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Detailed information for vg0514548093:

Variant ID: vg0514548093 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 14548093
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 120. )

Flanking Sequence (100 bp) in Reference Genome:


ACGGGTTGAATCAGGATACAATAAAGCATCCTCGATTATAATTTGTGTACCCATTGGGAGTGTAATAGTTGCTCGTCCTGAGCCAACTATCACAGTATCG[C/T]
GCCCAGCGATAGTCAAAACTTTGCCTTCTCTCTTTTTGAGAGTTTGAAAGTATTTGATCTCCCTAAGTATAGAGTTTGTGGTACCACTGTCCACAAGACA

Reverse complement sequence

TGTCTTGTGGACAGTGGTACCACAAACTCTATACTTAGGGAGATCAAATACTTTCAAACTCTCAAAAAGAGAGAAGGCAAAGTTTTGACTATCGCTGGGC[G/A]
CGATACTGTGATAGTTGGCTCAGGACGAGCAACTATTACACTCCCAATGGGTACACAAATTATAATCGAGGATGCTTTATTGTATCCTGATTCAACCCGT

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 79.90% 6.30% 13.01% 0.83% NA
All Indica  2759 69.80% 9.60% 19.43% 1.12% NA
All Japonica  1512 99.10% 0.10% 0.20% 0.53% NA
Aus  269 66.50% 11.20% 22.30% 0.00% NA
Indica I  595 75.80% 2.00% 18.82% 3.36% NA
Indica II  465 52.30% 15.70% 30.75% 1.29% NA
Indica III  913 75.80% 10.50% 13.69% 0.00% NA
Indica Intermediate  786 68.80% 10.70% 19.85% 0.64% NA
Temperate Japonica  767 98.60% 0.30% 0.26% 0.91% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.00% 0.41% 0.41% NA
VI/Aromatic  96 99.00% 0.00% 1.04% 0.00% NA
Intermediate  90 82.20% 1.10% 16.67% 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
vg0514548093 C -> T LOC_Os05g25100.1 upstream_gene_variant ; 4824.0bp to feature; MODIFIER silent_mutation Average:8.927; most accessible tissue: Zhenshan97 root, score: 12.891 N N N N
vg0514548093 C -> T LOC_Os05g25110.1 intron_variant ; MODIFIER silent_mutation Average:8.927; most accessible tissue: Zhenshan97 root, score: 12.891 N N N N
vg0514548093 C -> DEL N N silent_mutation Average:8.927; most accessible tissue: Zhenshan97 root, score: 12.891 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0514548093 3.88E-06 NA mr1962_2 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