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Detailed information for vg0116085125:

Variant ID: vg0116085125 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 16085125
Reference Allele: TAlternative Allele: A
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 73. )

Flanking Sequence (100 bp) in Reference Genome:


TGTGGGTATTTTGTATATACTAAGTTTTGTTAATTAGGGGACATAAACAATACTAAAGTTATATATGAGAATTCAAGCATTAAAAATACACTTCATAACA[T/A]
GAACGTACTTAACAAAAATGTACTTTAGTCTATGGTGCTTAAATATTTATAAATTCTCTAAACATACTAATTATTTCTGCTCTTATTTCAAACTAAATTC

Reverse complement sequence

GAATTTAGTTTGAAATAAGAGCAGAAATAATTAGTATGTTTAGAGAATTTATAAATATTTAAGCACCATAGACTAAAGTACATTTTTGTTAAGTACGTTC[A/T]
TGTTATGAAGTGTATTTTTAATGCTTGAATTCTCATATATAACTTTAGTATTGTTTATGTCCCCTAATTAACAAAACTTAGTATATACAAAATACCCACA

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 24.20% 14.20% 25.86% 35.74% NA
All Indica  2759 5.50% 0.80% 39.51% 54.11% NA
All Japonica  1512 50.70% 41.50% 5.29% 2.51% NA
Aus  269 38.30% 0.70% 11.15% 49.81% NA
Indica I  595 0.70% 0.70% 17.48% 81.18% NA
Indica II  465 14.60% 2.20% 48.82% 34.41% NA
Indica III  913 2.10% 0.10% 52.35% 45.45% NA
Indica Intermediate  786 7.90% 1.00% 35.75% 55.34% NA
Temperate Japonica  767 20.60% 71.40% 7.04% 0.91% NA
Tropical Japonica  504 89.70% 1.80% 3.37% 5.16% NA
Japonica Intermediate  241 64.70% 29.50% 3.73% 2.07% NA
VI/Aromatic  96 92.70% 0.00% 2.08% 5.21% NA
Intermediate  90 36.70% 20.00% 22.22% 21.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0116085125 T -> A LOC_Os01g28730.1 upstream_gene_variant ; 1498.0bp to feature; MODIFIER silent_mutation Average:7.986; most accessible tissue: Minghui63 flag leaf, score: 15.952 N N N N
vg0116085125 T -> A LOC_Os01g28720.1 downstream_gene_variant ; 3317.0bp to feature; MODIFIER silent_mutation Average:7.986; most accessible tissue: Minghui63 flag leaf, score: 15.952 N N N N
vg0116085125 T -> A LOC_Os01g28740.1 downstream_gene_variant ; 4439.0bp to feature; MODIFIER silent_mutation Average:7.986; most accessible tissue: Minghui63 flag leaf, score: 15.952 N N N N
vg0116085125 T -> A LOC_Os01g28720-LOC_Os01g28730 intergenic_region ; MODIFIER silent_mutation Average:7.986; most accessible tissue: Minghui63 flag leaf, score: 15.952 N N N N
vg0116085125 T -> DEL N N silent_mutation Average:7.986; most accessible tissue: Minghui63 flag leaf, score: 15.952 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0116085125 NA 2.90E-11 Plant_height Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0116085125 NA 2.37E-07 mr1013 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
vg0116085125 NA 2.33E-07 mr1031 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
vg0116085125 NA 2.78E-06 mr1056 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
vg0116085125 NA 7.97E-06 mr1063 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
vg0116085125 NA 1.58E-08 mr1163 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
vg0116085125 NA 2.69E-06 mr1183 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
vg0116085125 NA 9.41E-06 mr1205 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
vg0116085125 NA 1.03E-06 mr1330 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
vg0116085125 NA 5.43E-07 mr1548 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
vg0116085125 NA 2.82E-07 mr1627 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
vg0116085125 NA 2.83E-07 mr1668 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
vg0116085125 9.60E-06 1.27E-07 mr1826 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
vg0116085125 NA 7.04E-06 mr1359_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
vg0116085125 NA 4.12E-07 mr1548_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