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Detailed information for vg0333652898:

Variant ID: vg0333652898 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 33652898
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACTCTTTTTTTTTTGAACTTCAAAAATCAGGAAGTTAATGGTGAGGGTGGTGGCAGATTCACAATTCATCACAAGATTTTTTTAAGAGCAATTTTACGGT[T/C]
CATAAGAAGGTACCATGATGTAAAAAAATTTAGTATAAAATTTGGTATCTCTTGGTACCTAGTTACTATGAGGTACCAAATTTATAATAGAAAAAGTGGT

Reverse complement sequence

ACCACTTTTTCTATTATAAATTTGGTACCTCATAGTAACTAGGTACCAAGAGATACCAAATTTTATACTAAATTTTTTTACATCATGGTACCTTCTTATG[A/G]
ACCGTAAAATTGCTCTTAAAAAAATCTTGTGATGAATTGTGAATCTGCCACCACCCTCACCATTAACTTCCTGATTTTTGAAGTTCAAAAAAAAAAGAGT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 82.00% 18.00% 0.06% 0.00% NA
All Indica  2759 79.30% 20.60% 0.11% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 0.70% 99.30% 0.00% 0.00% NA
Indica I  595 70.40% 29.60% 0.00% 0.00% NA
Indica II  465 94.60% 5.20% 0.22% 0.00% NA
Indica III  913 78.00% 21.80% 0.22% 0.00% NA
Indica Intermediate  786 78.40% 21.60% 0.00% 0.00% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 90.00% 10.00% 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
vg0333652898 T -> C LOC_Os03g59110.1 intron_variant ; MODIFIER silent_mutation Average:30.231; most accessible tissue: Callus, score: 54.683 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0333652898 NA 1.38E-06 mr1126 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
vg0333652898 NA 9.16E-07 mr1286 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
vg0333652898 NA 2.05E-06 mr1665 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
vg0333652898 2.59E-07 NA mr1707 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
vg0333652898 NA 2.13E-07 mr1764 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
vg0333652898 NA 5.72E-06 mr1777 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
vg0333652898 NA 1.09E-06 mr1979 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
vg0333652898 4.78E-06 4.72E-09 mr1707_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
vg0333652898 NA 4.14E-06 mr1723_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
vg0333652898 3.02E-06 2.48E-07 mr1834_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