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Detailed information for vg0137882391:

Variant ID: vg0137882391 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 37882391
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.01, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:


GAGAGCTCCGAAAGATGAACAGTGAAGAATCCGATTTTGCCGCCGTGAAGCCAAGTCCAAGAACAAACGCTTTGAAGCGCTCGAACCAGGCCCGGGGAGC[C/T]
TGTTTGAGGCCGTAGAGAGAACGATTCAGGCAACATACGACGTCGGGGTGCTTGGCGTCGACGAAGCCGGTAGGTTGGCGACAGTAGACCGTTTCTGAGA

Reverse complement sequence

TCTCAGAAACGGTCTACTGTCGCCAACCTACCGGCTTCGTCGACGCCAAGCACCCCGACGTCGTATGTTGCCTGAATCGTTCTCTCTACGGCCTCAAACA[G/A]
GCTCCCCGGGCCTGGTTCGAGCGCTTCAAAGCGTTTGTTCTTGGACTTGGCTTCACGGCGGCAAAATCGGATTCTTCACTGTTCATCTTTCGGAGCTCTC

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 58.70% 40.00% 0.32% 0.97% NA
All Indica  2759 34.30% 63.70% 0.51% 1.52% NA
All Japonica  1512 97.90% 2.10% 0.07% 0.00% NA
Aus  269 70.60% 29.00% 0.00% 0.37% NA
Indica I  595 35.80% 63.20% 0.50% 0.50% NA
Indica II  465 17.00% 75.90% 0.86% 6.24% NA
Indica III  913 45.30% 54.10% 0.22% 0.33% NA
Indica Intermediate  786 30.40% 68.10% 0.64% 0.89% NA
Temperate Japonica  767 97.90% 2.00% 0.13% 0.00% NA
Tropical Japonica  504 98.00% 2.00% 0.00% 0.00% NA
Japonica Intermediate  241 97.50% 2.50% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 71.10% 25.60% 0.00% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0137882391 C -> T LOC_Os01g65290.1 synonymous_variant ; p.Gln97Gln; LOW synonymous_codon Average:58.387; most accessible tissue: Minghui63 root, score: 77.29 N N N N
vg0137882391 C -> DEL LOC_Os01g65290.1 N frameshift_variant Average:58.387; most accessible tissue: Minghui63 root, score: 77.29 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0137882391 6.84E-09 2.05E-26 mr1375 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
vg0137882391 2.21E-06 1.29E-08 mr1375 Ind_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
vg0137882391 1.07E-20 NA mr1517 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
vg0137882391 2.23E-18 2.14E-21 mr1517 Ind_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
vg0137882391 9.99E-19 5.29E-74 mr1538 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
vg0137882391 3.98E-13 9.64E-15 mr1538 Ind_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
vg0137882391 1.02E-24 NA mr1517_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
vg0137882391 2.68E-20 4.67E-22 mr1517_2 Ind_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
vg0137882391 1.02E-20 NA mr1538_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
vg0137882391 1.01E-14 1.76E-19 mr1538_2 Ind_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