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Detailed information for vg1212601474:

Variant ID: vg1212601474 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 12601474
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 313. )

Flanking Sequence (100 bp) in Reference Genome:


TCTGAAACTTGTGTACGCCCCGTAATGGCATGACCCGAAGATACACAAAATCGTACACTGCGAATTCCAGATTACGGCGTCGGTTTGAAGCAATGTTGCA[G/A]
CAAGCACGGGATCAGTTCTTGAACTCATTCATGCAGACCCGCAAGGGGACACTTGTTCAGAAGTACAAAATAAAAGTGGTTGCTAATGATCCTGGGACCA

Reverse complement sequence

TGGTCCCAGGATCATTAGCAACCACTTTTATTTTGTACTTCTGAACAAGTGTCCCCTTGCGGGTCTGCATGAATGAGTTCAAGAACTGATCCCGTGCTTG[C/T]
TGCAACATTGCTTCAAACCGACGCCGTAATCTGGAATTCGCAGTGTACGATTTTGTGTATCTTCGGGTCATGCCATTACGGGGCGTACACAAGTTTCAGA

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 93.40% 5.40% 1.18% 0.00% NA
All Indica  2759 88.90% 9.20% 1.92% 0.00% NA
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.80% 0.30% 0.84% 0.00% NA
Indica II  465 69.90% 24.70% 5.38% 0.00% NA
Indica III  913 93.30% 6.20% 0.44% 0.00% NA
Indica Intermediate  786 87.40% 10.20% 2.42% 0.00% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 0.00% 3.33% 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
vg1212601474 G -> A LOC_Os12g22320.1 synonymous_variant ; p.Gln3Gln; LOW synonymous_codon Average:58.734; most accessible tissue: Minghui63 panicle, score: 70.194 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1212601474 NA 4.54E-07 mr1425 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
vg1212601474 NA 8.16E-06 mr1002_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
vg1212601474 NA 2.28E-06 mr1024_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
vg1212601474 NA 3.17E-06 mr1425_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
vg1212601474 7.41E-06 NA mr1584_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
vg1212601474 1.15E-06 1.15E-06 mr1584_2 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
vg1212601474 NA 9.98E-06 mr1892_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