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Detailed information for vg1227343398:

Variant ID: vg1227343398 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 27343398
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:


ATAGTGTAAATGAAGATGGTGTTGAAATGGGAAGTGTTGCACAAAAGTGGTGAAGAAGAAAAAATGTTACATTCTCTGCAGCTTGTCGAGCTTCCCAATG[T/C]
TAGGTGAAATGATGCCCCCAAGCTGCATGTAAGGGAGATTTCTGGTAGAAAAGGAAAACATGAAAGAAGAGATTATTCAGGGGGCGAGGAATCCAATGAG

Reverse complement sequence

CTCATTGGATTCCTCGCCCCCTGAATAATCTCTTCTTTCATGTTTTCCTTTTCTACCAGAAATCTCCCTTACATGCAGCTTGGGGGCATCATTTCACCTA[A/G]
CATTGGGAAGCTCGACAAGCTGCAGAGAATGTAACATTTTTTCTTCTTCACCACTTTTGTGCAACACTTCCCATTTCAACACCATCTTCATTTACACTAT

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 66.60% 33.40% 0.00% 0.00% NA
All Indica  2759 97.80% 2.20% 0.00% 0.00% NA
All Japonica  1512 7.30% 92.70% 0.00% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 99.20% 0.80% 0.00% 0.00% NA
Indica II  465 98.70% 1.30% 0.00% 0.00% NA
Indica III  913 96.60% 3.40% 0.00% 0.00% NA
Indica Intermediate  786 97.60% 2.40% 0.00% 0.00% NA
Temperate Japonica  767 12.10% 87.90% 0.00% 0.00% NA
Tropical Japonica  504 0.80% 99.20% 0.00% 0.00% NA
Japonica Intermediate  241 5.40% 94.60% 0.00% 0.00% NA
VI/Aromatic  96 21.90% 78.10% 0.00% 0.00% NA
Intermediate  90 58.90% 41.10% 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
vg1227343398 T -> C LOC_Os12g44090.1 missense_variant ; p.Asn111Ser; MODERATE nonsynonymous_codon Average:58.389; most accessible tissue: Zhenshan97 panicle, score: 87.126 unknown unknown TOLERATED 1.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1227343398 NA 8.52E-29 mr1024 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
vg1227343398 NA 5.30E-32 mr1922 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
vg1227343398 9.07E-06 6.55E-27 mr1024_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
vg1227343398 NA 1.31E-14 mr1162_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
vg1227343398 NA 1.52E-19 mr1657_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
vg1227343398 NA 1.99E-30 mr1891_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
vg1227343398 NA 8.62E-20 mr1922_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