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Detailed information for vg0222523726:

Variant ID: vg0222523726 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 22523726
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCTATTAGTACGAATTCGTCTAGCTATCGATCGGCACTGCAATCTAGCACCACCTATCACCATGCTGGCGGATCTTAGTAAAACCCACAAAAATCTCATG[T/C]
AAAGGTTCCACGAAATTGAAGAGTTGACATTAAGTTTGATTGCTGTGGTTTTTTTTTTTGTTGTTGAAAGTTTCTTATACTGAATGGGAAGAGTTTTACT

Reverse complement sequence

AGTAAAACTCTTCCCATTCAGTATAAGAAACTTTCAACAACAAAAAAAAAAACCACAGCAATCAAACTTAATGTCAACTCTTCAATTTCGTGGAACCTTT[A/G]
CATGAGATTTTTGTGGGTTTTACTAAGATCCGCCAGCATGGTGATAGGTGGTGCTAGATTGCAGTGCCGATCGATAGCTAGACGAATTCGTACTAATAGG

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 55.80% 44.00% 0.25% 0.00% NA
All Indica  2759 82.60% 17.00% 0.36% 0.00% NA
All Japonica  1512 4.10% 95.80% 0.07% 0.00% NA
Aus  269 95.20% 4.50% 0.37% 0.00% NA
Indica I  595 67.10% 32.10% 0.84% 0.00% NA
Indica II  465 90.10% 9.50% 0.43% 0.00% NA
Indica III  913 88.80% 11.00% 0.22% 0.00% NA
Indica Intermediate  786 82.70% 17.20% 0.13% 0.00% NA
Temperate Japonica  767 0.80% 99.20% 0.00% 0.00% NA
Tropical Japonica  504 10.10% 89.70% 0.20% 0.00% NA
Japonica Intermediate  241 2.10% 97.90% 0.00% 0.00% NA
VI/Aromatic  96 10.40% 89.60% 0.00% 0.00% NA
Intermediate  90 32.20% 67.80% 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
vg0222523726 T -> C LOC_Os02g37254-LOC_Os02g37260 intergenic_region ; MODIFIER silent_mutation Average:31.922; most accessible tissue: Callus, score: 73.056 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0222523726 NA 1.08E-26 mr1072 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
vg0222523726 NA 2.03E-28 mr1075 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
vg0222523726 NA 2.66E-22 mr1150 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
vg0222523726 NA 4.79E-08 mr1222 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
vg0222523726 4.16E-06 NA mr1225 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
vg0222523726 NA 1.50E-37 mr1072_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
vg0222523726 NA 1.03E-38 mr1075_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
vg0222523726 NA 1.70E-26 mr1149_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
vg0222523726 NA 3.81E-17 mr1592_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
vg0222523726 NA 2.28E-11 mr1595_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
vg0222523726 NA 4.30E-09 mr1600_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