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Detailed information for vg0131232372:

Variant ID: vg0131232372 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 31232372
Reference Allele: TAlternative Allele: G
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCTCTCGTAGCGTGGCTAGGCCCCTTCCCGCTGCTTAGAGTTTGTTTTTAGCCGCCGTAGTTTCTCTAGCTTCAGTTTTTTTATTTTACTTTTTCTCCCT[T/G]
CCCCTAGTATAAGCTGGTCTGGCTAACTGCGTGGTGTAACTAAAACTCTTTTCGTTTAATATATTGACGTGCAATTCTTTTACGCGTTTGCGAAAAAAAA

Reverse complement sequence

TTTTTTTTCGCAAACGCGTAAAAGAATTGCACGTCAATATATTAAACGAAAAGAGTTTTAGTTACACCACGCAGTTAGCCAGACCAGCTTATACTAGGGG[A/C]
AGGGAGAAAAAGTAAAATAAAAAAACTGAAGCTAGAGAAACTACGGCGGCTAAAAACAAACTCTAAGCAGCGGGAAGGGGCCTAGCCACGCTACGAGAGG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.40% 2.00% 0.61% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 91.90% 6.20% 1.92% 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  465 100.00% 0.00% 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 84.50% 11.90% 3.65% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 0.80% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0131232372 T -> G LOC_Os01g54270.1 upstream_gene_variant ; 3806.0bp to feature; MODIFIER silent_mutation Average:55.016; most accessible tissue: Zhenshan97 flower, score: 68.001 N N N N
vg0131232372 T -> G LOC_Os01g54280.1 upstream_gene_variant ; 1929.0bp to feature; MODIFIER silent_mutation Average:55.016; most accessible tissue: Zhenshan97 flower, score: 68.001 N N N N
vg0131232372 T -> G LOC_Os01g54290.1 upstream_gene_variant ; 2143.0bp to feature; MODIFIER silent_mutation Average:55.016; most accessible tissue: Zhenshan97 flower, score: 68.001 N N N N
vg0131232372 T -> G LOC_Os01g54280-LOC_Os01g54290 intergenic_region ; MODIFIER silent_mutation Average:55.016; most accessible tissue: Zhenshan97 flower, score: 68.001 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0131232372 1.41E-06 NA mr1154 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