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Detailed information for vg1218885143:

Variant ID: vg1218885143 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 18885143
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.94, C: 0.07, others allele: 0.00, population size: 159. )

Flanking Sequence (100 bp) in Reference Genome:


ATTTAAGGGGAACTGATCGTATGACACCACATCATCTCGATCAGGGTTTAGAAATATACCATATAGTTTATACTCGAGTATCACAAACCATTTACCTGTA[T/C]
ATGGTAATGGTTAAAGTTGCCCTTTGCGGCTATAGTTGCCTCCTGCGCGAGGACTTAAAAATAAGAACCACTATACAGAGGTGCCATATTGCTAATTAAC

Reverse complement sequence

GTTAATTAGCAATATGGCACCTCTGTATAGTGGTTCTTATTTTTAAGTCCTCGCGCAGGAGGCAACTATAGCCGCAAAGGGCAACTTTAACCATTACCAT[A/G]
TACAGGTAAATGGTTTGTGATACTCGAGTATAAACTATATGGTATATTTCTAAACCCTGATCGAGATGATGTGGTGTCATACGATCAGTTCCCCTTAAAT

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 83.60% 14.70% 1.65% 0.00% NA
All Indica  2759 81.60% 17.20% 1.23% 0.00% NA
All Japonica  1512 98.90% 1.10% 0.00% 0.00% NA
Aus  269 22.30% 69.50% 8.18% 0.00% NA
Indica I  595 91.30% 7.70% 1.01% 0.00% NA
Indica II  465 79.40% 20.00% 0.65% 0.00% NA
Indica III  913 80.80% 17.70% 1.42% 0.00% NA
Indica Intermediate  786 76.50% 22.00% 1.53% 0.00% NA
Temperate Japonica  767 99.20% 0.80% 0.00% 0.00% NA
Tropical Japonica  504 99.00% 1.00% 0.00% 0.00% NA
Japonica Intermediate  241 97.50% 2.50% 0.00% 0.00% NA
VI/Aromatic  96 74.00% 10.40% 15.62% 0.00% NA
Intermediate  90 83.30% 8.90% 7.78% 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
vg1218885143 T -> C LOC_Os12g31380.1 upstream_gene_variant ; 2729.0bp to feature; MODIFIER silent_mutation Average:30.143; most accessible tissue: Zhenshan97 root, score: 51.776 N N N N
vg1218885143 T -> C LOC_Os12g31390.1 downstream_gene_variant ; 777.0bp to feature; MODIFIER silent_mutation Average:30.143; most accessible tissue: Zhenshan97 root, score: 51.776 N N N N
vg1218885143 T -> C LOC_Os12g31390-LOC_Os12g31400 intergenic_region ; MODIFIER silent_mutation Average:30.143; most accessible tissue: Zhenshan97 root, score: 51.776 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1218885143 NA 2.85E-09 mr1458 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
vg1218885143 2.37E-06 2.37E-06 mr1682 Ind_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
vg1218885143 NA 3.59E-06 mr1754 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
vg1218885143 NA 2.68E-06 mr1457_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
vg1218885143 NA 1.54E-10 mr1458_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