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Detailed information for vg0129888300:

Variant ID: vg0129888300 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 29888300
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTCTAAATTTGACGCCGTTGACTTTTTTAAATATATATGACCGTTTGTTTTATTAAAAAATCTAAATTTGACGCCGTTGACTTTTTTAAATATATATGAC[C/T]
GTTTGTCTTATTAAAAAATTTAAGTAATTATTAATTCTTTTTCTATCATTTGATTCATTGATAAATATATTTTTATGTATACGTATAGTTTTACATATTT

Reverse complement sequence

AAATATGTAAAACTATACGTATACATAAAAATATATTTATCAATGAATCAAATGATAGAAAAAGAATTAATAATTACTTAAATTTTTTAATAAGACAAAC[G/A]
GTCATATATATTTAAAAAAGTCAACGGCGTCAAATTTAGATTTTTTAATAAAACAAACGGTCATATATATTTAAAAAAGTCAACGGCGTCAAATTTAGAG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.20% 3.00% 2.09% 0.61% NA
All Indica  2759 97.80% 0.10% 0.98% 1.05% NA
All Japonica  1512 86.80% 8.80% 4.37% 0.00% NA
Aus  269 97.40% 1.90% 0.74% 0.00% NA
Indica I  595 99.50% 0.00% 0.00% 0.50% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 96.50% 0.10% 1.31% 2.08% NA
Indica Intermediate  786 96.80% 0.40% 1.91% 0.89% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 62.90% 25.00% 12.10% 0.00% NA
Japonica Intermediate  241 95.40% 2.50% 2.07% 0.00% NA
VI/Aromatic  96 97.90% 1.00% 1.04% 0.00% NA
Intermediate  90 95.60% 1.10% 3.33% 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
vg0129888300 C -> T LOC_Os01g52000.1 upstream_gene_variant ; 2198.0bp to feature; MODIFIER silent_mutation Average:29.987; most accessible tissue: Callus, score: 63.435 N N N N
vg0129888300 C -> T LOC_Os01g52000-LOC_Os01g52010 intergenic_region ; MODIFIER silent_mutation Average:29.987; most accessible tissue: Callus, score: 63.435 N N N N
vg0129888300 C -> DEL N N silent_mutation Average:29.987; most accessible tissue: Callus, score: 63.435 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0129888300 NA 3.30E-06 mr1154 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
vg0129888300 NA 1.39E-07 mr1518 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
vg0129888300 NA 7.84E-11 mr1539 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
vg0129888300 NA 1.14E-07 mr1584 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
vg0129888300 NA 7.89E-08 mr1676 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
vg0129888300 NA 5.81E-07 mr1723 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
vg0129888300 NA 8.17E-16 mr1732 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
vg0129888300 NA 3.90E-07 mr1097_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
vg0129888300 NA 4.54E-07 mr1206_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
vg0129888300 NA 7.99E-06 mr1428_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
vg0129888300 7.20E-07 NA mr1539_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
vg0129888300 NA 2.24E-17 mr1539_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
vg0129888300 2.15E-07 NA mr1540_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
vg0129888300 NA 3.32E-19 mr1540_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
vg0129888300 NA 1.17E-06 mr1596_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
vg0129888300 NA 4.91E-09 mr1668_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
vg0129888300 1.10E-06 NA mr1715_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
vg0129888300 NA 1.06E-06 mr1715_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
vg0129888300 NA 3.65E-06 mr1723_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
vg0129888300 5.32E-07 NA mr1732_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
vg0129888300 NA 1.51E-17 mr1732_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