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Detailed information for vg0141112730:

Variant ID: vg0141112730 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 41112730
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.97, G: 0.03, others allele: 0.00, population size: 111. )

Flanking Sequence (100 bp) in Reference Genome:


GATCACTGGATGTAAGGAATAATGTTGTTAGAGACAAAATGATTAGAAAAGATGCAAAAGAAGAATAATGATCGTTGGGTCCCCTGATTTTGATAAACAC[A/G]
ATAGATGAGATAATAGCATGTGCATGTGCTACCTTCGGTTTTTTTTTTTTGAGCTGCTACCTTCGTATTTAGATTATTAGATATATATAACACTGTTGAT

Reverse complement sequence

ATCAACAGTGTTATATATATCTAATAATCTAAATACGAAGGTAGCAGCTCAAAAAAAAAAAACCGAAGGTAGCACATGCACATGCTATTATCTCATCTAT[T/C]
GTGTTTATCAAAATCAGGGGACCCAACGATCATTATTCTTCTTTTGCATCTTTTCTAATCATTTTGTCTCTAACAACATTATTCCTTACATCCAGTGATC

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 59.00% 40.90% 0.06% 0.00% NA
All Indica  2759 91.30% 8.70% 0.07% 0.00% NA
All Japonica  1512 3.50% 96.40% 0.07% 0.00% NA
Aus  269 66.90% 33.10% 0.00% 0.00% NA
Indica I  595 93.90% 6.10% 0.00% 0.00% NA
Indica II  465 97.80% 2.20% 0.00% 0.00% NA
Indica III  913 89.70% 10.30% 0.00% 0.00% NA
Indica Intermediate  786 87.20% 12.60% 0.25% 0.00% NA
Temperate Japonica  767 1.00% 98.80% 0.13% 0.00% NA
Tropical Japonica  504 5.80% 94.20% 0.00% 0.00% NA
Japonica Intermediate  241 6.60% 93.40% 0.00% 0.00% NA
VI/Aromatic  96 4.20% 95.80% 0.00% 0.00% NA
Intermediate  90 38.90% 61.10% 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
vg0141112730 A -> G LOC_Os01g71050.1 downstream_gene_variant ; 4255.0bp to feature; MODIFIER silent_mutation Average:45.141; most accessible tissue: Callus, score: 86.704 N N N N
vg0141112730 A -> G LOC_Os01g71040.1 intron_variant ; MODIFIER silent_mutation Average:45.141; most accessible tissue: Callus, score: 86.704 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0141112730 7.41E-06 NA mr1101 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
vg0141112730 1.16E-06 NA mr1098_2 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
vg0141112730 NA 2.44E-15 mr1148_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
vg0141112730 NA 4.26E-10 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