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Detailed information for vg0130651782:

Variant ID: vg0130651782 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 30651782
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGCAGGCCGACCCGCGAGTTTAAATAAATAATAATTTATGGGTTTTCGCGTCGTGGCCCGGCTTGCCGCATCTAAATATACAAGTGAATCGATCTATAAA[C/T]
CTATCTATAAATCAAATTCATAGTTAATCCGTTAGTCAAACCGGCGGGTTACGCACTATTTTTACCTATAAGCGGGTTCGCGGGTAAACCCACTTGCACC

Reverse complement sequence

GGTGCAAGTGGGTTTACCCGCGAACCCGCTTATAGGTAAAAATAGTGCGTAACCCGCCGGTTTGACTAACGGATTAACTATGAATTTGATTTATAGATAG[G/A]
TTTATAGATCGATTCACTTGTATATTTAGATGCGGCAAGCCGGGCCACGACGCGAAAACCCATAAATTATTATTTATTTAAACTCGCGGGTCGGCCTGCT

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 93.10% 6.60% 0.32% 0.00% NA
All Indica  2759 99.60% 0.40% 0.00% 0.00% NA
All Japonica  1512 85.40% 13.60% 0.99% 0.00% NA
Aus  269 96.70% 3.30% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.00% 1.00% 0.00% 0.00% NA
Temperate Japonica  767 87.10% 11.90% 1.04% 0.00% NA
Tropical Japonica  504 87.30% 11.90% 0.79% 0.00% NA
Japonica Intermediate  241 76.30% 22.40% 1.24% 0.00% NA
VI/Aromatic  96 22.90% 77.10% 0.00% 0.00% NA
Intermediate  90 85.60% 14.40% 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
vg0130651782 C -> T LOC_Os01g53340.1 upstream_gene_variant ; 1534.0bp to feature; MODIFIER silent_mutation Average:55.181; most accessible tissue: Callus, score: 87.384 N N N N
vg0130651782 C -> T LOC_Os01g53350.1 upstream_gene_variant ; 3507.0bp to feature; MODIFIER silent_mutation Average:55.181; most accessible tissue: Callus, score: 87.384 N N N N
vg0130651782 C -> T LOC_Os01g53350.2 upstream_gene_variant ; 3507.0bp to feature; MODIFIER silent_mutation Average:55.181; most accessible tissue: Callus, score: 87.384 N N N N
vg0130651782 C -> T LOC_Os01g53330.1 downstream_gene_variant ; 2435.0bp to feature; MODIFIER silent_mutation Average:55.181; most accessible tissue: Callus, score: 87.384 N N N N
vg0130651782 C -> T LOC_Os01g53340-LOC_Os01g53350 intergenic_region ; MODIFIER silent_mutation Average:55.181; most accessible tissue: Callus, score: 87.384 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0130651782 NA 3.03E-11 mr1070 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
vg0130651782 NA 1.56E-10 mr1128 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
vg0130651782 3.13E-06 NA mr1128_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