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Detailed information for vg0122836087:

Variant ID: vg0122836087 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 22836087
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGGCGGTGCGGATCTGGCGCAGGAGCAGCCGGGGCCGCGACCTGCCCCACGACAGCGCCGGTCCTCTGCCCCCGTCGGTGGCTCTCCCCTCTCCCTTCTC[C/T]
GGCATCGTCGGGCGAAGGAAGCCGGCAAGCTTCTTCAGCCCCACCACCTTCCCCATCGACCCAGCGAGCATCCAGCGGCCCTCCTCCCCTGGCCGACGAG

Reverse complement sequence

CTCGTCGGCCAGGGGAGGAGGGCCGCTGGATGCTCGCTGGGTCGATGGGGAAGGTGGTGGGGCTGAAGAAGCTTGCCGGCTTCCTTCGCCCGACGATGCC[G/A]
GAGAAGGGAGAGGGGAGAGCCACCGACGGGGGCAGAGGACCGGCGCTGTCGTGGGGCAGGTCGCGGCCCCGGCTGCTCCTGCGCCAGATCCGCACCGCCC

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 94.80% 5.20% 0.00% 0.00% NA
All Indica  2759 94.70% 5.30% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 64.30% 35.70% 0.00% 0.00% NA
Indica I  595 91.40% 8.60% 0.00% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 96.70% 3.30% 0.00% 0.00% NA
Indica Intermediate  786 92.00% 8.00% 0.00% 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  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0122836087 C -> T LOC_Os01g40450.1 synonymous_variant ; p.Pro437Pro; LOW synonymous_codon Average:76.636; most accessible tissue: Zhenshan97 young leaf, score: 92.356 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0122836087 2.03E-06 2.03E-06 mr1852 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