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Detailed information for vg0127445565:

Variant ID: vg0127445565 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 27445565
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, C: 0.00, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:


GGGTACGGCGTTTGCTCCAGTGACCACAATACGATTGGGATGTCTGCTTCGTGTAAATTGGCGGTAATGTGGAGGTCGACTTTGCCTTGGTTGCAGGCAG[T/C]
CCCTCGAGTAATGCCCTGGTTCTTTGCAGTTGTAACAAATCAACGTCTTCTTTACTGAGCTGTCCATCTGGGGACGATCATTTTGACTTGGAGTTGGAAT

Reverse complement sequence

ATTCCAACTCCAAGTCAAAATGATCGTCCCCAGATGGACAGCTCAGTAAAGAAGACGTTGATTTGTTACAACTGCAAAGAACCAGGGCATTACTCGAGGG[A/G]
CTGCCTGCAACCAAGGCAAAGTCGACCTCCACATTACCGCCAATTTACACGAAGCAGACATCCCAATCGTATTGTGGTCACTGGAGCAAACGCCGTACCC

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 65.80% 6.80% 2.03% 25.39% NA
All Indica  2759 46.20% 9.80% 2.43% 41.57% NA
All Japonica  1512 99.90% 0.00% 0.00% 0.07% NA
Aus  269 55.80% 17.80% 10.41% 15.99% NA
Indica I  595 30.80% 4.40% 3.87% 61.01% NA
Indica II  465 41.10% 9.20% 1.72% 47.96% NA
Indica III  913 56.20% 10.00% 1.86% 31.98% NA
Indica Intermediate  786 49.20% 14.10% 2.42% 34.22% NA
Temperate Japonica  767 99.90% 0.00% 0.00% 0.13% 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 86.70% 2.20% 1.11% 10.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0127445565 T -> DEL LOC_Os01g47960.1 N frameshift_variant Average:6.962; most accessible tissue: Callus, score: 28.943 N N N N
vg0127445565 T -> C LOC_Os01g47960.1 missense_variant ; p.Asp459Gly; MODERATE nonsynonymous_codon ; D459G Average:6.962; most accessible tissue: Callus, score: 28.943 possibly damaging 1.551 DELETERIOUS 0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0127445565 5.75E-09 4.04E-15 mr1216 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
vg0127445565 2.98E-08 3.76E-15 mr1216 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