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Detailed information for vg1223208705:

Variant ID: vg1223208705 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 23208705
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACCTTAGCTCAATCTCAATCCCCTCCATGCCGCCTCCTTCGCCTGTCTCTAATTGCTGCTGCCTTCGTGCCTCTCCGCTCGCCGCCACCACAGCAACCAC[C/T]
GTCCTCCCACATGTCGGTGCTGCCCTTTCCTCCCTCCCTATCGCGCCATCCTCTCCGATGCCATCTCCTCCTCCTCATCACTGGATGCGGGTGAGGAGTT

Reverse complement sequence

AACTCCTCACCCGCATCCAGTGATGAGGAGGAGGAGATGGCATCGGAGAGGATGGCGCGATAGGGAGGGAGGAAAGGGCAGCACCGACATGTGGGAGGAC[G/A]
GTGGTTGCTGTGGTGGCGGCGAGCGGAGAGGCACGAAGGCAGCAGCAATTAGAGACAGGCGAAGGAGGCGGCATGGAGGGGATTGAGATTGAGCTAAGGT

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 97.90% 1.70% 0.47% 0.00% NA
All Indica  2759 99.70% 0.00% 0.25% 0.00% NA
All Japonica  1512 94.00% 5.10% 0.93% 0.00% NA
Aus  269 99.60% 0.00% 0.37% 0.00% NA
Indica I  595 99.30% 0.00% 0.67% 0.00% NA
Indica II  465 99.80% 0.00% 0.22% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.00% 0.25% 0.00% NA
Temperate Japonica  767 98.30% 1.20% 0.52% 0.00% NA
Tropical Japonica  504 85.90% 12.30% 1.79% 0.00% NA
Japonica Intermediate  241 97.10% 2.50% 0.41% 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
vg1223208705 C -> T LOC_Os12g37800.1 upstream_gene_variant ; 242.0bp to feature; MODIFIER silent_mutation Average:38.492; most accessible tissue: Callus, score: 71.054 N N N N
vg1223208705 C -> T LOC_Os12g37790.1 downstream_gene_variant ; 2756.0bp to feature; MODIFIER silent_mutation Average:38.492; most accessible tissue: Callus, score: 71.054 N N N N
vg1223208705 C -> T LOC_Os12g37790-LOC_Os12g37800 intergenic_region ; MODIFIER silent_mutation Average:38.492; most accessible tissue: Callus, score: 71.054 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1223208705 NA 5.82E-06 mr1236 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
vg1223208705 NA 3.76E-06 mr1518 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
vg1223208705 NA 1.31E-07 mr1676 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
vg1223208705 NA 4.41E-09 mr1951 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
vg1223208705 3.82E-06 3.71E-12 mr1676_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