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Detailed information for vg1212722693:

Variant ID: vg1212722693 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 12722693
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACAGGTTCGTGAGCTACTGTTGTGAGACATTAACCGTGCCAACCACAAGCCAGCGTAGGCAACGGCTTTACCTTTTGTATAGCATGATTCATTACGGGGT[G/A]
CCAGACTGATAAGCGGTGAGAAGTCCGTGGGGGTCGCTGGGGAGTCCATGCCTCTGGTTATATTTATAGAGGGGGTGATTATGATCCAGGAATGGTGCAC

Reverse complement sequence

GTGCACCATTCCTGGATCATAATCACCCCCTCTATAAATATAACCAGAGGCATGGACTCCCCAGCGACCCCCACGGACTTCTCACCGCTTATCAGTCTGG[C/T]
ACCCCGTAATGAATCATGCTATACAAAAGGTAAAGCCGTTGCCTACGCTGGCTTGTGGTTGGCACGGTTAATGTCTCACAACAGTAGCTCACGAACCTGT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.70% 5.40% 0.42% 0.42% NA
All Indica  2759 90.60% 9.00% 0.36% 0.04% NA
All Japonica  1512 98.20% 0.00% 0.53% 1.26% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 95.30% 4.00% 0.67% 0.00% NA
Indica II  465 96.80% 2.80% 0.43% 0.00% NA
Indica III  913 86.20% 13.80% 0.00% 0.00% NA
Indica Intermediate  786 88.70% 10.70% 0.51% 0.13% NA
Temperate Japonica  767 97.30% 0.00% 0.52% 2.22% NA
Tropical Japonica  504 99.60% 0.00% 0.20% 0.20% NA
Japonica Intermediate  241 98.30% 0.00% 1.24% 0.41% NA
VI/Aromatic  96 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 94.40% 3.30% 2.22% 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
vg1212722693 G -> DEL N N silent_mutation Average:51.903; most accessible tissue: Minghui63 panicle, score: 74.563 N N N N
vg1212722693 G -> A LOC_Os12g22540.1 splice_region_variant&intron_variant ; LOW silent_mutation Average:51.903; most accessible tissue: Minghui63 panicle, score: 74.563 N N N N
vg1212722693 G -> A LOC_Os12g22530.1 downstream_gene_variant ; 4239.0bp to feature; MODIFIER silent_mutation Average:51.903; most accessible tissue: Minghui63 panicle, score: 74.563 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1212722693 NA 2.90E-06 mr1063 Ind_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
vg1212722693 NA 4.15E-06 mr1088 Ind_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
vg1212722693 NA 1.61E-06 mr1180 Ind_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
vg1212722693 NA 2.82E-06 mr1246 Ind_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
vg1212722693 NA 4.38E-07 mr1063_2 Ind_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
vg1212722693 NA 4.51E-06 mr1246_2 Ind_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