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Detailed information for vg0713719162:

Variant ID: vg0713719162 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 13719162
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.57, T: 0.43, others allele: 0.00, population size: 61. )

Flanking Sequence (100 bp) in Reference Genome:


AGGAGTTGCATGCTTGGAGCTGTTTGCAACAAATAAGTCTGGCCTTGTTTGGTTGGGGAAAAATTTTGGGTTTGGTTGTCACATCGGATATACGGACACA[C/T]
ATTTGAAGTATTAAATGTAGTCTAATAACTATAAAAATTACAGATTCCGCTAGGAAAATGAAAGATGAATTTATTAGGCCTAATTAAGAGTAGTGATATA

Reverse complement sequence

TATATCACTACTCTTAATTAGGCCTAATAAATTCATCTTTCATTTTCCTAGCGGAATCTGTAATTTTTATAGTTATTAGACTACATTTAATACTTCAAAT[G/A]
TGTGTCCGTATATCCGATGTGACAACCAAACCCAAAATTTTTCCCCAACCAAACAAGGCCAGACTTATTTGTTGCAAACAGCTCCAAGCATGCAACTCCT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 29.90% 26.40% 1.27% 42.45% NA
All Indica  2759 40.80% 1.50% 1.78% 55.93% NA
All Japonica  1512 2.40% 68.70% 0.46% 28.44% NA
Aus  269 77.70% 21.60% 0.00% 0.74% NA
Indica I  595 59.80% 0.80% 1.34% 37.98% NA
Indica II  465 16.80% 2.80% 3.01% 77.42% NA
Indica III  913 41.40% 0.70% 1.64% 56.30% NA
Indica Intermediate  786 39.90% 2.20% 1.53% 56.36% NA
Temperate Japonica  767 1.00% 61.50% 0.52% 36.90% NA
Tropical Japonica  504 4.00% 92.10% 0.00% 3.97% NA
Japonica Intermediate  241 3.70% 42.30% 1.24% 52.70% NA
VI/Aromatic  96 24.00% 74.00% 1.04% 1.04% NA
Intermediate  90 21.10% 42.20% 3.33% 33.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0713719162 C -> DEL N N silent_mutation Average:13.073; most accessible tissue: Callus, score: 45.928 N N N N
vg0713719162 C -> T LOC_Os07g24150-LOC_Os07g24160 intergenic_region ; MODIFIER silent_mutation Average:13.073; most accessible tissue: Callus, score: 45.928 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0713719162 NA 1.60E-07 mr1559 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
vg0713719162 NA 9.76E-15 mr1592 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
vg0713719162 NA 3.02E-26 mr1888 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
vg0713719162 NA 4.36E-06 mr1095_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
vg0713719162 NA 2.07E-20 mr1146_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
vg0713719162 NA 9.84E-13 mr1217_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
vg0713719162 NA 1.21E-10 mr1222_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
vg0713719162 NA 1.01E-06 mr1418_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
vg0713719162 NA 2.28E-09 mr1506_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
vg0713719162 NA 1.90E-07 mr1683_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
vg0713719162 NA 7.02E-07 mr1824_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
vg0713719162 NA 4.71E-13 mr1838_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
vg0713719162 NA 1.77E-19 mr1922_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
vg0713719162 NA 6.96E-12 mr1986_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