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Detailed information for vg0319293489:

Variant ID: vg0319293489 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 19293489
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.98, C: 0.02, others allele: 0.00, population size: 50. )

Flanking Sequence (100 bp) in Reference Genome:


TCAGAAGCGTTTGAAGAAGCTCAAGGCAAGTCACACAGATCCCAAAAAAACCCTTTGAGCATGTTGAACCCGTTTAAAGCTAATGTTTTATTTCAACTTA[T/C]
GCATTATTTTCGAATGCGATCGGGTGGTGAGCCATTCCTAATTTCCCAGAGGGAAATCTGTGAAGAAGCTCAAGCAGGTTGCTAATGAGGTCGGTTTGCT

Reverse complement sequence

AGCAAACCGACCTCATTAGCAACCTGCTTGAGCTTCTTCACAGATTTCCCTCTGGGAAATTAGGAATGGCTCACCACCCGATCGCATTCGAAAATAATGC[A/G]
TAAGTTGAAATAAAACATTAGCTTTAAACGGGTTCAACATGCTCAAAGGGTTTTTTTGGGATCTGTGTGACTTGCCTTGAGCTTCTTCAAACGCTTCTGA

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 58.10% 39.30% 1.04% 1.59% NA
All Indica  2759 31.90% 63.90% 1.56% 2.65% NA
All Japonica  1512 99.00% 0.80% 0.13% 0.07% NA
Aus  269 82.50% 17.10% 0.37% 0.00% NA
Indica I  595 46.20% 51.80% 1.34% 0.67% NA
Indica II  465 24.50% 68.00% 3.01% 4.52% NA
Indica III  913 30.70% 67.00% 0.33% 1.97% NA
Indica Intermediate  786 26.70% 67.20% 2.29% 3.82% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 98.40% 1.40% 0.20% 0.00% NA
Japonica Intermediate  241 97.90% 1.20% 0.41% 0.41% NA
VI/Aromatic  96 94.80% 2.10% 2.08% 1.04% NA
Intermediate  90 64.40% 34.40% 1.11% 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
vg0319293489 T -> C LOC_Os03g33750.1 upstream_gene_variant ; 274.0bp to feature; MODIFIER silent_mutation Average:61.775; most accessible tissue: Minghui63 root, score: 72.958 N N N N
vg0319293489 T -> C LOC_Os03g33740.1 downstream_gene_variant ; 3130.0bp to feature; MODIFIER silent_mutation Average:61.775; most accessible tissue: Minghui63 root, score: 72.958 N N N N
vg0319293489 T -> C LOC_Os03g33740-LOC_Os03g33750 intergenic_region ; MODIFIER silent_mutation Average:61.775; most accessible tissue: Minghui63 root, score: 72.958 N N N N
vg0319293489 T -> DEL N N silent_mutation Average:61.775; most accessible tissue: Minghui63 root, score: 72.958 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0319293489 NA 8.17E-06 mr1179 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
vg0319293489 NA 1.60E-07 mr1221 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
vg0319293489 NA 2.06E-08 mr1624 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
vg0319293489 NA 3.56E-07 mr1735 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
vg0319293489 NA 3.01E-07 mr1735 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
vg0319293489 NA 1.38E-07 mr1756 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
vg0319293489 NA 2.49E-07 mr1785 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
vg0319293489 NA 4.89E-06 mr1837 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
vg0319293489 NA 7.10E-07 mr1844 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
vg0319293489 NA 3.33E-09 mr1624_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
vg0319293489 NA 1.93E-07 mr1837_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
vg0319293489 NA 4.96E-09 mr1850_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
vg0319293489 NA 2.25E-06 mr1925_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