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Detailed information for vg0720597910:

Variant ID: vg0720597910 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 20597910
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 313. )

Flanking Sequence (100 bp) in Reference Genome:


TAAGGGAAAAATAATTCAAAAGTAATACGCATGCTCTTGAAAAAAATTGTAAATCCTAATTTTATACAATGTAGCTACACTATAACTATCATGTAACTAG[T/A]
ACATAATTGAGGTATAAGTACTATGTAACTACTCTGTATTAATTACGGTGTAAGTGTTAAGTAACTACTATGTAACTAAAGTGTAAGTGCTATGTAAGTA

Reverse complement sequence

TACTTACATAGCACTTACACTTTAGTTACATAGTAGTTACTTAACACTTACACCGTAATTAATACAGAGTAGTTACATAGTACTTATACCTCAATTATGT[A/T]
CTAGTTACATGATAGTTATAGTGTAGCTACATTGTATAAAATTAGGATTTACAATTTTTTTCAAGAGCATGCGTATTACTTTTGAATTATTTTTCCCTTA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.00% 3.40% 0.28% 0.25% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 88.00% 10.40% 0.86% 0.79% 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 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 95.20% 2.20% 1.04% 1.56% NA
Tropical Japonica  504 78.80% 21.20% 0.00% 0.00% NA
Japonica Intermediate  241 84.20% 13.70% 2.07% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 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
vg0720597910 T -> DEL N N silent_mutation Average:35.138; most accessible tissue: Callus, score: 63.772 N N N N
vg0720597910 T -> A LOC_Os07g34380.1 downstream_gene_variant ; 4751.0bp to feature; MODIFIER silent_mutation Average:35.138; most accessible tissue: Callus, score: 63.772 N N N N
vg0720597910 T -> A LOC_Os07g34370.1 intron_variant ; MODIFIER silent_mutation Average:35.138; most accessible tissue: Callus, score: 63.772 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0720597910 NA 2.76E-07 mr1213 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
vg0720597910 NA 6.44E-07 mr1225 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
vg0720597910 NA 1.16E-14 mr1410 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
vg0720597910 NA 2.29E-08 mr1746 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
vg0720597910 NA 2.30E-13 mr1410_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
vg0720597910 7.03E-08 1.20E-13 mr1993_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