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Detailed information for vg1222407333:

Variant ID: vg1222407333 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 22407333
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.86, T: 0.14, others allele: 0.00, population size: 63. )

Flanking Sequence (100 bp) in Reference Genome:


CGATGATGAGATTACAAGTGCCGGATTCAGTTTTCCTTGGAGGGGGATTACAAGTGCTGGATTCAGCTTTCCTAGGAGGCTTAAGCACATAGTCATAAGG[A/T]
ACAGTTATCCCTCTATCAGCTGCCTGAAAACATTGAAGCTTATCACCGAGATATTCATGCTAATGGTTCGACATGGAAGCGGTTACACCAAAGAAGAGAC

Reverse complement sequence

GTCTCTTCTTTGGTGTAACCGCTTCCATGTCGAACCATTAGCATGAATATCTCGGTGATAAGCTTCAATGTTTTCAGGCAGCTGATAGAGGGATAACTGT[T/A]
CCTTATGACTATGTGCTTAAGCCTCCTAGGAAAGCTGAATCCAGCACTTGTAATCCCCCTCCAAGGAAAACTGAATCCGGCACTTGTAATCTCATCATCG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 38.60% 17.70% 0.78% 42.89% NA
All Indica  2759 10.20% 29.10% 0.98% 59.73% NA
All Japonica  1512 86.30% 0.70% 0.26% 12.76% NA
Aus  269 32.70% 4.50% 1.86% 60.97% NA
Indica I  595 10.90% 29.60% 0.84% 58.66% NA
Indica II  465 4.90% 17.00% 0.86% 77.20% NA
Indica III  913 10.60% 34.70% 1.31% 53.34% NA
Indica Intermediate  786 12.30% 29.30% 0.76% 57.63% NA
Temperate Japonica  767 91.50% 0.10% 0.13% 8.21% NA
Tropical Japonica  504 77.20% 1.20% 0.40% 21.23% NA
Japonica Intermediate  241 88.80% 1.20% 0.41% 9.54% NA
VI/Aromatic  96 92.70% 2.10% 0.00% 5.21% NA
Intermediate  90 67.80% 12.20% 1.11% 18.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1222407333 A -> DEL LOC_Os12g36590.1 N frameshift_variant Average:11.756; most accessible tissue: Callus, score: 65.404 N N N N
vg1222407333 A -> T LOC_Os12g36590.1 missense_variant ; p.Asn673Tyr; MODERATE nonsynonymous_codon Average:11.756; most accessible tissue: Callus, score: 65.404 unknown unknown TOLERATED 0.65

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1222407333 NA 2.64E-06 mr1015 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
vg1222407333 NA 5.24E-07 mr1021 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
vg1222407333 NA 5.58E-07 mr1031 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
vg1222407333 NA 1.12E-13 mr1032 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
vg1222407333 NA 4.16E-07 mr1032 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
vg1222407333 NA 4.05E-06 mr1165 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
vg1222407333 NA 8.48E-07 mr1291 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
vg1222407333 NA 9.16E-06 mr1471 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
vg1222407333 NA 2.85E-06 mr1477 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
vg1222407333 NA 1.42E-06 mr1478 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
vg1222407333 NA 4.92E-06 mr1553 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
vg1222407333 NA 4.19E-08 mr1660 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
vg1222407333 NA 3.96E-06 mr1660 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
vg1222407333 5.33E-06 NA mr1738 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
vg1222407333 5.23E-06 5.22E-06 mr1738 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
vg1222407333 NA 9.03E-06 mr1815 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
vg1222407333 2.89E-06 2.88E-06 mr1848_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
vg1222407333 NA 1.30E-06 mr1925_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