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Detailed information for vg1222877206:

Variant ID: vg1222877206 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 22877206
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:


TGGCAGCTCTATTTAGCCAAAACAAATAAAAGAATGATGGGACCCATTTGTCAGCCCAGTCCGTCTTCTTCTCCCCATCCTCTCTTTCGCTCGATCTCAG[C/T]
TACTGTCGCCGATGACCATCTCCACCAGACGTGCACCGAAGGCAAAGCCAAGACAAGCAGCGCTGAGATTTAGGGGTGACACGAGGCAGTGGAACTAACA

Reverse complement sequence

TGTTAGTTCCACTGCCTCGTGTCACCCCTAAATCTCAGCGCTGCTTGTCTTGGCTTTGCCTTCGGTGCACGTCTGGTGGAGATGGTCATCGGCGACAGTA[G/A]
CTGAGATCGAGCGAAAGAGAGGATGGGGAGAAGAAGACGGACTGGGCTGACAAATGGGTCCCATCATTCTTTTATTTGTTTTGGCTAAATAGAGCTGCCA

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 81.40% 18.50% 0.11% 0.00% NA
All Indica  2759 69.00% 30.80% 0.18% 0.00% NA
All Japonica  1512 99.60% 0.40% 0.00% 0.00% NA
Aus  269 97.00% 3.00% 0.00% 0.00% NA
Indica I  595 86.70% 13.30% 0.00% 0.00% NA
Indica II  465 73.50% 26.50% 0.00% 0.00% NA
Indica III  913 51.60% 48.10% 0.33% 0.00% NA
Indica Intermediate  786 73.00% 26.70% 0.25% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 99.20% 0.80% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 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
vg1222877206 C -> T LOC_Os12g37290.1 downstream_gene_variant ; 4993.0bp to feature; MODIFIER silent_mutation Average:63.582; most accessible tissue: Minghui63 young leaf, score: 78.443 N N N N
vg1222877206 C -> T LOC_Os12g37280.1 intron_variant ; MODIFIER silent_mutation Average:63.582; most accessible tissue: Minghui63 young leaf, score: 78.443 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1222877206 NA 1.68E-06 mr1038 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
vg1222877206 3.34E-06 1.44E-06 mr1389 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
vg1222877206 7.78E-06 3.05E-07 mr1389 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
vg1222877206 3.48E-07 1.40E-07 mr1038_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
vg1222877206 2.85E-07 5.60E-08 mr1038_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
vg1222877206 2.93E-08 4.27E-08 mr1389_2 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
vg1222877206 7.25E-08 3.15E-09 mr1389_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