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Detailed information for vg0116357536:

Variant ID: vg0116357536 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 16357536
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 331. )

Flanking Sequence (100 bp) in Reference Genome:


TCACGGGCTTCGGCCCGACGCAACAAGCAAGCCATGTGAATCAAGGCACCGTGACCTGGGCTCAAGTCCCACAATTCGACCTAAGCCAGATGACAAGCAC[G/A]
GTTTCGGCAGATATGCAAGGAATGCAGTTTAGAACCGGGCCACAGCCGAACACAATGGCTCAACCGCATGTACAGCCAATGAACTGTCCTTTCGCCACCT

Reverse complement sequence

AGGTGGCGAAAGGACAGTTCATTGGCTGTACATGCGGTTGAGCCATTGTGTTCGGCTGTGGCCCGGTTCTAAACTGCATTCCTTGCATATCTGCCGAAAC[C/T]
GTGCTTGTCATCTGGCTTAGGTCGAATTGTGGGACTTGAGCCCAGGTCACGGTGCCTTGATTCACATGGCTTGCTTGTTGCGTCGGGCCGAAGCCCGTGA

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% 3.20% 0.97% 0.00% NA
All Indica  2759 99.10% 0.90% 0.00% 0.00% NA
All Japonica  1512 90.50% 6.50% 3.04% 0.00% NA
Aus  269 92.90% 7.10% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.30% 0.70% 0.00% 0.00% NA
Indica Intermediate  786 97.80% 2.20% 0.00% 0.00% NA
Temperate Japonica  767 82.80% 12.10% 5.08% 0.00% NA
Tropical Japonica  504 99.60% 0.20% 0.20% 0.00% NA
Japonica Intermediate  241 95.90% 1.70% 2.49% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 90.00% 10.00% 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
vg0116357536 G -> A LOC_Os01g29200.1 upstream_gene_variant ; 4095.0bp to feature; MODIFIER silent_mutation Average:72.79; most accessible tissue: Zhenshan97 young leaf, score: 88.637 N N N N
vg0116357536 G -> A LOC_Os01g29190.1 intron_variant ; MODIFIER silent_mutation Average:72.79; most accessible tissue: Zhenshan97 young leaf, score: 88.637 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0116357536 3.75E-06 NA mr1112 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