Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1214707367:

Variant ID: vg1214707367 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 14707367
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGCACATAAACCATTTCTTGCATACTTAATTAAACTCCTACTCTGAAACATTGATATGGTGCTATGCAATAGTTCTTTCAATCTTGCAACTAATGTCAAG[C/T]
AACTTTGTTATGGCCTTCTTGTTCCATGATTCAGGTGGCCTTGTAATGCTAGTATATGACCTTCTCATCGAGAAAATACTTAGTTAATGAGGAAGAATAT

Reverse complement sequence

ATATTCTTCCTCATTAACTAAGTATTTTCTCGATGAGAAGGTCATATACTAGCATTACAAGGCCACCTGAATCATGGAACAAGAAGGCCATAACAAAGTT[G/A]
CTTGACATTAGTTGCAAGATTGAAAGAACTATTGCATAGCACCATATCAATGTTTCAGAGTAGGAGTTTAATTAAGTATGCAAGAAATGGTTTATGTGCT

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 92.10% 7.90% 0.00% 0.00% NA
All Indica  2759 86.80% 13.20% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 79.30% 20.70% 0.00% 0.00% NA
Indica II  465 98.90% 1.10% 0.00% 0.00% NA
Indica III  913 86.60% 13.40% 0.00% 0.00% NA
Indica Intermediate  786 85.40% 14.60% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 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
vg1214707367 C -> T LOC_Os12g25440.1 downstream_gene_variant ; 417.0bp to feature; MODIFIER silent_mutation Average:9.582; most accessible tissue: Zhenshan97 panicle, score: 16.188 N N N N
vg1214707367 C -> T LOC_Os12g25420-LOC_Os12g25440 intergenic_region ; MODIFIER silent_mutation Average:9.582; most accessible tissue: Zhenshan97 panicle, score: 16.188 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1214707367 1.31E-06 1.31E-06 mr1323 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
vg1214707367 6.31E-06 NA mr1326 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
vg1214707367 2.15E-07 2.15E-07 mr1540 Ind_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
vg1214707367 NA 2.96E-06 mr1630 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
vg1214707367 2.16E-06 5.47E-07 mr1732 Ind_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