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Detailed information for vg0823915309:

Variant ID: vg0823915309 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 23915309
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 313. )

Flanking Sequence (100 bp) in Reference Genome:


GAAGTTTCAAGTCTGCACAGTATGGAGGTTCTGATTTTGATATCAGGATTTATGGCTTGAAGTGCATCATTGATCTTCATGCTGCTCCTGGCTCTCAAAA[C/T]
GGAATGGAACACAGTGCAAGTAGGGATGGTTCAGTAGATTGGCCTTCACCAGCTAACATCGAGAAAACACTGGATGTCATTAATTTTCTGGCTCAAAGGT

Reverse complement sequence

ACCTTTGAGCCAGAAAATTAATGACATCCAGTGTTTTCTCGATGTTAGCTGGTGAAGGCCAATCTACTGAACCATCCCTACTTGCACTGTGTTCCATTCC[G/A]
TTTTGAGAGCCAGGAGCAGCATGAAGATCAATGATGCACTTCAAGCCATAAATCCTGATATCAAAATCAGAACCTCCATACTGTGCAGACTTGAAACTTC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.80% 2.90% 0.21% 0.00% NA
All Indica  2759 99.90% 0.00% 0.07% 0.00% NA
All Japonica  1512 90.70% 8.90% 0.46% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.00% 0.17% 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 99.70% 0.10% 0.13% 0.00% NA
Temperate Japonica  767 99.50% 0.10% 0.39% 0.00% NA
Tropical Japonica  504 75.40% 23.80% 0.79% 0.00% NA
Japonica Intermediate  241 94.60% 5.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 94.40% 4.40% 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
vg0823915309 C -> T LOC_Os08g37750.1 synonymous_variant ; p.Asn302Asn; LOW synonymous_codon Average:59.822; most accessible tissue: Callus, score: 88.226 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0823915309 NA 2.47E-06 mr1414 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
vg0823915309 NA 7.78E-07 mr1583 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
vg0823915309 NA 4.39E-07 mr1696 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
vg0823915309 NA 4.94E-06 mr1830 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
vg0823915309 NA 3.40E-10 mr1852 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
vg0823915309 NA 3.76E-06 mr1243_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