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Detailed information for vg0412431746:

Variant ID: vg0412431746 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 12431746
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.93, G: 0.08, others allele: 0.00, population size: 118. )

Flanking Sequence (100 bp) in Reference Genome:


CCTGGTTCTTTTTAAAGAAAAGTCCAAGATCTCTTGTGCCATTAAGATATCGAAAGACATTCTTAACTCCAGTCCAATGGTGTTTGGTAGGAGCAGCGCT[A/G]
TATCTTGCTAATAGATTAACCGAGAAAGCAATATCTGGCCTTGTACTATTTGCAAGGTACATAAGTGCGCCAATAGCACTAAGATATGGAAAATCAGGAC

Reverse complement sequence

GTCCTGATTTTCCATATCTTAGTGCTATTGGCGCACTTATGTACCTTGCAAATAGTACAAGGCCAGATATTGCTTTCTCGGTTAATCTATTAGCAAGATA[T/C]
AGCGCTGCTCCTACCAAACACCATTGGACTGGAGTTAAGAATGTCTTTCGATATCTTAATGGCACAAGAGATCTTGGACTTTTCTTTAAAAAGAACCAGG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 37.30% 27.40% 24.29% 10.94% NA
All Indica  2759 4.80% 44.60% 39.29% 11.27% NA
All Japonica  1512 99.00% 0.50% 0.26% 0.20% NA
Aus  269 0.40% 12.30% 15.61% 71.75% NA
Indica I  595 5.20% 17.50% 57.98% 19.33% NA
Indica II  465 6.00% 57.00% 27.74% 9.25% NA
Indica III  913 3.90% 58.10% 32.86% 5.15% NA
Indica Intermediate  786 4.80% 42.20% 39.44% 13.49% NA
Temperate Japonica  767 99.60% 0.30% 0.00% 0.13% NA
Tropical Japonica  504 98.60% 0.60% 0.79% 0.00% NA
Japonica Intermediate  241 97.90% 1.20% 0.00% 0.83% NA
VI/Aromatic  96 88.50% 6.20% 1.04% 4.17% NA
Intermediate  90 54.40% 20.00% 18.89% 6.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0412431746 A -> DEL LOC_Os04g21960.1 N frameshift_variant Average:13.925; most accessible tissue: Minghui63 young leaf, score: 29.964 N N N N
vg0412431746 A -> G LOC_Os04g21960.1 synonymous_variant ; p.Tyr653Tyr; LOW synonymous_codon Average:13.925; most accessible tissue: Minghui63 young leaf, score: 29.964 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0412431746 NA 5.06E-35 mr1350 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
vg0412431746 NA 2.02E-15 mr1040_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
vg0412431746 1.19E-07 NA mr1071_2 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
vg0412431746 1.87E-07 NA mr1080_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
vg0412431746 4.40E-06 NA mr1100_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
vg0412431746 3.62E-09 4.82E-09 mr1203_2 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
vg0412431746 NA 2.31E-17 mr1281_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
vg0412431746 4.82E-06 NA mr1619_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