Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1011204876:

Variant ID: vg1011204876 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 11204876
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGTTGTCCTTTAGCAAAATTTAGTGATTGGAGAAAAACTAGCTCCAACAAAAATGTCCTATGGCCCTATTTGCTTAGACTTATAAGCCAACTTATAAGTC[G/A]
AAAAGTTTAAACCTAAACAAACAAGTAGCTTTTTTTTGTTTTTTTAAAGCCATAAACCACTACTACACTATTAAAAAACCAAAAGTTAGATTTGAGAATA

Reverse complement sequence

TATTCTCAAATCTAACTTTTGGTTTTTTAATAGTGTAGTAGTGGTTTATGGCTTTAAAAAAACAAAAAAAAGCTACTTGTTTGTTTAGGTTTAAACTTTT[C/T]
GACTTATAAGTTGGCTTATAAGTCTAAGCAAATAGGGCCATAGGACATTTTTGTTGGAGCTAGTTTTTCTCCAATCACTAAATTTTGCTAAAGGACAACA

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 95.70% 4.30% 0.02% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 87.40% 12.60% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 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 85.80% 14.20% 0.00% 0.00% NA
Tropical Japonica  504 94.80% 5.20% 0.00% 0.00% NA
Japonica Intermediate  241 77.20% 22.80% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 90.00% 8.90% 1.11% 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
vg1011204876 G -> A LOC_Os10g21810.1 upstream_gene_variant ; 1813.0bp to feature; MODIFIER silent_mutation Average:81.231; most accessible tissue: Minghui63 flower, score: 90.393 N N N N
vg1011204876 G -> A LOC_Os10g21810.2 upstream_gene_variant ; 1244.0bp to feature; MODIFIER silent_mutation Average:81.231; most accessible tissue: Minghui63 flower, score: 90.393 N N N N
vg1011204876 G -> A LOC_Os10g21810-LOC_Os10g21820 intergenic_region ; MODIFIER silent_mutation Average:81.231; most accessible tissue: Minghui63 flower, score: 90.393 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1011204876 1.81E-06 NA mr1137 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
vg1011204876 NA 2.27E-06 mr1149 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
vg1011204876 1.24E-06 NA mr1617 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
vg1011204876 NA 2.95E-06 mr1071_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
vg1011204876 2.46E-06 NA mr1080_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
vg1011204876 NA 1.92E-07 mr1080_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
vg1011204876 8.88E-09 NA mr1137_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
vg1011204876 NA 4.33E-09 mr1137_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
vg1011204876 NA 4.39E-06 mr1149_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
vg1011204876 NA 3.63E-06 mr1203_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
vg1011204876 NA 5.96E-06 mr1441_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
vg1011204876 8.86E-08 NA mr1617_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
vg1011204876 NA 3.44E-08 mr1617_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
vg1011204876 NA 5.06E-08 mr1705_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