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Detailed information for vg0815721034:

Variant ID: vg0815721034 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 15721034
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTCGTCCGGGGCTCGAAGAGAGAGCTTGTGCTCCTACCTGCGACCCGAAGATGGCTAGCCTTGGTTTCTAGATGGCTACCACACCCGAGGGCGTCCTCGG[C/T]
TCCCGGGGCACCTGGCGTGTTCAGAGTATTCCTGGACACCTGGTTTTTCTCCTTGGCGTCTTGAAGATGCATGTCTTGTTTGCCTCGTTGTATTCTACCG

Reverse complement sequence

CGGTAGAATACAACGAGGCAAACAAGACATGCATCTTCAAGACGCCAAGGAGAAAAACCAGGTGTCCAGGAATACTCTGAACACGCCAGGTGCCCCGGGA[G/A]
CCGAGGACGCCCTCGGGTGTGGTAGCCATCTAGAAACCAAGGCTAGCCATCTTCGGGTCGCAGGTAGGAGCACAAGCTCTCTCTTCGAGCCCCGGACGAG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 85.70% 13.30% 0.97% 0.00% NA
All Indica  2759 99.70% 0.20% 0.07% 0.00% NA
All Japonica  1512 56.90% 40.20% 2.84% 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 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.40% 0.40% 0.25% 0.00% NA
Temperate Japonica  767 32.90% 62.20% 4.95% 0.00% NA
Tropical Japonica  504 89.30% 10.50% 0.20% 0.00% NA
Japonica Intermediate  241 66.00% 32.40% 1.66% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 82.20% 16.70% 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
vg0815721034 C -> T LOC_Os08g25820.1 downstream_gene_variant ; 4508.0bp to feature; MODIFIER silent_mutation Average:66.842; most accessible tissue: Zhenshan97 young leaf, score: 83.623 N N N N
vg0815721034 C -> T LOC_Os08g25830.1 downstream_gene_variant ; 2017.0bp to feature; MODIFIER silent_mutation Average:66.842; most accessible tissue: Zhenshan97 young leaf, score: 83.623 N N N N
vg0815721034 C -> T LOC_Os08g25820.2 downstream_gene_variant ; 4508.0bp to feature; MODIFIER silent_mutation Average:66.842; most accessible tissue: Zhenshan97 young leaf, score: 83.623 N N N N
vg0815721034 C -> T LOC_Os08g25830-LOC_Os08g25839 intergenic_region ; MODIFIER silent_mutation Average:66.842; most accessible tissue: Zhenshan97 young leaf, score: 83.623 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0815721034 NA 7.52E-06 mr1029 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
vg0815721034 1.21E-06 NA mr1125 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
vg0815721034 NA 9.55E-08 mr1125 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
vg0815721034 9.38E-07 2.54E-07 mr1343 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
vg0815721034 2.13E-06 2.12E-06 mr1343 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
vg0815721034 NA 9.63E-06 mr1548 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
vg0815721034 1.14E-06 2.85E-06 mr1621 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
vg0815721034 1.73E-07 1.73E-07 mr1621 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
vg0815721034 NA 6.13E-09 mr1746 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
vg0815721034 7.42E-06 NA mr1806 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
vg0815721034 2.81E-06 2.81E-06 mr1806 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
vg0815721034 NA 7.52E-09 mr1471_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
vg0815721034 NA 1.06E-07 mr1526_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