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Detailed information for vg0324949842:

Variant ID: vg0324949842 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 24949842
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:


AATGATGTGACGGAAAAGTTGAAAGTTTGTGTGTGTAGGAAAGTTTTGATGTGATGAAAAGGTTGGAAGTTTAAAGAATTATTTTGGAACTAAACACGGC[G/A]
TAAAAGAAAAGGAGTGAATTAAAAGTAAAATAAAAATGTAATTTATTTCTCATATCTTTGACAATATAATGAGCCTTGTTGGAGCGACTGCAAGGGAATT

Reverse complement sequence

AATTCCCTTGCAGTCGCTCCAACAAGGCTCATTATATTGTCAAAGATATGAGAAATAAATTACATTTTTATTTTACTTTTAATTCACTCCTTTTCTTTTA[C/T]
GCCGTGTTTAGTTCCAAAATAATTCTTTAAACTTCCAACCTTTTCATCACATCAAAACTTTCCTACACACACAAACTTTCAACTTTTCCGTCACATCATT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.30% 2.80% 2.96% 0.00% NA
All Indica  2759 96.90% 1.40% 1.67% 0.00% NA
All Japonica  1512 88.00% 5.90% 6.08% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 95.00% 1.30% 3.70% 0.00% NA
Indica II  465 99.60% 0.00% 0.43% 0.00% NA
Indica III  913 99.70% 0.20% 0.11% 0.00% NA
Indica Intermediate  786 93.50% 3.80% 2.67% 0.00% NA
Temperate Japonica  767 79.90% 11.30% 8.74% 0.00% NA
Tropical Japonica  504 97.60% 0.00% 2.38% 0.00% NA
Japonica Intermediate  241 93.80% 0.80% 5.39% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 1.10% 2.22% 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
vg0324949842 G -> A LOC_Os03g44370.1 upstream_gene_variant ; 1226.0bp to feature; MODIFIER silent_mutation Average:48.078; most accessible tissue: Zhenshan97 panicle, score: 57.341 N N N N
vg0324949842 G -> A LOC_Os03g44370-LOC_Os03g44380 intergenic_region ; MODIFIER silent_mutation Average:48.078; most accessible tissue: Zhenshan97 panicle, score: 57.341 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0324949842 7.61E-08 NA mr1210 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
vg0324949842 7.61E-07 NA mr1305 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
vg0324949842 3.61E-09 NA mr1586 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
vg0324949842 1.07E-06 1.07E-06 mr1703 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
vg0324949842 7.59E-06 NA mr1765 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
vg0324949842 6.82E-07 NA mr1305_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
vg0324949842 7.71E-07 NA mr1585_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