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Detailed information for vg0119924762:

Variant ID: vg0119924762 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 19924762
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:


CACGCAAACCTGCAGACGGAGATCAGGGCACATCAAAGAAGAAAGATGATGAAGACGATGCCCCGACTGGTTTTCAAGATCATCGCAAAGAACTTAATCA[C/T]
ATTTTCGGCGGACCCCTGGCTTATGAGTCCAAGAGAAAACAGAAGCTAACAGAACGGGAGATCAATGCGGTTCAGCCTAACATGCCCCAATATCTTCGGT

Reverse complement sequence

ACCGAAGATATTGGGGCATGTTAGGCTGAACCGCATTGATCTCCCGTTCTGTTAGCTTCTGTTTTCTCTTGGACTCATAAGCCAGGGGTCCGCCGAAAAT[G/A]
TGATTAAGTTCTTTGCGATGATCTTGAAAACCAGTCGGGGCATCGTCTTCATCATCTTTCTTCTTTGATGTGCCCTGATCTCCGTCTGCAGGTTTGCGTG

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 73.30% 26.70% 0.04% 0.00% NA
All Indica  2759 55.60% 44.40% 0.04% 0.00% NA
All Japonica  1512 99.20% 0.80% 0.00% 0.00% NA
Aus  269 94.10% 5.60% 0.37% 0.00% NA
Indica I  595 50.90% 48.90% 0.17% 0.00% NA
Indica II  465 92.30% 7.70% 0.00% 0.00% NA
Indica III  913 32.90% 67.10% 0.00% 0.00% NA
Indica Intermediate  786 63.90% 36.10% 0.00% 0.00% NA
Temperate Japonica  767 98.40% 1.60% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 91.10% 8.90% 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
vg0119924762 C -> T LOC_Os01g36000.1 synonymous_variant ; p.His606His; LOW synonymous_codon Average:52.677; most accessible tissue: Minghui63 flag leaf, score: 83.621 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0119924762 NA 2.70E-06 mr1042 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
vg0119924762 NA 8.56E-08 mr1133 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
vg0119924762 2.55E-06 NA mr1519 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
vg0119924762 8.22E-06 1.60E-07 mr1519 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
vg0119924762 NA 2.76E-11 mr1519_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