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Detailed information for vg1217311558:

Variant ID: vg1217311558 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 17311558
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTCCTCTACAAGGTATCGACGTGCAGATTCCAGTGATGGTGTCCGCAAATAAGCATGCATATTGCAATATATATAAACTGAATTGTCACTACTACAGACC[C/T]
TATTTTTCCGTATGCTTGAATCGATTATCCCGTGCGGTGGCTCGGCCCACCTACAGCGTCTCGTCTGGGAAAATCAGTATTTTCGCGTGTGGTGCAGTAA

Reverse complement sequence

TTACTGCACCACACGCGAAAATACTGATTTTCCCAGACGAGACGCTGTAGGTGGGCCGAGCCACCGCACGGGATAATCGATTCAAGCATACGGAAAAATA[G/A]
GGTCTGTAGTAGTGACAATTCAGTTTATATATATTGCAATATGCATGCTTATTTGCGGACACCATCACTGGAATCTGCACGTCGATACCTTGTAGAGGAC

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 94.00% 6.00% 0.00% 0.00% NA
All Indica  2759 99.70% 0.30% 0.00% 0.00% NA
All Japonica  1512 83.60% 16.40% 0.00% 0.00% NA
Aus  269 92.20% 7.80% 0.00% 0.00% NA
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.20% 0.80% 0.00% 0.00% NA
Temperate Japonica  767 83.70% 16.30% 0.00% 0.00% NA
Tropical Japonica  504 93.30% 6.70% 0.00% 0.00% NA
Japonica Intermediate  241 63.10% 36.90% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 93.30% 6.70% 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
vg1217311558 C -> T LOC_Os12g29230.1 intron_variant ; MODIFIER silent_mutation Average:50.946; most accessible tissue: Callus, score: 81.632 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1217311558 NA 1.46E-06 mr1180 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
vg1217311558 NA 3.02E-06 mr1183 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
vg1217311558 NA 1.36E-06 mr1503 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
vg1217311558 NA 4.28E-09 mr1807 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
vg1217311558 NA 1.05E-06 mr1051_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
vg1217311558 NA 8.88E-06 mr1617_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