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Detailed information for vg0413177353:

Variant ID: vg0413177353 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 13177353
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 327. )

Flanking Sequence (100 bp) in Reference Genome:


AACCAAAACTGGGTGATCATAATGTCCTATGTCCAAAACAGCACACTCTCCTGACAAGGTAGAGTATTCTGTCTCGCCTGTCCTCTCCTCCTCAAAATTG[A/G]
TTTAGGACATGAGGCTTCGAATGATCATTCGTTTCCTCTACATGTGTGTGCAGAACACAAGAAAATCTCACGACAAAATGAGGACTTTTCATTCATTATA

Reverse complement sequence

TATAATGAATGAAAAGTCCTCATTTTGTCGTGAGATTTTCTTGTGTTCTGCACACACATGTAGAGGAAACGAATGATCATTCGAAGCCTCATGTCCTAAA[T/C]
CAATTTTGAGGAGGAGAGGACAGGCGAGACAGAATACTCTACCTTGTCAGGAGAGTGTGCTGTTTTGGACATAGGACATTATGATCACCCAGTTTTGGTT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.30% 0.50% 0.15% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 97.90% 1.60% 0.46% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 96.00% 3.10% 0.91% 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  90 100.00% 0.00% 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
vg0413177353 A -> G LOC_Os04g23170.1 upstream_gene_variant ; 2690.0bp to feature; MODIFIER silent_mutation Average:58.604; most accessible tissue: Callus, score: 72.256 N N N N
vg0413177353 A -> G LOC_Os04g23180.1 intron_variant ; MODIFIER silent_mutation Average:58.604; most accessible tissue: Callus, score: 72.256 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0413177353 NA 9.27E-07 mr1210 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
vg0413177353 NA 6.06E-09 mr1585 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
vg0413177353 NA 1.10E-08 mr1586 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
vg0413177353 2.26E-06 2.26E-06 mr1674 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
vg0413177353 NA 4.03E-07 mr1305_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
vg0413177353 NA 7.72E-09 mr1585_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
vg0413177353 NA 6.62E-06 mr1765_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