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Detailed information for vg1124320687:

Variant ID: vg1124320687 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 24320687
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:


CCACACACTAGCTTTGCAATTAGAGAAGCCATGATGAGGTGTTTAATTGAGTGGGGCTTGAGTAGCAAACTGTTCACCTTAGACAATGCTATTAACAACA[C/T]
ACTGTTTGTCAAGAATTAGTGAAAAATCTCAAGGATGAGTTGGTATTGGAAGGTACTTCCTCCGTCCCACAATACTTGTCTACTAGCATTCAAAAATTGT

Reverse complement sequence

ACAATTTTTGAATGCTAGTAGACAAGTATTGTGGGACGGAGGAAGTACCTTCCAATACCAACTCATCCTTGAGATTTTTCACTAATTCTTGACAAACAGT[G/A]
TGTTGTTAATAGCATTGTCTAAGGTGAACAGTTTGCTACTCAAGCCCCACTCAATTAAACACCTCATCATGGCTTCTCTAATTGCAAAGCTAGTGTGTGG

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 90.70% 7.70% 0.11% 1.54% NA
All Indica  2759 99.00% 0.40% 0.00% 0.58% NA
All Japonica  1512 77.40% 22.50% 0.07% 0.00% NA
Aus  269 77.00% 0.40% 1.49% 21.19% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 97.80% 1.90% 0.00% 0.22% NA
Indica III  913 99.20% 0.00% 0.00% 0.77% NA
Indica Intermediate  786 98.70% 0.30% 0.00% 1.02% NA
Temperate Japonica  767 92.70% 7.20% 0.13% 0.00% NA
Tropical Japonica  504 52.80% 47.20% 0.00% 0.00% NA
Japonica Intermediate  241 80.50% 19.50% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 87.80% 12.20% 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
vg1124320687 C -> T LOC_Os11g40700.1 downstream_gene_variant ; 3195.0bp to feature; MODIFIER silent_mutation Average:37.416; most accessible tissue: Callus, score: 69.183 N N N N
vg1124320687 C -> T LOC_Os11g40690-LOC_Os11g40700 intergenic_region ; MODIFIER silent_mutation Average:37.416; most accessible tissue: Callus, score: 69.183 N N N N
vg1124320687 C -> DEL N N silent_mutation Average:37.416; most accessible tissue: Callus, score: 69.183 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1124320687 2.67E-06 NA mr1238 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
vg1124320687 NA 4.37E-07 mr1248 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
vg1124320687 NA 4.95E-07 mr1554 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
vg1124320687 8.29E-06 7.25E-13 mr1900 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
vg1124320687 NA 7.00E-06 mr1900 Jap_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
vg1124320687 2.41E-10 NA mr1238_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
vg1124320687 1.16E-06 NA mr1238_2 Jap_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
vg1124320687 NA 5.20E-09 mr1354_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
vg1124320687 2.23E-10 NA mr1484_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
vg1124320687 NA 2.34E-07 mr1554_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
vg1124320687 3.06E-07 NA mr1609_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
vg1124320687 1.51E-06 1.51E-06 mr1609_2 Jap_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
vg1124320687 3.16E-08 NA mr1841_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
vg1124320687 1.62E-09 NA mr1900_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
vg1124320687 1.40E-06 NA mr1900_2 Jap_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
vg1124320687 2.24E-09 NA mr1945_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