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Detailed information for vg0817537465:

Variant ID: vg0817537465 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 17537465
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTCATCCAATCCGAATCTGATTTAGGTTTTGGCCAAGGGGGTGTGTGCCCTAGGGCAACCCTTGGACATCCCTAATCATATTTATTCAATAGCCATCATC[G/A]
TTTAGAGTCGGGTTTTGCTTAGATTAATCTATCAAGAATAGTTTCGCCGCTAGTTCGGTTTGTGGAACCCCAAATTCGAGTGCTCAATCATTCATATGAA

Reverse complement sequence

TTCATATGAATGATTGAGCACTCGAATTTGGGGTTCCACAAACCGAACTAGCGGCGAAACTATTCTTGATAGATTAATCTAAGCAAAACCCGACTCTAAA[C/T]
GATGATGGCTATTGAATAAATATGATTAGGGATGTCCAAGGGTTGCCCTAGGGCACACACCCCCTTGGCCAAAACCTAAATCAGATTCGGATTGGATGAG

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 96.60% 3.40% 0.00% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 89.80% 10.20% 0.00% 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 99.80% 0.20% 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 99.00% 1.00% 0.00% 0.00% NA
Tropical Japonica  504 76.00% 24.00% 0.00% 0.00% NA
Japonica Intermediate  241 89.60% 10.40% 0.00% 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
vg0817537465 G -> A LOC_Os08g28700.1 downstream_gene_variant ; 734.0bp to feature; MODIFIER silent_mutation Average:63.517; most accessible tissue: Zhenshan97 root, score: 85.677 N N N N
vg0817537465 G -> A LOC_Os08g28690-LOC_Os08g28700 intergenic_region ; MODIFIER silent_mutation Average:63.517; most accessible tissue: Zhenshan97 root, score: 85.677 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0817537465 NA 1.61E-07 mr1040 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
vg0817537465 NA 4.63E-14 mr1301 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
vg0817537465 5.50E-06 4.82E-16 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
vg0817537465 NA 8.02E-08 mr1951 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
vg0817537465 NA 2.25E-09 mr1980 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
vg0817537465 3.44E-06 5.75E-16 mr1301_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
vg0817537465 4.37E-08 1.57E-17 mr1410_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
vg0817537465 NA 3.11E-11 mr1533_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
vg0817537465 NA 7.12E-09 mr1676_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
vg0817537465 NA 8.89E-06 mr1836_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
vg0817537465 3.44E-06 2.84E-12 mr1993_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