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Detailed information for vg1225855844:

Variant ID: vg1225855844 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 25855844
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.83, A: 0.18, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:


ATTAATTAGTCCTAATGTTTTTATGTTAAGTAATTATTTATTGTTCCGAGCTACTTCAACTGCATACATTCTAGCGGACCCATCGTTTCGCTTATTCACG[A/G]
AATAAGACAAACGTCATATTTACAAACGAAAAGTAATTTGTGAGTAAAACTTTTACATAGCGATCTAAAAGCAAAGGCTAAAAACTAAACTTCAATGAAA

Reverse complement sequence

TTTCATTGAAGTTTAGTTTTTAGCCTTTGCTTTTAGATCGCTATGTAAAAGTTTTACTCACAAATTACTTTTCGTTTGTAAATATGACGTTTGTCTTATT[T/C]
CGTGAATAAGCGAAACGATGGGTCCGCTAGAATGTATGCAGTTGAAGTAGCTCGGAACAATAAATAATTACTTAACATAAAAACATTAGGACTAATTAAT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 51.10% 33.40% 8.59% 6.88% NA
All Indica  2759 72.20% 3.80% 13.37% 10.62% NA
All Japonica  1512 7.00% 92.80% 0.20% 0.00% NA
Aus  269 81.00% 0.40% 9.29% 9.29% NA
Indica I  595 55.00% 8.40% 26.39% 10.25% NA
Indica II  465 78.50% 2.80% 10.97% 7.74% NA
Indica III  913 81.30% 0.70% 4.27% 13.80% NA
Indica Intermediate  786 71.10% 4.50% 15.52% 8.91% NA
Temperate Japonica  767 1.20% 98.80% 0.00% 0.00% NA
Tropical Japonica  504 9.90% 89.90% 0.20% 0.00% NA
Japonica Intermediate  241 19.50% 79.70% 0.83% 0.00% NA
VI/Aromatic  96 69.80% 21.90% 4.17% 4.17% NA
Intermediate  90 36.70% 54.40% 5.56% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1225855844 A -> DEL N N silent_mutation Average:49.162; most accessible tissue: Minghui63 root, score: 84.323 N N N N
vg1225855844 A -> G LOC_Os12g41730.1 downstream_gene_variant ; 3587.0bp to feature; MODIFIER silent_mutation Average:49.162; most accessible tissue: Minghui63 root, score: 84.323 N N N N
vg1225855844 A -> G LOC_Os12g41730-LOC_Os12g41740 intergenic_region ; MODIFIER silent_mutation Average:49.162; most accessible tissue: Minghui63 root, score: 84.323 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1225855844 NA 1.08E-20 mr1102 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
vg1225855844 NA 7.60E-15 mr1146 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
vg1225855844 NA 4.40E-10 mr1198 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
vg1225855844 NA 1.83E-08 mr1302 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
vg1225855844 NA 6.14E-08 mr1506 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
vg1225855844 NA 1.66E-17 mr1529 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
vg1225855844 NA 5.77E-13 mr1579 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
vg1225855844 NA 3.61E-15 mr1653 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
vg1225855844 NA 6.60E-28 mr1723 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
vg1225855844 NA 1.54E-10 mr1730 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
vg1225855844 NA 1.19E-09 mr1866 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
vg1225855844 NA 2.10E-14 mr1924 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
vg1225855844 NA 1.22E-06 mr1979 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
vg1225855844 NA 1.04E-08 mr1986 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
vg1225855844 NA 9.21E-17 mr1146_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