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Detailed information for vg1114877180:

Variant ID: vg1114877180 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 14877180
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CAATATTACCAAAATAGGAGAGAACTAGTGATGCTTGCAATACATATGTTTGTTAGAATAATAATATTCCACTAGTATTAGGTTTACTAACCTTTTGCAG[A/T]
GAATGATCATAAAGTAGAGGAGAATCGACATCAACTCAGACGATAAATCAATCGGACGATGTCGAGAACCAGACTTGTGTGTGAATAGGCCAAGAACTCA

Reverse complement sequence

TGAGTTCTTGGCCTATTCACACACAAGTCTGGTTCTCGACATCGTCCGATTGATTTATCGTCTGAGTTGATGTCGATTCTCCTCTACTTTATGATCATTC[T/A]
CTGCAAAAGGTTAGTAAACCTAATACTAGTGGAATATTATTATTCTAACAAACATATGTATTGCAAGCATCACTAGTTCTCTCCTATTTTGGTAATATTG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 92.40% 7.30% 0.30% 0.00% NA
All Indica  2759 99.00% 0.90% 0.11% 0.00% NA
All Japonica  1512 78.70% 20.60% 0.73% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.80% 0.70% 0.50% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 97.30% 2.70% 0.00% 0.00% NA
Temperate Japonica  767 65.60% 33.00% 1.43% 0.00% NA
Tropical Japonica  504 99.20% 0.80% 0.00% 0.00% NA
Japonica Intermediate  241 77.60% 22.40% 0.00% 0.00% NA
VI/Aromatic  96 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg1114877180 A -> T LOC_Os11g26010.1 3_prime_UTR_variant ; 1678.0bp to feature; MODIFIER silent_mutation Average:23.866; most accessible tissue: Minghui63 young leaf, score: 48.378 N N N N
vg1114877180 A -> T LOC_Os11g26020.1 upstream_gene_variant ; 3404.0bp to feature; MODIFIER silent_mutation Average:23.866; most accessible tissue: Minghui63 young leaf, score: 48.378 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1114877180 2.15E-06 NA mr1359 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
vg1114877180 NA 2.80E-06 mr1382 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
vg1114877180 NA 6.92E-07 mr1424 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
vg1114877180 NA 4.50E-07 mr1445 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
vg1114877180 NA 2.96E-06 mr1830 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
vg1114877180 2.10E-06 NA mr1904 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