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Detailed information for vg1216678067:

Variant ID: vg1216678067 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 16678067
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TAGTCAAACCACGAACAAGATCCAAACCACTTAACCTCGTGAGATGATCAAAACCAACATATCCAAGTCCACAATGCCAAAACATTACATCCTTATTAAA[T/C]
TTAGCAACCAAACATGTTATTACAAGTGAAACATGATTTTCAAAATCAGCTTTAAATACTCTTCCATAGCGAGAAATATTCAACACAGAATCACCACAAG

Reverse complement sequence

CTTGTGGTGATTCTGTGTTGAATATTTCTCGCTATGGAAGAGTATTTAAAGCTGATTTTGAAAATCATGTTTCACTTGTAATAACATGTTTGGTTGCTAA[A/G]
TTTAATAAGGATGTAATGTTTTGGCATTGTGGACTTGGATATGTTGGTTTTGATCATCTCACGAGGTTAAGTGGTTTGGATCTTGTTCGTGGTTTGACTA

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 52.50% 18.40% 0.61% 28.52% NA
All Indica  2759 74.60% 1.80% 0.58% 23.05% NA
All Japonica  1512 22.80% 52.40% 0.26% 24.60% NA
Aus  269 10.80% 1.50% 1.49% 86.25% NA
Indica I  595 89.40% 1.30% 0.00% 9.24% NA
Indica II  465 74.60% 2.40% 1.51% 21.51% NA
Indica III  913 70.90% 0.10% 0.44% 28.59% NA
Indica Intermediate  786 67.60% 3.80% 0.64% 27.99% NA
Temperate Japonica  767 13.00% 84.40% 0.00% 2.61% NA
Tropical Japonica  504 30.40% 5.80% 0.79% 63.10% NA
Japonica Intermediate  241 37.80% 48.10% 0.00% 14.11% NA
VI/Aromatic  96 9.40% 0.00% 3.12% 87.50% NA
Intermediate  90 45.60% 25.60% 2.22% 26.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1216678067 T -> C LOC_Os12g28240.1 synonymous_variant ; p.Lys176Lys; LOW synonymous_codon Average:11.713; most accessible tissue: Callus, score: 29.034 N N N N
vg1216678067 T -> DEL LOC_Os12g28240.1 N frameshift_variant Average:11.713; most accessible tissue: Callus, score: 29.034 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1216678067 NA 3.19E-10 mr1011_2 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
vg1216678067 NA 8.76E-09 mr1011_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
vg1216678067 NA 7.47E-09 mr1030_2 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
vg1216678067 NA 7.09E-06 mr1030_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
vg1216678067 NA 6.58E-17 mr1162_2 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
vg1216678067 1.18E-08 1.18E-08 mr1162_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
vg1216678067 NA 2.36E-06 mr1715_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
vg1216678067 NA 1.26E-07 mr1749_2 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
vg1216678067 NA 3.22E-08 mr1754_2 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
vg1216678067 NA 2.24E-14 mr1790_2 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
vg1216678067 NA 9.31E-10 mr1821_2 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