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Detailed information for vg0810915454:

Variant ID: vg0810915454 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 10915454
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 345. )

Flanking Sequence (100 bp) in Reference Genome:


GAAAAGATAATCTTCTCTCGAACCAGATTACTCCAAAGCCAAGTGCTTCAATCATCTTTGCCATGGTCTCCCGAGTACTTTTACCAAATATGAAGACTGT[G/C]
GAGGGCTGAAAAATAAAGTCAAGTGCATCGACTAGATGCACCTAATAGGTGTAGCCCCCGACTATGTGGTTTGCTGAACAAACTAAGCATACAGTCAAGG

Reverse complement sequence

CCTTGACTGTATGCTTAGTTTGTTCAGCAAACCACATAGTCGGGGGCTACACCTATTAGGTGCATCTAGTCGATGCACTTGACTTTATTTTTCAGCCCTC[C/G]
ACAGTCTTCATATTTGGTAAAAGTACTCGGGAGACCATGGCAAAGATGATTGAAGCACTTGGCTTTGGAGTAATCTGGTTCGAGAGAAGATTATCTTTTC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.30% 5.50% 0.21% 0.00% NA
All Indica  2759 90.40% 9.30% 0.33% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 98.90% 1.10% 0.00% 0.00% NA
Indica I  595 98.00% 1.80% 0.17% 0.00% NA
Indica II  465 95.10% 4.90% 0.00% 0.00% NA
Indica III  913 81.20% 18.20% 0.66% 0.00% NA
Indica Intermediate  786 92.50% 7.30% 0.25% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 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 98.90% 0.00% 1.11% 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
vg0810915454 G -> C LOC_Os08g17800.1 upstream_gene_variant ; 3206.0bp to feature; MODIFIER silent_mutation Average:53.828; most accessible tissue: Minghui63 young leaf, score: 75.937 N N N N
vg0810915454 G -> C LOC_Os08g17810.1 downstream_gene_variant ; 4593.0bp to feature; MODIFIER silent_mutation Average:53.828; most accessible tissue: Minghui63 young leaf, score: 75.937 N N N N
vg0810915454 G -> C LOC_Os08g17784-LOC_Os08g17800 intergenic_region ; MODIFIER silent_mutation Average:53.828; most accessible tissue: Minghui63 young leaf, score: 75.937 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0810915454 NA 5.39E-06 mr1309 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
vg0810915454 7.98E-07 3.68E-06 mr1318 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
vg0810915454 1.16E-07 1.16E-07 mr1900 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