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Detailed information for vg0208158153:

Variant ID: vg0208158153 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 8158153
Reference Allele: CAlternative Allele: G
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, G: 0.01, others allele: 0.00, population size: 124. )

Flanking Sequence (100 bp) in Reference Genome:


CGGAAAAAATAGGTACGATAAATTGCATATAAAATAATGCGTACCTATCTAGATATTGCCAGATATATCTACGAAATTAGTAGATTAACTTGAAAATTAA[C/G]
CTACTAAATACCTTTGGTTTGTCCGGATGGCATATGCACATATAACTAAAGTCACCATGCATATATGCCGTATGGATGTGTGTTGTCTGATCTTTGAATC

Reverse complement sequence

GATTCAAAGATCAGACAACACACATCCATACGGCATATATGCATGGTGACTTTAGTTATATGTGCATATGCCATCCGGACAAACCAAAGGTATTTAGTAG[G/C]
TTAATTTTCAAGTTAATCTACTAATTTCGTAGATATATCTGGCAATATCTAGATAGGTACGCATTATTTTATATGCAATTTATCGTACCTATTTTTTCCG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 78.20% 21.80% 0.04% 0.00% NA
All Indica  2759 63.50% 36.40% 0.07% 0.00% NA
All Japonica  1512 99.50% 0.50% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 46.60% 53.10% 0.34% 0.00% NA
Indica II  465 78.70% 21.30% 0.00% 0.00% NA
Indica III  913 67.10% 32.90% 0.00% 0.00% NA
Indica Intermediate  786 63.20% 36.80% 0.00% 0.00% NA
Temperate Japonica  767 99.10% 0.90% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 81.10% 18.90% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0208158153 C -> G LOC_Os02g14750.1 intron_variant ; MODIFIER silent_mutation Average:43.795; most accessible tissue: Zhenshan97 root, score: 85.175 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0208158153 1.91E-06 1.57E-06 mr1171 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
vg0208158153 2.15E-06 2.53E-07 mr1171 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
vg0208158153 NA 1.76E-06 mr1629 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
vg0208158153 NA 1.85E-06 mr1671 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