Search for Variation information by Variation ID:

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

Detailed information for vg1207257056:

Variant ID: vg1207257056 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 7257056
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, C: 0.01, others allele: 0.00, population size: 213. )

Flanking Sequence (100 bp) in Reference Genome:


GGAGGACTGCGAAAGTGAAAAGGAGGTGCAGAAACTAGAGCGCATGTTAGCGGACCACAAAACAGCGTTGTACCCAGGTTGCGAGAAGGGCTACAAAAAG[T/C]
TGAGTACCATCCTAGAATTCTTGCAATGGAAGGCTAAAAATGGTGTAAGTGACAAGGCATTCGGCGAGTTATTGAAACTCGTAAAGAACATTCTTCCGAA

Reverse complement sequence

TTCGGAAGAATGTTCTTTACGAGTTTCAATAACTCGCCGAATGCCTTGTCACTTACACCATTTTTAGCCTTCCATTGCAAGAATTCTAGGATGGTACTCA[A/G]
CTTTTTGTAGCCCTTCTCGCAACCTGGGTACAACGCTGTTTTGTGGTCCGCTAACATGCGCTCTAGTTTCTGCACCTCCTTTTCACTTTCGCAGTCCTCC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 88.10% 11.20% 0.72% 0.00% NA
All Indica  2759 87.50% 12.00% 0.47% 0.00% NA
All Japonica  1512 98.50% 0.10% 1.32% 0.00% NA
Aus  269 47.20% 52.80% 0.00% 0.00% NA
Indica I  595 89.60% 9.60% 0.84% 0.00% NA
Indica II  465 90.30% 9.00% 0.65% 0.00% NA
Indica III  913 88.60% 11.30% 0.11% 0.00% NA
Indica Intermediate  786 83.10% 16.40% 0.51% 0.00% NA
Temperate Japonica  767 97.30% 0.10% 2.61% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 49.00% 50.00% 1.04% 0.00% NA
Intermediate  90 95.60% 4.40% 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
vg1207257056 T -> C LOC_Os12g13070.1 synonymous_variant ; p.Leu162Leu; LOW synonymous_codon Average:26.959; most accessible tissue: Minghui63 panicle, score: 53.77 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1207257056 6.92E-06 6.44E-06 mr1324 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
vg1207257056 1.62E-06 1.46E-08 mr1347 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
vg1207257056 NA 6.39E-06 mr1347 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
vg1207257056 NA 3.62E-08 mr1705 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
vg1207257056 NA 3.57E-06 mr1734 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
vg1207257056 NA 4.78E-06 mr1808 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
vg1207257056 1.48E-06 1.29E-08 mr1815 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
vg1207257056 5.99E-07 8.25E-06 mr1964 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