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Detailed information for vg1217121743:

Variant ID: vg1217121743 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 17121743
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.98, C: 0.01, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:


TTGATGAAAGTTACTCAAAGCATTCCAAATTTCATGAGCAGCTCAAAAATGCGCAACACGATCATAATCCGAACGAGAAATACCACTCAAAAGAATGTTG[T/C]
GAGCTTTGCAATTTTGTTCAAAAGCAGTTTTTTCAGCAGCAGTATTAATAGCTTCAGGAATCACATAGGGACGAGAAACTTTTCTCCAAATATCATAAAC

Reverse complement sequence

GTTTATGATATTTGGAGAAAAGTTTCTCGTCCCTATGTGATTCCTGAAGCTATTAATACTGCTGCTGAAAAAACTGCTTTTGAACAAAATTGCAAAGCTC[A/G]
CAACATTCTTTTGAGTGGTATTTCTCGTTCGGATTATGATCGTGTTGCGCATTTTTGAGCTGCTCATGAAATTTGGAATGCTTTGAGTAACTTTCATCAA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 90.30% 6.70% 0.11% 2.84% NA
All Indica  2759 97.20% 1.30% 0.07% 1.45% NA
All Japonica  1512 93.70% 0.20% 0.20% 5.95% NA
Aus  269 18.60% 81.00% 0.00% 0.37% NA
Indica I  595 97.10% 0.00% 0.17% 2.69% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 96.70% 1.30% 0.00% 1.97% NA
Indica Intermediate  786 96.30% 2.80% 0.13% 0.76% NA
Temperate Japonica  767 97.70% 0.00% 0.00% 2.35% NA
Tropical Japonica  504 90.10% 0.00% 0.60% 9.33% NA
Japonica Intermediate  241 88.40% 1.20% 0.00% 10.37% NA
VI/Aromatic  96 41.70% 58.30% 0.00% 0.00% NA
Intermediate  90 90.00% 6.70% 0.00% 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
vg1217121743 T -> C LOC_Os12g28950.1 missense_variant ; p.His46Arg; MODERATE nonsynonymous_codon ; H46R Average:23.195; most accessible tissue: Minghui63 flag leaf, score: 32.882 unknown unknown TOLERATED 1.00
vg1217121743 T -> DEL LOC_Os12g28950.1 N frameshift_variant Average:23.195; most accessible tissue: Minghui63 flag leaf, score: 32.882 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1217121743 NA 8.37E-10 mr1570 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
vg1217121743 2.70E-06 NA mr1741 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
vg1217121743 NA 7.96E-07 mr1803 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
vg1217121743 NA 9.78E-06 mr1158_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
vg1217121743 NA 1.32E-10 mr1166_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
vg1217121743 NA 1.74E-06 mr1369_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
vg1217121743 NA 3.91E-07 mr1453_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
vg1217121743 NA 3.59E-06 mr1522_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
vg1217121743 NA 1.73E-07 mr1567_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
vg1217121743 NA 2.57E-08 mr1762_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
vg1217121743 NA 1.58E-07 mr1765_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
vg1217121743 NA 3.61E-06 mr1929_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
vg1217121743 NA 3.58E-10 mr1942_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