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Detailed information for vg1219149829:

Variant ID: vg1219149829 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 19149829
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.00, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:


ACTTAGGAGCTTACCTTGGTGGCCGCTTCTCCATGCAGTCCTCAACTTGCCCCAAAGATGGCTTGAACAACGATAGCCGAGCAGCTAATGCCTTTTCAAA[C/T]
GGAACTGACCCAGTCATCGCCCTGGAAATGTTTTTTTTTTTTCAAAAAATAAAATAAAAATTGAACGCTTGAATGGAAATTTCCATGGATTAATTGGCAA

Reverse complement sequence

TTGCCAATTAATCCATGGAAATTTCCATTCAAGCGTTCAATTTTTATTTTATTTTTTGAAAAAAAAAAAACATTTCCAGGGCGATGACTGGGTCAGTTCC[G/A]
TTTGAAAAGGCATTAGCTGCTCGGCTATCGTTGTTCAAGCCATCTTTGGGGCAAGTTGAGGACTGCATGGAGAAGCGGCCACCAAGGTAAGCTCCTAAGT

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 71.90% 28.00% 0.17% 0.00% NA
All Indica  2759 96.10% 3.70% 0.18% 0.00% NA
All Japonica  1512 35.10% 64.70% 0.13% 0.00% NA
Aus  269 52.80% 46.80% 0.37% 0.00% NA
Indica I  595 98.30% 1.50% 0.17% 0.00% NA
Indica II  465 98.70% 1.30% 0.00% 0.00% NA
Indica III  913 96.30% 3.70% 0.00% 0.00% NA
Indica Intermediate  786 92.70% 6.70% 0.51% 0.00% NA
Temperate Japonica  767 58.10% 41.70% 0.13% 0.00% NA
Tropical Japonica  504 4.80% 95.20% 0.00% 0.00% NA
Japonica Intermediate  241 25.30% 74.30% 0.41% 0.00% NA
VI/Aromatic  96 14.60% 85.40% 0.00% 0.00% NA
Intermediate  90 64.40% 35.60% 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
vg1219149829 C -> T LOC_Os12g31820.1 synonymous_variant ; p.Pro126Pro; LOW synonymous_codon Average:59.516; most accessible tissue: Minghui63 flag leaf, score: 81.566 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1219149829 NA 8.69E-09 mr1047 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
vg1219149829 NA 4.63E-06 mr1189 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
vg1219149829 NA 7.40E-08 mr1617 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
vg1219149829 NA 4.91E-06 mr1729 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
vg1219149829 NA 1.71E-07 mr1779 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
vg1219149829 NA 1.33E-09 mr1084_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
vg1219149829 NA 3.54E-08 mr1205_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
vg1219149829 NA 3.56E-14 mr1454_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
vg1219149829 NA 8.09E-17 mr1521_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
vg1219149829 NA 4.96E-30 mr1580_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
vg1219149829 NA 4.33E-10 mr1646_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
vg1219149829 NA 3.24E-07 mr1668_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
vg1219149829 NA 1.11E-28 mr1825_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