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Detailed information for vg1115847531:

Variant ID: vg1115847531 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 15847531
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AATCCTCTGAAGTGTATAAGTAAACAAATATTGTTCAACATACTCAACATACACAAAAAAAACAACTATTCCAGAAAAAGGGGCAATTTTTGCTAGAGTA[C/T]
ACCCAAAATATGTGCAATTTGTTGATAGACGTCGAAAAAATATGTCACGGCTGAAGCACGTCCTAAAAAACTGGTAATCTGCTAGAGAACACTTTCGGTT

Reverse complement sequence

AACCGAAAGTGTTCTCTAGCAGATTACCAGTTTTTTAGGACGTGCTTCAGCCGTGACATATTTTTTCGACGTCTATCAACAAATTGCACATATTTTGGGT[G/A]
TACTCTAGCAAAAATTGCCCCTTTTTCTGGAATAGTTGTTTTTTTTGTGTATGTTGAGTATGTTGAACAATATTTGTTTACTTATACACTTCAGAGGATT

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 94.50% 4.70% 0.78% 0.00% NA
All Indica  2759 99.50% 0.40% 0.07% 0.00% NA
All Japonica  1512 84.30% 13.50% 2.25% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.80% 1.00% 0.17% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.40% 0.50% 0.13% 0.00% NA
Temperate Japonica  767 94.40% 2.70% 2.87% 0.00% NA
Tropical Japonica  504 77.40% 22.40% 0.20% 0.00% NA
Japonica Intermediate  241 66.40% 29.00% 4.56% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 93.30% 5.60% 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
vg1115847531 C -> T LOC_Os11g27530.1 downstream_gene_variant ; 3130.0bp to feature; MODIFIER silent_mutation Average:28.907; most accessible tissue: Callus, score: 56.305 N N N N
vg1115847531 C -> T LOC_Os11g27540.1 downstream_gene_variant ; 3584.0bp to feature; MODIFIER silent_mutation Average:28.907; most accessible tissue: Callus, score: 56.305 N N N N
vg1115847531 C -> T LOC_Os11g27540.2 downstream_gene_variant ; 3168.0bp to feature; MODIFIER silent_mutation Average:28.907; most accessible tissue: Callus, score: 56.305 N N N N
vg1115847531 C -> T LOC_Os11g27530-LOC_Os11g27540 intergenic_region ; MODIFIER silent_mutation Average:28.907; most accessible tissue: Callus, score: 56.305 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1115847531 NA 9.11E-06 mr1113 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
vg1115847531 NA 8.48E-07 mr1114 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
vg1115847531 NA 4.27E-07 mr1117 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
vg1115847531 NA 1.12E-07 mr1118 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
vg1115847531 NA 2.35E-06 mr1119 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
vg1115847531 NA 1.66E-07 mr1123 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
vg1115847531 4.89E-06 1.63E-06 mr1150 Jap_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
vg1115847531 3.02E-06 9.16E-09 mr1240 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
vg1115847531 NA 5.31E-06 mr1242 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
vg1115847531 3.36E-06 5.89E-09 mr1496 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
vg1115847531 NA 1.07E-06 mr1961 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
vg1115847531 NA 2.14E-06 mr1063_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
vg1115847531 NA 1.27E-08 mr1183_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