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Detailed information for vg0517984725:

Variant ID: vg0517984725 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 17984725
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.65, G: 0.34, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:


TCTTCATAAGATTTATTCAACACCGTCTAAAAATAAAATATAGTTATAATATTATAATCTGTCTTTTATTCTGAAAAATATATGCAAGGAAATAAGGAAT[G/T]
GAGATATGCCTATTTGAAGAGTTGTAGGTTCACACCTTTTCTCTTTATAAATTGCCACTCCACTCATGCATTTTCCCCTTACAATTTTAGGCTCATATCC

Reverse complement sequence

GGATATGAGCCTAAAATTGTAAGGGGAAAATGCATGAGTGGAGTGGCAATTTATAAAGAGAAAAGGTGTGAACCTACAACTCTTCAAATAGGCATATCTC[C/A]
ATTCCTTATTTCCTTGCATATATTTTTCAGAATAAAAGACAGATTATAATATTATAACTATATTTTATTTTTAGACGGTGTTGAATAAATCTTATGAAGA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 83.00% 16.90% 0.11% 0.00% NA
All Indica  2759 95.00% 4.90% 0.11% 0.00% NA
All Japonica  1512 57.40% 42.50% 0.13% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 76.30% 23.00% 0.65% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 96.40% 3.60% 0.00% 0.00% NA
Temperate Japonica  767 79.00% 20.90% 0.13% 0.00% NA
Tropical Japonica  504 38.10% 61.70% 0.20% 0.00% NA
Japonica Intermediate  241 29.00% 71.00% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 81.10% 18.90% 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
vg0517984725 G -> T LOC_Os05g30970.1 intron_variant ; MODIFIER silent_mutation Average:58.232; most accessible tissue: Callus, score: 84.034 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0517984725 NA 9.64E-06 mr1002 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
vg0517984725 NA 2.09E-07 mr1039 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
vg0517984725 NA 7.54E-07 mr1044 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
vg0517984725 3.02E-06 3.02E-06 mr1406 Jap_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
vg0517984725 NA 3.03E-06 mr1408 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
vg0517984725 NA 5.16E-06 mr1482 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
vg0517984725 NA 2.63E-06 mr1002_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
vg0517984725 NA 1.74E-07 mr1039_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
vg0517984725 NA 3.65E-07 mr1167_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
vg0517984725 NA 5.37E-07 mr1363_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
vg0517984725 NA 4.44E-06 mr1399_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
vg0517984725 NA 5.08E-07 mr1544_2 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
vg0517984725 NA 2.64E-06 mr1654_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