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Detailed information for vg1209894319:

Variant ID: vg1209894319 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 9894319
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:


ATACGAACATGCTAAGTGTTTCATATGTAATGCATCCCACGCACATTGCAGATTCCACTAGGTGCTGTTACTCTTCGACCTGGAGGCCTGCACCGTCAAC[A/G]
TATATGACTCAATGGATAAAAAAGAGTCTACGTTTGACAAGGTTTTCGAACTTATAGACAGGTATTGTCATAAGTTCCTATGTTAATTAAGAATCTTGTT

Reverse complement sequence

AACAAGATTCTTAATTAACATAGGAACTTATGACAATACCTGTCTATAAGTTCGAAAACCTTGTCAAACGTAGACTCTTTTTTATCCATTGAGTCATATA[T/C]
GTTGACGGTGCAGGCCTCCAGGTCGAAGAGTAACAGCACCTAGTGGAATCTGCAATGTGCGTGGGATGCATTACATATGAAACACTTAGCATGTTCGTAT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 43.50% 18.60% 34.28% 3.58% NA
All Indica  2759 46.20% 13.90% 37.84% 2.03% NA
All Japonica  1512 43.50% 31.10% 24.07% 1.39% NA
Aus  269 21.60% 1.90% 53.16% 23.42% NA
Indica I  595 46.10% 5.00% 46.89% 2.02% NA
Indica II  465 32.30% 33.50% 31.83% 2.37% NA
Indica III  913 57.10% 8.30% 32.53% 2.08% NA
Indica Intermediate  786 42.10% 15.40% 40.71% 1.78% NA
Temperate Japonica  767 25.00% 49.50% 24.51% 0.91% NA
Tropical Japonica  504 68.70% 7.30% 23.02% 0.99% NA
Japonica Intermediate  241 49.40% 22.00% 24.90% 3.73% NA
VI/Aromatic  96 31.20% 2.10% 42.71% 23.96% NA
Intermediate  90 40.00% 22.20% 31.11% 6.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1209894319 A -> DEL N N silent_mutation Average:25.087; most accessible tissue: Minghui63 young leaf, score: 50.756 N N N N
vg1209894319 A -> G LOC_Os12g17290.1 intron_variant ; MODIFIER silent_mutation Average:25.087; most accessible tissue: Minghui63 young leaf, score: 50.756 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1209894319 NA 4.69E-09 mr1002 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
vg1209894319 NA 9.89E-08 mr1002 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
vg1209894319 NA 6.68E-08 mr1425 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
vg1209894319 NA 2.13E-06 mr1425 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
vg1209894319 2.56E-07 2.06E-15 mr1002_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
vg1209894319 NA 1.06E-06 mr1002_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
vg1209894319 NA 1.50E-08 mr1002_2 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
vg1209894319 NA 8.68E-07 mr1928_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