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Detailed information for vg0102327347:

Variant ID: vg0102327347 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 2327347
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

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:


GCGTGAATTTGGGTTTTGGCATATCGGCGGGGCTAAGGGTTCCAGGCCATTAAGCAGCCAAAATAAGAGATTTGCTCCGATCCAATAAAAAGTATTTCAA[G/T]
GTACCAGTACCTCATGATACGGCCTTAAAATACTTTTTGCTGGACTGGAGCAAATCTCACAAAATAAATCACATTACTCCTGTAAATTTTCTCTTCTTTT

Reverse complement sequence

AAAAGAAGAGAAAATTTACAGGAGTAATGTGATTTATTTTGTGAGATTTGCTCCAGTCCAGCAAAAAGTATTTTAAGGCCGTATCATGAGGTACTGGTAC[C/A]
TTGAAATACTTTTTATTGGATCGGAGCAAATCTCTTATTTTGGCTGCTTAATGGCCTGGAACCCTTAGCCCCGCCGATATGCCAAAACCCAAATTCACGC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.20% 5.70% 0.02% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 82.30% 17.70% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 71.40% 28.60% 0.00% 0.00% NA
Tropical Japonica  504 99.00% 1.00% 0.00% 0.00% NA
Japonica Intermediate  241 81.70% 17.80% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0102327347 G -> T LOC_Os01g04970.1 upstream_gene_variant ; 1277.0bp to feature; MODIFIER silent_mutation Average:30.313; most accessible tissue: Minghui63 panicle, score: 50.413 N N N N
vg0102327347 G -> T LOC_Os01g04960-LOC_Os01g04970 intergenic_region ; MODIFIER silent_mutation Average:30.313; most accessible tissue: Minghui63 panicle, score: 50.413 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0102327347 NA 1.89E-10 Heading_date Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0102327347 NA 4.77E-06 mr1354_2 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
vg0102327347 NA 8.94E-06 mr1902_2 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
vg0102327347 3.75E-07 3.75E-07 mr1958_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