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Detailed information for vg1218320965:

Variant ID: vg1218320965 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 18320965
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, C: 0.02, others allele: 0.00, population size: 213. )

Flanking Sequence (100 bp) in Reference Genome:


TGGGGTAGTTAGGGGTGAACTAAACACAGCCTAAACAAGCCCTAAATGTTGGTGGAGACTAGAGAATGCACAAAAATGACTTCAGATGAATTTCGAAGGC[T/C]
TGAAAAGACATCCTACCATGTTTCCTAACGTACTCGTATGAATTTCGACAGGCTTGAAAAGACATACTACCCTGTTTCCTAATGTACTCGTATGACGTTG

Reverse complement sequence

CAACGTCATACGAGTACATTAGGAAACAGGGTAGTATGTCTTTTCAAGCCTGTCGAAATTCATACGAGTACGTTAGGAAACATGGTAGGATGTCTTTTCA[A/G]
GCCTTCGAAATTCATCTGAAGTCATTTTTGTGCATTCTCTAGTCTCCACCAACATTTAGGGCTTGTTTAGGCTGTGTTTAGTTCACCCCTAACTACCCCA

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 66.90% 33.00% 0.06% 0.00% NA
All Indica  2759 52.80% 47.10% 0.11% 0.00% NA
All Japonica  1512 98.40% 1.60% 0.00% 0.00% NA
Aus  269 24.20% 75.80% 0.00% 0.00% NA
Indica I  595 13.80% 86.20% 0.00% 0.00% NA
Indica II  465 75.50% 24.50% 0.00% 0.00% NA
Indica III  913 65.00% 34.90% 0.11% 0.00% NA
Indica Intermediate  786 54.70% 45.00% 0.25% 0.00% NA
Temperate Japonica  767 98.80% 1.20% 0.00% 0.00% NA
Tropical Japonica  504 99.00% 1.00% 0.00% 0.00% NA
Japonica Intermediate  241 95.90% 4.10% 0.00% 0.00% NA
VI/Aromatic  96 83.30% 16.70% 0.00% 0.00% NA
Intermediate  90 82.20% 17.80% 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
vg1218320965 T -> C LOC_Os12g30520.1 upstream_gene_variant ; 1898.0bp to feature; MODIFIER silent_mutation Average:44.778; most accessible tissue: Callus, score: 72.615 N N N N
vg1218320965 T -> C LOC_Os12g30520-LOC_Os12g30540 intergenic_region ; MODIFIER silent_mutation Average:44.778; most accessible tissue: Callus, score: 72.615 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1218320965 NA 8.87E-08 mr1514 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
vg1218320965 NA 5.39E-07 mr1646 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
vg1218320965 2.85E-06 2.83E-06 mr1954 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
vg1218320965 NA 3.87E-08 mr1482_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
vg1218320965 NA 1.86E-08 mr1829_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
vg1218320965 NA 3.69E-15 mr1902_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