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Detailed information for vg0233356353:

Variant ID: vg0233356353 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 33356353
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGATTGCGTCGTCACTGAGCAGCTGGCAGCAGCAACCAGGGAGATTGCGTCAGTGCCGAGCAGCTGTGATTGCCATGGAGTGAATTACGTCGGCGCCGGC[C/T]
GCTGGCGACACGCGATGCAGTTTCGATTTTTGGCTTTTCGCCAAATCGCTATCGCCCGGTCACCGATCGCTAAGCGCGTGCGCGTGAAGAGGACAAGAGG

Reverse complement sequence

CCTCTTGTCCTCTTCACGCGCACGCGCTTAGCGATCGGTGACCGGGCGATAGCGATTTGGCGAAAAGCCAAAAATCGAAACTGCATCGCGTGTCGCCAGC[G/A]
GCCGGCGCCGACGTAATTCACTCCATGGCAATCACAGCTGCTCGGCACTGACGCAATCTCCCTGGTTGCTGCTGCCAGCTGCTCAGTGACGACGCAATCT

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 98.50% 1.20% 0.23% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 95.50% 3.80% 0.66% 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  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 91.50% 7.30% 1.17% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 0.80% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 1.10% 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
vg0233356353 C -> T LOC_Os02g54460.1 missense_variant ; p.Arg42Cys; MODERATE nonsynonymous_codon ; R42C Average:62.935; most accessible tissue: Minghui63 root, score: 74.1 unknown unknown DELETERIOUS 0.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0233356353 NA 1.33E-09 Heading_date Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0233356353 3.07E-06 3.07E-06 mr1038 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
vg0233356353 NA 2.12E-07 mr1354 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
vg0233356353 5.08E-07 5.08E-07 mr1389 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
vg0233356353 5.66E-06 2.47E-06 mr1038_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
vg0233356353 NA 5.17E-08 mr1354_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
vg0233356353 5.74E-07 5.74E-07 mr1389_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