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Detailed information for vg1219406576:

Variant ID: vg1219406576 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 19406576
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.79, T: 0.21, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:


TCAATCAAATTGTTCTTTTACATTTACCTTCAGCCATGTTTTCTACTTTATCTTCTACCTAACATTAGTCTGTCTATCCTTCTCGATTTGCACACCACGG[C/T]
GACAATCTGAGCGGCGATCTGCTGCTTGGCTTGCTGCGTGGCGACCAGCTGCGCCCAATGGCCTTGAAGGTGAGGTGGAGGTTGGTGATGACGTCGTTCG

Reverse complement sequence

CGAACGACGTCATCACCAACCTCCACCTCACCTTCAAGGCCATTGGGCGCAGCTGGTCGCCACGCAGCAAGCCAAGCAGCAGATCGCCGCTCAGATTGTC[G/A]
CCGTGGTGTGCAAATCGAGAAGGATAGACAGACTAATGTTAGGTAGAAGATAAAGTAGAAAACATGGCTGAAGGTAAATGTAAAAGAACAATTTGATTGA

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 54.70% 43.30% 0.13% 1.84% NA
All Indica  2759 30.80% 65.80% 0.22% 3.12% NA
All Japonica  1512 97.80% 2.10% 0.00% 0.07% NA
Aus  269 36.80% 63.20% 0.00% 0.00% NA
Indica I  595 59.20% 40.80% 0.00% 0.00% NA
Indica II  465 14.20% 68.80% 0.65% 16.34% NA
Indica III  913 20.70% 79.20% 0.11% 0.00% NA
Indica Intermediate  786 31.00% 67.40% 0.25% 1.27% NA
Temperate Japonica  767 98.30% 1.70% 0.00% 0.00% NA
Tropical Japonica  504 99.00% 1.00% 0.00% 0.00% NA
Japonica Intermediate  241 93.80% 5.80% 0.00% 0.41% NA
VI/Aromatic  96 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 75.60% 24.40% 0.00% 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
vg1219406576 C -> DEL LOC_Os12g32160.1 N frameshift_variant Average:47.244; most accessible tissue: Zhenshan97 young leaf, score: 64.205 N N N N
vg1219406576 C -> T LOC_Os12g32160.1 synonymous_variant ; p.Ser216Ser; LOW synonymous_codon Average:47.244; most accessible tissue: Zhenshan97 young leaf, score: 64.205 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1219406576 NA 2.12E-07 mr1457 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
vg1219406576 2.01E-11 NA mr1458 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
vg1219406576 1.06E-10 8.59E-21 mr1458 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
vg1219406576 NA 2.46E-06 mr1686 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
vg1219406576 NA 3.40E-07 mr1457_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
vg1219406576 1.16E-07 NA mr1458_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
vg1219406576 3.83E-08 2.01E-16 mr1458_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
vg1219406576 NA 7.59E-06 mr1756_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