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Detailed information for vg1214243584:

Variant ID: vg1214243584 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 14243584
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGAAAGCAAGAACTTGTCGAAACAAAACTAAAGCAAAAGAGTAGCGATGCACCAAAGTTGCATTGAACGTGTGTGTTGTTAATTACATAGGGCTCGGGGT[C/T]
TATTTATACCCTGGAATTACAAGACATGCCCACACCAGACACGACTATTATCTCTAACAAACTCTAAGATACCATAAGTCTTTGCGGCAGACTTTTGCCC

Reverse complement sequence

GGGCAAAAGTCTGCCGCAAAGACTTATGGTATCTTAGAGTTTGTTAGAGATAATAGTCGTGTCTGGTGTGGGCATGTCTTGTAATTCCAGGGTATAAATA[G/A]
ACCCCGAGCCCTATGTAATTAACAACACACACGTTCAATGCAACTTTGGTGCATCGCTACTCTTTTGCTTTAGTTTTGTTTCGACAAGTTCTTGCTTTCG

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 86.60% 3.90% 2.62% 6.88% NA
All Indica  2759 85.10% 0.50% 3.01% 11.42% NA
All Japonica  1512 86.20% 10.90% 2.45% 0.40% NA
Aus  269 97.80% 1.90% 0.37% 0.00% NA
Indica I  595 56.50% 0.30% 8.07% 35.13% NA
Indica II  465 96.10% 0.00% 1.29% 2.58% NA
Indica III  913 96.70% 0.40% 0.88% 1.97% NA
Indica Intermediate  786 86.80% 0.90% 2.67% 9.67% NA
Temperate Japonica  767 95.70% 2.90% 1.30% 0.13% NA
Tropical Japonica  504 78.80% 18.50% 2.18% 0.60% NA
Japonica Intermediate  241 71.80% 20.70% 6.64% 0.83% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 88.90% 3.30% 3.33% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1214243584 C -> DEL N N silent_mutation Average:20.229; most accessible tissue: Minghui63 young leaf, score: 39.381 N N N N
vg1214243584 C -> T LOC_Os12g24820.1 upstream_gene_variant ; 668.0bp to feature; MODIFIER silent_mutation Average:20.229; most accessible tissue: Minghui63 young leaf, score: 39.381 N N N N
vg1214243584 C -> T LOC_Os12g24810.1 downstream_gene_variant ; 1062.0bp to feature; MODIFIER silent_mutation Average:20.229; most accessible tissue: Minghui63 young leaf, score: 39.381 N N N N
vg1214243584 C -> T LOC_Os12g24830.1 downstream_gene_variant ; 4232.0bp to feature; MODIFIER silent_mutation Average:20.229; most accessible tissue: Minghui63 young leaf, score: 39.381 N N N N
vg1214243584 C -> T LOC_Os12g24810-LOC_Os12g24820 intergenic_region ; MODIFIER silent_mutation Average:20.229; most accessible tissue: Minghui63 young leaf, score: 39.381 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1214243584 NA 3.67E-10 mr1018 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
vg1214243584 NA 4.99E-09 mr1019 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
vg1214243584 NA 1.55E-09 mr1022 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
vg1214243584 NA 1.74E-09 mr1236 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
vg1214243584 NA 4.50E-08 mr1558_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
vg1214243584 NA 5.88E-09 mr1916_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
vg1214243584 NA 2.66E-06 mr1944_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