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Detailed information for vg0412456522:

Variant ID: vg0412456522 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 12456522
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AATTCCTATATAATAAAGCTTAGTTCCTGAGCATCTGTTTTTCTTCTTTTCTACCCCCCCGTCTGCTCTTCCTCCAGATGGTCTACACCAGGAATGGTAG[C/T]
CGCACAACAGGCGAGGGCAGCAACGGCAAAGAACGCACTGACGGTGTGCATCCCAACAGCGATTCCAGCAATGGTCCGCCACCACTCCCCGAGAATCCGA

Reverse complement sequence

TCGGATTCTCGGGGAGTGGTGGCGGACCATTGCTGGAATCGCTGTTGGGATGCACACCGTCAGTGCGTTCTTTGCCGTTGCTGCCCTCGCCTGTTGTGCG[G/A]
CTACCATTCCTGGTGTAGACCATCTGGAGGAAGAGCAGACGGGGGGGTAGAAAAGAAGAAAAACAGATGCTCAGGAACTAAGCTTTATTATATAGGAATT

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 95.80% 1.70% 2.52% 0.00% NA
All Indica  2759 94.00% 2.40% 3.59% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 89.60% 3.30% 7.06% 0.00% NA
Indica I  595 96.50% 0.30% 3.19% 0.00% NA
Indica II  465 96.10% 1.30% 2.58% 0.00% NA
Indica III  913 91.10% 4.80% 4.05% 0.00% NA
Indica Intermediate  786 94.10% 1.90% 3.94% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 3.30% 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
vg0412456522 C -> T LOC_Os04g22000.1 synonymous_variant ; p.Ser316Ser; LOW synonymous_codon Average:40.99; most accessible tissue: Minghui63 young leaf, score: 55.178 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0412456522 2.82E-06 7.48E-06 mr1312 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
vg0412456522 NA 6.64E-06 mr1403 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
vg0412456522 6.21E-06 6.21E-06 mr1463 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
vg0412456522 NA 6.91E-06 mr1569 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
vg0412456522 3.35E-06 NA mr1669 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
vg0412456522 1.44E-06 7.23E-07 mr1669 Ind_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
vg0412456522 NA 5.92E-06 mr1846 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
vg0412456522 NA 8.91E-06 mr1818_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
vg0412456522 NA 8.28E-14 mr1846_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
vg0412456522 NA 2.08E-11 mr1846_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