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Detailed information for vg0820510689:

Variant ID: vg0820510689 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 20510689
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATTAGGTCATTATGCATTTAGACTTGTGCTCACACTATCACAACACACACTTGCTATATATATTGGTCTCTGTTTCACTGGGTTCGGCCTGACTAGGGGC[G/A]
GCCAGACCGGCCACACTGGCGGTCTGACCGGCGTGCCCTGGCCGGTCTGACCGGCGCCACAATGGCAGTCTGACCGGCGCATAAGGCCGGTCTAACAGGC

Reverse complement sequence

GCCTGTTAGACCGGCCTTATGCGCCGGTCAGACTGCCATTGTGGCGCCGGTCAGACCGGCCAGGGCACGCCGGTCAGACCGCCAGTGTGGCCGGTCTGGC[C/T]
GCCCCTAGTCAGGCCGAACCCAGTGAAACAGAGACCAATATATATAGCAAGTGTGTGTTGTGATAGTGTGAGCACAAGTCTAAATGCATAATGACCTAAT

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 87.40% 12.60% 0.02% 0.00% NA
All Indica  2759 79.70% 20.30% 0.04% 0.00% NA
All Japonica  1512 98.20% 1.80% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 77.30% 22.50% 0.17% 0.00% NA
Indica II  465 95.10% 4.90% 0.00% 0.00% NA
Indica III  913 71.60% 28.40% 0.00% 0.00% NA
Indica Intermediate  786 81.70% 18.30% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 94.60% 5.40% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 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
vg0820510689 G -> A LOC_Os08g33040.1 upstream_gene_variant ; 1275.0bp to feature; MODIFIER silent_mutation Average:70.078; most accessible tissue: Minghui63 young leaf, score: 86.554 N N N N
vg0820510689 G -> A LOC_Os08g33030-LOC_Os08g33040 intergenic_region ; MODIFIER silent_mutation Average:70.078; most accessible tissue: Minghui63 young leaf, score: 86.554 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0820510689 4.08E-06 4.08E-06 mr1419_2 Ind_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
vg0820510689 NA 6.89E-07 mr1466_2 Ind_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
vg0820510689 NA 8.01E-06 mr1467_2 Ind_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
vg0820510689 3.96E-06 3.96E-06 mr1488_2 Ind_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
vg0820510689 NA 1.66E-06 mr1653_2 Ind_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
vg0820510689 NA 2.91E-07 mr1759_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
vg0820510689 NA 2.61E-07 mr1759_2 Ind_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
vg0820510689 NA 5.89E-06 mr1823_2 Ind_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
vg0820510689 NA 1.29E-06 mr1824_2 Ind_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
vg0820510689 NA 9.87E-06 mr1831_2 Ind_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