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Detailed information for vg1217086772:

Variant ID: vg1217086772 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 17086772
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:


CCAATCGAAGAAACAAACCACGAAAGTGTTGAAAAGCTTCGTCCTTAGTTGCCATAAAGAAAACCCAAGAATATCGAGAAAAATCATCAACAATAACCAA[C/T]
ACATACCACTTACCTCCAACAGATTGCATGTCGCGACCGGGAAAATTGCCTTTTTCCGAACGCTAGTGTATTAATCCCCGTCCCAGGAAAAGCCGGGGTA

Reverse complement sequence

TACCCCGGCTTTTCCTGGGACGGGGATTAATACACTAGCGTTCGGAAAAAGGCAATTTTCCCGGTCGCGACATGCAATCTGTTGGAGGTAAGTGGTATGT[G/A]
TTGGTTATTGTTGATGATTTTTCTCGATATTCTTGGGTTTTCTTTATGGCAACTAAGGACGAAGCTTTTCAACACTTTCGTGGTTTGTTTCTTCGATTGG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 42.50% 8.00% 28.90% 20.55% NA
All Indica  2759 18.90% 13.20% 44.55% 23.34% NA
All Japonica  1512 73.90% 0.30% 5.89% 19.91% NA
Aus  269 91.40% 1.90% 6.32% 0.37% NA
Indica I  595 4.20% 20.50% 52.27% 23.03% NA
Indica II  465 22.80% 6.20% 47.96% 23.01% NA
Indica III  913 20.00% 12.60% 40.31% 27.05% NA
Indica Intermediate  786 26.30% 12.60% 41.60% 19.47% NA
Temperate Japonica  767 96.30% 0.30% 0.39% 3.00% NA
Tropical Japonica  504 41.10% 0.20% 14.48% 44.25% NA
Japonica Intermediate  241 71.40% 0.40% 5.39% 22.82% NA
VI/Aromatic  96 78.10% 1.00% 13.54% 7.29% NA
Intermediate  90 55.60% 4.40% 20.00% 20.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1217086772 C -> DEL LOC_Os12g28900.1 N frameshift_variant Average:11.977; most accessible tissue: Minghui63 panicle, score: 20.733 N N N N
vg1217086772 C -> T LOC_Os12g28900.1 synonymous_variant ; p.Val10Val; LOW synonymous_codon Average:11.977; most accessible tissue: Minghui63 panicle, score: 20.733 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1217086772 NA 6.77E-06 mr1450 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
vg1217086772 NA 4.61E-06 mr1511 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
vg1217086772 NA 2.44E-07 mr1680 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
vg1217086772 NA 5.68E-13 mr1707 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
vg1217086772 NA 2.92E-06 mr1707 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
vg1217086772 NA 4.27E-09 mr1728 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
vg1217086772 NA 7.74E-12 mr1860 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
vg1217086772 NA 2.05E-06 mr1860 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
vg1217086772 NA 4.51E-06 mr1904 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
vg1217086772 NA 7.13E-08 mr1990 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
vg1217086772 NA 1.19E-08 mr1707_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