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Detailed information for vg0621417288:

Variant ID: vg0621417288 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 21417288
Reference Allele: GAlternative Allele: T
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, G: 0.01, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:


AGCATATAAAATCAGAGTATGTATCTGCAGTCTGTGTGTGAGAGAGAGATATGTATATATACGTGAAATATATGGTTACGTACCCCTCCTTTGGACCTCC[G/T]
TGAGGTGCAGCCCATGATCACCTCCTCCAGTCCAGAACCAGAGGTCGACCTCCCATCAAACTTTCGCGGTTGGTGTGGCCGTTCATCCTCCTGCTGATCA

Reverse complement sequence

TGATCAGCAGGAGGATGAACGGCCACACCAACCGCGAAAGTTTGATGGGAGGTCGACCTCTGGTTCTGGACTGGAGGAGGTGATCATGGGCTGCACCTCA[C/A]
GGAGGTCCAAAGGAGGGGTACGTAACCATATATTTCACGTATATATACATATCTCTCTCTCACACACAGACTGCAGATACATACTCTGATTTTATATGCT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 76.20% 23.80% 0.04% 0.00% NA
All Indica  2759 98.50% 1.50% 0.00% 0.00% NA
All Japonica  1512 32.10% 67.70% 0.13% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 96.10% 3.90% 0.00% 0.00% NA
Indica III  913 99.30% 0.70% 0.00% 0.00% NA
Indica Intermediate  786 97.80% 2.20% 0.00% 0.00% NA
Temperate Japonica  767 46.90% 52.80% 0.26% 0.00% NA
Tropical Japonica  504 12.70% 87.30% 0.00% 0.00% NA
Japonica Intermediate  241 25.70% 74.30% 0.00% 0.00% NA
VI/Aromatic  96 78.10% 21.90% 0.00% 0.00% NA
Intermediate  90 58.90% 41.10% 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
vg0621417288 G -> T LOC_Os06g36480.1 synonymous_variant ; p.Arg444Arg; LOW synonymous_codon Average:62.681; most accessible tissue: Callus, score: 89.385 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0621417288 4.73E-06 4.73E-06 mr1327 Jap_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
vg0621417288 7.88E-06 7.88E-06 mr1464 Jap_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
vg0621417288 NA 6.47E-07 mr1510 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
vg0621417288 NA 5.76E-08 mr1648 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
vg0621417288 NA 1.90E-11 mr1871 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
vg0621417288 NA 2.85E-10 mr1905 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
vg0621417288 NA 6.16E-16 mr1324_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
vg0621417288 NA 1.09E-06 mr1548_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
vg0621417288 NA 7.77E-09 mr1623_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
vg0621417288 1.57E-06 NA mr1933_2 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