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Detailed information for vg1207399356:

Variant ID: vg1207399356 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 7399356
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCGGTCGAGACGGTCCTCGACTTAATATTTTTCTGTCCAAAATAAACTGTTCTAGTTTATTCTATGCGCGGTCGACCGAAAAACTATGATACATTAAAAT[C/T]
GACCTGATCCGGATGGTCCCGGACTTAATACTTTTTTTTTCCAAAATAAACCGATTTGCTTCCCGATCCAAACAGTCCCGGACTTAATATTTCTGCTTCA

Reverse complement sequence

TGAAGCAGAAATATTAAGTCCGGGACTGTTTGGATCGGGAAGCAAATCGGTTTATTTTGGAAAAAAAAAGTATTAAGTCCGGGACCATCCGGATCAGGTC[G/A]
ATTTTAATGTATCATAGTTTTTCGGTCGACCGCGCATAGAATAAACTAGAACAGTTTATTTTGGACAGAAAAATATTAAGTCGAGGACCGTCTCGACCGG

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 90.80% 9.10% 0.13% 0.00% NA
All Indica  2759 84.30% 15.50% 0.22% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 82.40% 17.00% 0.67% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 78.90% 21.10% 0.00% 0.00% NA
Indica Intermediate  786 83.20% 16.50% 0.25% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 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  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg1207399356 C -> T LOC_Os12g13290-LOC_Os12g13295 intergenic_region ; MODIFIER silent_mutation Average:67.428; most accessible tissue: Minghui63 panicle, score: 82.797 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1207399356 2.43E-06 4.23E-07 mr1171 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
vg1207399356 NA 1.45E-06 mr1171 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
vg1207399356 NA 8.15E-06 mr1216 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
vg1207399356 NA 5.79E-06 mr1875_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