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Detailed information for vg1217240129:

Variant ID: vg1217240129 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 17240129
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.51, G: 0.49, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:


AGTGCATCGCCCACCCGTGGCTGCATGAGTAACCCAAGCAAAGAAGCTTCACAAAGAAGGCGAGCCATCGCTGGTCTTTTGATATGATGCTAATGGACAA[A/G]
TTGATGCTTAATTATGCACTTGATTTTACACGCAACGTGGTTGGGGGGAGGGTTCTGTGTCCCAATGGGAGGTGCCGGGCCCACCCCGGCACTCTAGTAG

Reverse complement sequence

CTACTAGAGTGCCGGGGTGGGCCCGGCACCTCCCATTGGGACACAGAACCCTCCCCCCAACCACGTTGCGTGTAAAATCAAGTGCATAATTAAGCATCAA[T/C]
TTGTCCATTAGCATCATATCAAAAGACCAGCGATGGCTCGCCTTCTTTGTGAAGCTTCTTTGCTTGGGTTACTCATGCAGCCACGGGTGGGCGATGCACT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 25.30% 3.20% 8.76% 62.65% NA
All Indica  2759 3.00% 0.50% 3.88% 92.61% NA
All Japonica  1512 69.90% 0.20% 8.33% 21.56% NA
Aus  269 9.70% 28.60% 53.16% 8.55% NA
Indica I  595 1.80% 0.00% 1.34% 96.81% NA
Indica II  465 3.40% 0.40% 7.53% 88.60% NA
Indica III  913 1.50% 0.50% 2.41% 95.51% NA
Indica Intermediate  786 5.50% 0.80% 5.34% 88.42% NA
Temperate Japonica  767 96.20% 0.00% 0.00% 3.78% NA
Tropical Japonica  504 30.60% 0.00% 22.42% 47.02% NA
Japonica Intermediate  241 68.50% 1.20% 5.39% 24.90% NA
VI/Aromatic  96 2.10% 57.30% 23.96% 16.67% NA
Intermediate  90 32.20% 5.60% 16.67% 45.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1217240129 A -> DEL N N silent_mutation Average:35.457; most accessible tissue: Minghui63 young leaf, score: 77.243 N N N N
vg1217240129 A -> G LOC_Os12g29120.1 upstream_gene_variant ; 2049.0bp to feature; MODIFIER silent_mutation Average:35.457; most accessible tissue: Minghui63 young leaf, score: 77.243 N N N N
vg1217240129 A -> G LOC_Os12g29130.1 downstream_gene_variant ; 4631.0bp to feature; MODIFIER silent_mutation Average:35.457; most accessible tissue: Minghui63 young leaf, score: 77.243 N N N N
vg1217240129 A -> G LOC_Os12g29120-LOC_Os12g29130 intergenic_region ; MODIFIER silent_mutation Average:35.457; most accessible tissue: Minghui63 young leaf, score: 77.243 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1217240129 NA 1.21E-55 Grain_width 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
vg1217240129 NA 2.22E-08 mr1174 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
vg1217240129 NA 8.84E-08 mr1190 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
vg1217240129 6.96E-08 1.31E-90 mr1334 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
vg1217240129 1.71E-08 1.55E-11 mr1334 Ind_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
vg1217240129 NA 5.27E-15 mr1401 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
vg1217240129 NA 7.41E-07 mr1584 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
vg1217240129 NA 4.05E-07 mr1622 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
vg1217240129 NA 5.37E-07 mr1696 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
vg1217240129 NA 1.00E-09 mr1714 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
vg1217240129 NA 5.06E-07 mr1257_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
vg1217240129 8.41E-06 5.31E-96 mr1334_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
vg1217240129 2.99E-06 1.79E-09 mr1334_2 Ind_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