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Detailed information for vg0522018171:

Variant ID: vg0522018171 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 22018171
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.75, C: 0.25, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:


CAAAATCAAGATCTTTCTTAAGTTTAGGCAAACCACGAACAAGATCCAAACCACTTAACCTAGTGAGATGATCAAAACCAACATGTCCAAGTCTATGATA[C/T]
CAAAACATCACATCTTTATCAAACTTAGCAACCACACATGTTATCACAGGTGAAACAGAATTTTCAAAATCAGCTTTAAACACTCTTCCATAGCGAGAAA

Reverse complement sequence

TTTCTCGCTATGGAAGAGTGTTTAAAGCTGATTTTGAAAATTCTGTTTCACCTGTGATAACATGTGTGGTTGCTAAGTTTGATAAAGATGTGATGTTTTG[G/A]
TATCATAGACTTGGACATGTTGGTTTTGATCATCTCACTAGGTTAAGTGGTTTGGATCTTGTTCGTGGTTTGCCTAAACTTAAGAAAGATCTTGATTTTG

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 60.60% 39.30% 0.08% 0.00% NA
All Indica  2759 96.70% 3.20% 0.11% 0.00% NA
All Japonica  1512 1.20% 98.70% 0.07% 0.00% NA
Aus  269 49.10% 50.90% 0.00% 0.00% NA
Indica I  595 96.10% 3.90% 0.00% 0.00% NA
Indica II  465 96.30% 3.20% 0.43% 0.00% NA
Indica III  913 99.30% 0.70% 0.00% 0.00% NA
Indica Intermediate  786 94.10% 5.70% 0.13% 0.00% NA
Temperate Japonica  767 1.20% 98.70% 0.13% 0.00% NA
Tropical Japonica  504 0.80% 99.20% 0.00% 0.00% NA
Japonica Intermediate  241 2.10% 97.90% 0.00% 0.00% NA
VI/Aromatic  96 2.10% 97.90% 0.00% 0.00% NA
Intermediate  90 48.90% 51.10% 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
vg0522018171 C -> T LOC_Os05g37620.1 stop_gained ; p.Trp640*; HIGH stop_gained Average:14.01; most accessible tissue: Zhenshan97 flag leaf, score: 23.298 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0522018171 NA 2.60E-07 mr1162 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
vg0522018171 4.61E-07 4.61E-07 mr1584 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
vg0522018171 NA 9.07E-10 mr1595 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
vg0522018171 NA 5.96E-06 mr1184_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
vg0522018171 NA 5.74E-13 mr1325_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
vg0522018171 NA 3.22E-07 mr1329_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
vg0522018171 NA 5.86E-07 mr1524_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
vg0522018171 NA 3.55E-08 mr1600_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
vg0522018171 NA 9.30E-09 mr1690_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
vg0522018171 NA 5.21E-06 mr1982_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