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Detailed information for vg0212053945:

Variant ID: vg0212053945 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 12053945
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGCTTCCAAGCGCAGCCGCCGAATCCTCCATCTCCGGTCAGCATAGCTCCCGCTCGGCCGCGCCGCTCATCCCTCACCGGCACACCGCACCGTCCTCCAC[C/T]
GCTCGCCGTCGCCGCCGAGAAGAGGGACACAGCTGCCGTGCGCGTCCGAGTGGATGTGGTGTGAGGCGGCCGGGTTTGAACTAGCCAACGTCATATATAC

Reverse complement sequence

GTATATATGACGTTGGCTAGTTCAAACCCGGCCGCCTCACACCACATCCACTCGGACGCGCACGGCAGCTGTGTCCCTCTTCTCGGCGGCGACGGCGAGC[G/A]
GTGGAGGACGGTGCGGTGTGCCGGTGAGGGATGAGCGGCGCGGCCGAGCGGGAGCTATGCTGACCGGAGATGGAGGATTCGGCGGCTGCGCTTGGAAGCT

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 93.50% 5.90% 0.61% 0.00% NA
All Indica  2759 99.70% 0.30% 0.00% 0.00% NA
All Japonica  1512 80.80% 17.40% 1.85% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 98.90% 1.10% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.50% 0.50% 0.00% 0.00% NA
Temperate Japonica  767 96.00% 3.40% 0.65% 0.00% NA
Tropical Japonica  504 57.50% 38.90% 3.57% 0.00% NA
Japonica Intermediate  241 80.90% 17.00% 2.07% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 92.20% 6.70% 1.11% 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
vg0212053945 C -> T LOC_Os02g20420.1 upstream_gene_variant ; 1852.0bp to feature; MODIFIER silent_mutation Average:75.27; most accessible tissue: Minghui63 panicle, score: 82.797 N N N N
vg0212053945 C -> T LOC_Os02g20430.1 upstream_gene_variant ; 888.0bp to feature; MODIFIER silent_mutation Average:75.27; most accessible tissue: Minghui63 panicle, score: 82.797 N N N N
vg0212053945 C -> T LOC_Os02g20420-LOC_Os02g20430 intergenic_region ; MODIFIER silent_mutation Average:75.27; most accessible tissue: Minghui63 panicle, score: 82.797 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0212053945 NA 3.21E-07 mr1543 Jap_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
vg0212053945 NA 6.56E-06 mr1871 Jap_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
vg0212053945 1.75E-06 1.42E-08 mr1042_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
vg0212053945 NA 1.46E-07 mr1502_2 Jap_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
vg0212053945 9.78E-06 1.18E-09 mr1543_2 Jap_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
vg0212053945 4.55E-07 6.64E-11 mr1742_2 Jap_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
vg0212053945 1.15E-07 8.21E-10 mr1871_2 Jap_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