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Detailed information for vg0605296817:

Variant ID: vg0605296817 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 5296817
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.74, T: 0.25, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:


TGATCCCATCCAAGCACAGGAACTAGAAGTTGCAGATATCGTTTTCAAGGGTGATATAACTTTTCAGTATGCTCTCACTGTGCTCCCTGTGGTGTTTCCA[A/T]
GCGTGCAAAATCTGACTGTGCATGCTAATTTTGGGCTACAGGTGGGTCTAAGAAAACTTCGCAAGTCAATAATGATGACCATATCATACTTGTAGATTTT

Reverse complement sequence

AAAATCTACAAGTATGATATGGTCATCATTATTGACTTGCGAAGTTTTCTTAGACCCACCTGTAGCCCAAAATTAGCATGCACAGTCAGATTTTGCACGC[T/A]
TGGAAACACCACAGGGAGCACAGTGAGAGCATACTGAAAAGTTATATCACCCTTGAAAACGATATCTGCAACTTCTAGTTCCTGTGCTTGGATGGGATCA

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 87.10% 12.80% 0.04% 0.13% NA
All Indica  2759 79.60% 20.30% 0.00% 0.14% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.07% NA
Aus  269 88.10% 11.90% 0.00% 0.00% NA
Indica I  595 66.20% 33.80% 0.00% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 74.50% 25.40% 0.00% 0.11% NA
Indica Intermediate  786 83.70% 15.90% 0.00% 0.38% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.00% 0.80% 0.00% 0.20% 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 88.90% 7.80% 2.22% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0605296817 A -> T LOC_Os06g10300.1 missense_variant ; p.Ser354Cys; MODERATE nonsynonymous_codon ; S354C Average:46.285; most accessible tissue: Zhenshan97 panicle, score: 74.671 benign 0.276 TOLERATED 0.26
vg0605296817 A -> DEL LOC_Os06g10300.1 N frameshift_variant Average:46.285; most accessible tissue: Zhenshan97 panicle, score: 74.671 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0605296817 8.11E-21 6.15E-40 mr1201 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
vg0605296817 3.53E-18 1.26E-39 mr1201 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
vg0605296817 1.35E-17 9.92E-30 mr1219 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
vg0605296817 3.19E-16 4.66E-35 mr1219 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
vg0605296817 8.83E-19 4.83E-35 mr1274 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
vg0605296817 5.84E-20 3.82E-36 mr1274 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
vg0605296817 1.29E-19 1.31E-35 mr1201_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
vg0605296817 1.17E-17 1.65E-34 mr1201_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
vg0605296817 2.07E-16 3.13E-27 mr1219_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
vg0605296817 3.80E-16 6.20E-32 mr1219_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
vg0605296817 5.30E-15 1.26E-32 mr1274_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
vg0605296817 2.22E-16 5.27E-34 mr1274_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