2.40% 1.01% 0.00% NA
Indica II  465 91.60% 6.00% 2.15% 0.22% NA
Indica III  913 91.90% 6.70% 1.42% 0.00% NA
Indica Intermediate  786 89.70% 8.30% 1.91% 0.13% NA
Temperate Japonica  767 2.50% 84.60% 3.26% 9.65% NA
Tropical Japonica  504 2.40% 24.00% 58.53% 15.08% NA
Japonica Intermediate  241 2.90% 36.50% 19.50% 41.08% NA
VI/Aromatic  96 6.20% 3.10% 77.08% 13.54% NA
Intermediate  90 38.90% 31.10% 22.22% 7.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0814303967 T -> C LOC_Os08g23630.1 synonymous_variant ; p.Phe874Phe; LOW synonymous_codon Average:10.822; most accessible tissue: Zhenshan97 panicle, score: 24.575 N N N N
vg0814303967 T -> DEL LOC_Os08g23630.1 N frameshift_variant Average:10.822; most accessible tissue: Zhenshan97 panicle, score: 24.575 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0814303967 NA 8.97E-07 mr1134 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
vg0814303967 NA 6.05E-06 mr1135 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
vg0814303967 NA 2.06E-06 mr1708 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
vg0814303967 NA 4.76E-09 mr1134_2 Ind_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
vg0814303967 NA 4.43E-06 mr1194_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
vg0814303967 NA 2.55E-06 mr1504_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
vg0814303967 NA 1.12E-07 mr1521_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
vg0814303967 NA 6.73E-08 mr1672_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
vg0814303967 NA 4.64E-09 mr1746_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
vg0814303967 NA 2.00E-08 mr1794_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