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Detailed information for vg0903742271:

Variant ID: vg0903742271 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 3742271
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.03, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:


GTCGGGGATCTCGAGCAGGACCTTGCGGGGTTGGTTCGGCTGCGGTCAAGAAAGCAGAGTTGAGGTTGGCTATTGTCGACTATATATGTCTGACCTAGTT[G/A]
TCCGCCTCCGGGAAGGTTACTGGGTCGAACGGAGTTTACCTCAGTAGAGAGTTGACCACGCACGGTGAAGTGTTTGGCAGGAGTTCGAACCGGCTCGACT

Reverse complement sequence

AGTCGAGCCGGTTCGAACTCCTGCCAAACACTTCACCGTGCGTGGTCAACTCTCTACTGAGGTAAACTCCGTTCGACCCAGTAACCTTCCCGGAGGCGGA[C/T]
AACTAGGTCAGACATATATAGTCGACAATAGCCAACCTCAACTCTGCTTTCTTGACCGCAGCCGAACCAACCCCGCAAGGTCCTGCTCGAGATCCCCGAC

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 54.60% 45.40% 0.02% 0.00% NA
All Indica  2759 89.90% 10.10% 0.00% 0.00% NA
All Japonica  1512 0.80% 99.20% 0.00% 0.00% NA
Aus  269 17.80% 82.20% 0.00% 0.00% NA
Indica I  595 94.60% 5.40% 0.00% 0.00% NA
Indica II  465 85.20% 14.80% 0.00% 0.00% NA
Indica III  913 93.40% 6.60% 0.00% 0.00% NA
Indica Intermediate  786 85.10% 14.90% 0.00% 0.00% NA
Temperate Japonica  767 0.70% 99.30% 0.00% 0.00% NA
Tropical Japonica  504 1.00% 99.00% 0.00% 0.00% NA
Japonica Intermediate  241 0.80% 99.20% 0.00% 0.00% NA
VI/Aromatic  96 3.10% 96.90% 0.00% 0.00% NA
Intermediate  90 40.00% 58.90% 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
vg0903742271 G -> A LOC_Os09g07480.1 upstream_gene_variant ; 3412.0bp to feature; MODIFIER silent_mutation Average:72.329; most accessible tissue: Zhenshan97 young leaf, score: 84.624 N N N N
vg0903742271 G -> A LOC_Os09g07470.1 intron_variant ; MODIFIER silent_mutation Average:72.329; most accessible tissue: Zhenshan97 young leaf, score: 84.624 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0903742271 NA 5.21E-38 mr1208_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
vg0903742271 NA 3.20E-07 mr1446_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
vg0903742271 NA 2.01E-08 mr1660_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