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Detailed information for vg0125082086:

Variant ID: vg0125082086 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 25082086
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CAAAGATCGGCAAGCTGCTGGAATCCATCTAAGTACCTCGTAGATGCTCTAGGAGCCCTCCCCTAGCCATGTCTCACTCACATCACCCCGATCACCTTCA[C/T]
GGCTTAACTATGCCACTGCCGTCCTAGCCGTTAGCTCAACCACAAACCAAATTAACCCCTCCGCCGCCGCTCGCCGTCGCCGGAGAACCCTAGCTCCCTC

Reverse complement sequence

GAGGGAGCTAGGGTTCTCCGGCGACGGCGAGCGGCGGCGGAGGGGTTAATTTGGTTTGTGGTTGAGCTAACGGCTAGGACGGCAGTGGCATAGTTAAGCC[G/A]
TGAAGGTGATCGGGGTGATGTGAGTGAGACATGGCTAGGGGAGGGCTCCTAGAGCATCTACGAGGTACTTAGATGGATTCCAGCAGCTTGCCGATCTTTG

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 93.20% 6.80% 0.02% 0.00% NA
All Indica  2759 99.60% 0.40% 0.00% 0.00% NA
All Japonica  1512 85.40% 14.60% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.60% 0.40% 0.00% 0.00% NA
Indica Intermediate  786 99.40% 0.60% 0.00% 0.00% NA
Temperate Japonica  767 99.00% 1.00% 0.00% 0.00% NA
Tropical Japonica  504 63.10% 36.90% 0.00% 0.00% NA
Japonica Intermediate  241 88.80% 11.20% 0.00% 0.00% NA
VI/Aromatic  96 20.80% 78.10% 1.04% 0.00% NA
Intermediate  90 84.40% 15.60% 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
vg0125082086 C -> T LOC_Os01g43774.1 downstream_gene_variant ; 3537.0bp to feature; MODIFIER silent_mutation Average:52.339; most accessible tissue: Minghui63 root, score: 71.702 N N N N
vg0125082086 C -> T LOC_Os01g43774-LOC_Os01g43790 intergenic_region ; MODIFIER silent_mutation Average:52.339; most accessible tissue: Minghui63 root, score: 71.702 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0125082086 4.12E-06 NA mr1104_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
vg0125082086 2.41E-08 NA mr1155_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
vg0125082086 5.19E-07 NA mr1155_2 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
vg0125082086 3.85E-06 NA mr1226_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