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Detailed information for vg0714685745:

Variant ID: vg0714685745 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 14685745
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: 0.00, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:


ATACCTTTTATGGTGGAGGGGATAGCCTAGGAATACACAGAGAGAGGAGCGTGGGGCTAGCTTGTGCGGAGAGGTTGCGGAAAGGTTAGGGTAGCACTTA[C/T]
AGCCAAACACTCGAAGGTGGGTATAGCTAGGATGGGCACCAAAGAGGGCAAAGAAAGGTGTGTGATGTTGAAGGGTTTTGGTGGGATGCCGGTTTATGAG

Reverse complement sequence

CTCATAAACCGGCATCCCACCAAAACCCTTCAACATCACACACCTTTCTTTGCCCTCTTTGGTGCCCATCCTAGCTATACCCACCTTCGAGTGTTTGGCT[G/A]
TAAGTGCTACCCTAACCTTTCCGCAACCTCTCCGCACAAGCTAGCCCCACGCTCCTCTCTCTGTGTATTCCTAGGCTATCCCCTCCACCATAAAAGGTAT

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 82.90% 16.90% 0.21% 0.00% NA
All Indica  2759 73.00% 26.80% 0.22% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 87.00% 11.90% 1.12% 0.00% NA
Indica I  595 80.50% 19.30% 0.17% 0.00% NA
Indica II  465 87.30% 12.50% 0.22% 0.00% NA
Indica III  913 59.10% 40.70% 0.11% 0.00% NA
Indica Intermediate  786 74.90% 24.70% 0.38% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 87.50% 12.50% 0.00% 0.00% NA
Intermediate  90 84.40% 14.40% 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
vg0714685745 C -> T LOC_Os07g25620.1 intron_variant ; MODIFIER silent_mutation Average:61.792; most accessible tissue: Zhenshan97 young leaf, score: 75.039 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0714685745 NA 5.19E-06 mr1380_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
vg0714685745 NA 2.21E-06 mr1561_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
vg0714685745 NA 1.37E-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
vg0714685745 NA 1.88E-06 mr1908_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
vg0714685745 NA 3.65E-06 mr1996_2 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