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Detailed information for vg0118254834:

Variant ID: vg0118254834 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 18254834
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATCAAGTTGCGGCCCCACAACCAACTGGCAATTTCTGGCTGAAGCTCTAGAAACAAAGAAACAATTCCCCTTGGGCAAAATTCTCCTCGGCTATCTATAC[C/T]
AGATGTTGAGCAATGCATCGGCTAAGATAGCAGTCGGCTCAGTAGTTGGAGCAGGTGGACCCTGGTGGCTACTACAAACCTGGTTAAACCTTGCCGCCGT

Reverse complement sequence

ACGGCGGCAAGGTTTAACCAGGTTTGTAGTAGCCACCAGGGTCCACCTGCTCCAACTACTGAGCCGACTGCTATCTTAGCCGATGCATTGCTCAACATCT[G/A]
GTATAGATAGCCGAGGAGAATTTTGCCCAAGGGGAATTGTTTCTTTGTTTCTAGAGCTTCAGCCAGAAATTGCCAGTTGGTTGTGGGGCCGCAACTTGAT

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 97.70% 2.20% 0.02% 0.00% NA
All Indica  2759 97.10% 2.80% 0.04% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 90.00% 10.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 89.50% 10.30% 0.22% 0.00% NA
Indica III  913 99.50% 0.50% 0.00% 0.00% NA
Indica Intermediate  786 96.80% 3.20% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 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 98.90% 1.10% 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
vg0118254834 C -> T LOC_Os01g33142.1 upstream_gene_variant ; 4725.0bp to feature; MODIFIER silent_mutation Average:59.514; most accessible tissue: Zhenshan97 flag leaf, score: 81.008 N N N N
vg0118254834 C -> T LOC_Os01g33160.1 upstream_gene_variant ; 4731.0bp to feature; MODIFIER silent_mutation Average:59.514; most accessible tissue: Zhenshan97 flag leaf, score: 81.008 N N N N
vg0118254834 C -> T LOC_Os01g33150.1 intron_variant ; MODIFIER silent_mutation Average:59.514; most accessible tissue: Zhenshan97 flag leaf, score: 81.008 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0118254834 3.76E-06 NA mr1404_2 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