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Detailed information for vg0904680838:

Variant ID: vg0904680838 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 4680838
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 309. )

Flanking Sequence (100 bp) in Reference Genome:


ATAGCCTAGGCTATGACTCTTCACCATAATTAAAATAGGCATATAACACGCCAAGAGAATGACCATTGTAAAAACAAGTCATCCCAAATTAACCCAGACA[G/A]
CTTTTGCAGCCTAAAAAAGCTTTCAAAAATAGTATAACACTTTTCTGTCGGGTACCTTTTAATTTGCATTGCGATAATTCCGAAGAATTATATAACCGCA

Reverse complement sequence

TGCGGTTATATAATTCTTCGGAATTATCGCAATGCAAATTAAAAGGTACCCGACAGAAAAGTGTTATACTATTTTTGAAAGCTTTTTTAGGCTGCAAAAG[C/T]
TGTCTGGGTTAATTTGGGATGACTTGTTTTTACAATGGTCATTCTCTTGGCGTGTTATATGCCTATTTTAATTATGGTGAAGAGTCATAGCCTAGGCTAT

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 95.90% 1.20% 2.98% 0.00% NA
All Indica  2759 99.60% 0.40% 0.07% 0.00% NA
All Japonica  1512 88.30% 2.80% 8.86% 0.00% NA
Aus  269 97.80% 0.70% 1.49% 0.00% NA
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.10% 0.70% 0.22% 0.00% NA
Indica Intermediate  786 99.70% 0.30% 0.00% 0.00% NA
Temperate Japonica  767 99.20% 0.00% 0.78% 0.00% NA
Tropical Japonica  504 69.40% 8.30% 22.22% 0.00% NA
Japonica Intermediate  241 92.90% 0.40% 6.64% 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
vg0904680838 G -> A LOC_Os09g08860.1 upstream_gene_variant ; 491.0bp to feature; MODIFIER silent_mutation Average:53.52; most accessible tissue: Minghui63 flag leaf, score: 86.468 N N N N
vg0904680838 G -> A LOC_Os09g08870.1 downstream_gene_variant ; 3740.0bp to feature; MODIFIER silent_mutation Average:53.52; most accessible tissue: Minghui63 flag leaf, score: 86.468 N N N N
vg0904680838 G -> A LOC_Os09g08850-LOC_Os09g08860 intergenic_region ; MODIFIER silent_mutation Average:53.52; most accessible tissue: Minghui63 flag leaf, score: 86.468 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0904680838 NA 6.64E-06 mr1076 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
vg0904680838 4.34E-06 NA mr1742_2 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
vg0904680838 6.65E-07 3.83E-08 mr1871_2 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