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Detailed information for vg0138299108:

Variant ID: vg0138299108 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 38299108
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.01, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:


TCGGAGACTCGAATCGGAATTGGAATCTTGAGGTGGACGATTTTGATGGCGACGAGAAGGACAAGGAGATTAAATTGAGATCCACGGCACGACTTAGACT[C/T]
GCACACAAAGAACGAAAAATTTCGCATATAAGATTTTGCCGAATTAGTTTTTTTAACGCCTCACGAAAAGCGGAGCATTACATATTCGATAGTTATATTT

Reverse complement sequence

AAATATAACTATCGAATATGTAATGCTCCGCTTTTCGTGAGGCGTTAAAAAAACTAATTCGGCAAAATCTTATATGCGAAATTTTTCGTTCTTTGTGTGC[G/A]
AGTCTAAGTCGTGCCGTGGATCTCAATTTAATCTCCTTGTCCTTCTCGTCGCCATCAAAATCGTCCACCTCAAGATTCCAATTCCGATTCGAGTCTCCGA

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 94.90% 5.10% 0.00% 0.00% NA
All Indica  2759 98.50% 1.50% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 29.70% 70.30% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 97.90% 2.10% 0.00% 0.00% NA
Indica Intermediate  786 97.20% 2.80% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 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
vg0138299108 C -> T LOC_Os01g65986.1 upstream_gene_variant ; 891.0bp to feature; MODIFIER silent_mutation Average:43.506; most accessible tissue: Minghui63 panicle, score: 66.554 N N N N
vg0138299108 C -> T LOC_Os01g65980.1 downstream_gene_variant ; 1192.0bp to feature; MODIFIER silent_mutation Average:43.506; most accessible tissue: Minghui63 panicle, score: 66.554 N N N N
vg0138299108 C -> T LOC_Os01g65980-LOC_Os01g65986 intergenic_region ; MODIFIER silent_mutation Average:43.506; most accessible tissue: Minghui63 panicle, score: 66.554 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0138299108 NA 8.45E-10 mr1348 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
vg0138299108 NA 5.98E-06 mr1349 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
vg0138299108 NA 3.34E-10 mr1415 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
vg0138299108 NA 3.34E-10 mr1567 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