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Detailed information for vg0133776229:

Variant ID: vg0133776229 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 33776229
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTAGGGCCGTTTAGCATTGAAGCTGTTCTACCAAAATTTTAGTAACTTAGATAGTAGATAAGATAGTTTAGATTGAAACTAAACATTAGTAGTGTCCATG[C/T]
TTAATTTGGCCATATTCTAAGATCTTTTTCACCATACTACTAATTTTTGGCTTCATATTAATATCAAACCAAACATATCCTAGCTAACTTTGTCCTACTA

Reverse complement sequence

TAGTAGGACAAAGTTAGCTAGGATATGTTTGGTTTGATATTAATATGAAGCCAAAAATTAGTAGTATGGTGAAAAAGATCTTAGAATATGGCCAAATTAA[G/A]
CATGGACACTACTAATGTTTAGTTTCAATCTAAACTATCTTATCTACTATCTAAGTTACTAAAATTTTGGTAGAACAGCTTCAATGCTAAACGGCCCTAA

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 98.10% 1.80% 0.19% 0.00% NA
All Indica  2759 99.90% 0.10% 0.04% 0.00% NA
All Japonica  1512 94.50% 5.00% 0.46% 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  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.30% 0.13% 0.00% NA
Temperate Japonica  767 92.30% 6.80% 0.91% 0.00% NA
Tropical Japonica  504 98.80% 1.20% 0.00% 0.00% NA
Japonica Intermediate  241 92.50% 7.50% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 94.40% 4.40% 1.11% 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
vg0133776229 C -> T LOC_Os01g58440.1 upstream_gene_variant ; 2064.0bp to feature; MODIFIER silent_mutation Average:63.833; most accessible tissue: Minghui63 panicle, score: 88.281 N N N N
vg0133776229 C -> T LOC_Os01g58430-LOC_Os01g58440 intergenic_region ; MODIFIER silent_mutation Average:63.833; most accessible tissue: Minghui63 panicle, score: 88.281 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0133776229 3.73E-06 NA mr1446 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
vg0133776229 7.42E-06 6.65E-06 mr1496 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
vg0133776229 4.93E-06 5.62E-06 mr1917 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
vg0133776229 8.42E-06 5.83E-06 mr1936 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
vg0133776229 2.56E-06 8.76E-07 mr1008_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
vg0133776229 4.83E-06 4.82E-06 mr1113_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