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Detailed information for vg0821714774:

Variant ID: vg0821714774 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 21714774
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AACCTAGCGACAGCGGCAGTGGCGACTCGTGCTTGCGGTGGTGGCAGCAGGCGACGGTGAGTAGCAGCCGTCAGTAGCGTTCCGACCCGCGGCGAGGAGC[G/A]
GGAGCAGGTGGCAACGGTGACCCGCGCTTGAGGCGGCGGGGGCAGGTGGCATAGCAGCCGACGGTGGCGCCTCGACCCGCTGTGGGGAGCGAGCTACGCG

Reverse complement sequence

CGCGTAGCTCGCTCCCCACAGCGGGTCGAGGCGCCACCGTCGGCTGCTATGCCACCTGCCCCCGCCGCCTCAAGCGCGGGTCACCGTTGCCACCTGCTCC[C/T]
GCTCCTCGCCGCGGGTCGGAACGCTACTGACGGCTGCTACTCACCGTCGCCTGCTGCCACCACCGCAAGCACGAGTCGCCACTGCCGCTGTCGCTAGGTT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 77.00% 22.00% 0.36% 0.68% NA
All Indica  2759 97.80% 0.60% 0.54% 1.12% NA
All Japonica  1512 35.20% 64.80% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.20% 0.20% 0.17% 0.50% NA
Indica II  465 94.00% 0.90% 1.72% 3.44% NA
Indica III  913 99.80% 0.10% 0.00% 0.11% NA
Indica Intermediate  786 96.60% 1.30% 0.76% 1.40% NA
Temperate Japonica  767 2.30% 97.70% 0.00% 0.00% NA
Tropical Japonica  504 86.50% 13.50% 0.00% 0.00% NA
Japonica Intermediate  241 32.40% 67.60% 0.00% 0.00% NA
VI/Aromatic  96 83.30% 16.70% 0.00% 0.00% NA
Intermediate  90 65.60% 31.10% 2.22% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0821714774 G -> A LOC_Os08g34570-LOC_Os08g34580 intergenic_region ; MODIFIER silent_mutation Average:72.945; most accessible tissue: Minghui63 panicle, score: 88.893 N N N N
vg0821714774 G -> DEL N N silent_mutation Average:72.945; most accessible tissue: Minghui63 panicle, score: 88.893 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0821714774 NA 6.60E-08 mr1364 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
vg0821714774 NA 7.83E-06 mr1364 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
vg0821714774 NA 4.10E-07 mr1443 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
vg0821714774 NA 2.10E-06 mr1443 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
vg0821714774 NA 4.65E-11 mr1471 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
vg0821714774 NA 2.43E-06 mr1471 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
vg0821714774 NA 3.29E-06 mr1518 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
vg0821714774 NA 7.63E-37 mr1533 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
vg0821714774 NA 5.77E-07 mr1543 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
vg0821714774 NA 5.20E-18 mr1699 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
vg0821714774 NA 1.49E-06 mr1815 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
vg0821714774 NA 3.67E-06 mr1871 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
vg0821714774 NA 8.80E-33 mr1980 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
vg0821714774 NA 2.51E-38 mr1533_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
vg0821714774 NA 6.53E-21 mr1593_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
vg0821714774 NA 2.52E-16 mr1699_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