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Detailed information for vg1112946292:

Variant ID: vg1112946292 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 12946292
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.87, G: 0.13, others allele: 0.00, population size: 53. )

Flanking Sequence (100 bp) in Reference Genome:


ACCTCCATCATCTTCTTCATAATACCTCCCTTGTTGCTGCTTGTCATATTTCCTCTAATACTTGTTAATAATTCTAGCCGAATTCATCTAAAAACTTTTA[G/C]
TCCTGCTTCCATCGGCTGTTCTACCTGCTGTATGTACCATATTGACCAGGAAAGGGTTACCATCGACCTTCATCGGCTTCTTTGAGTCATCAAATTTAAT

Reverse complement sequence

ATTAAATTTGATGACTCAAAGAAGCCGATGAAGGTCGATGGTAACCCTTTCCTGGTCAATATGGTACATACAGCAGGTAGAACAGCCGATGGAAGCAGGA[C/G]
TAAAAGTTTTTAGATGAATTCGGCTAGAATTATTAACAAGTATTAGAGGAAATATGACAAGCAGCAACAAGGGAGGTATTATGAAGAAGATGATGGAGGT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 43.20% 17.90% 11.19% 27.70% NA
All Indica  2759 16.90% 20.90% 17.80% 44.36% NA
All Japonica  1512 95.50% 1.40% 0.53% 2.58% NA
Aus  269 1.50% 84.00% 6.32% 8.18% NA
Indica I  595 41.20% 17.10% 13.11% 28.57% NA
Indica II  465 14.80% 10.30% 18.49% 56.34% NA
Indica III  913 3.30% 28.00% 21.69% 46.99% NA
Indica Intermediate  786 15.60% 21.80% 16.41% 46.18% NA
Temperate Japonica  767 96.90% 2.10% 0.26% 0.78% NA
Tropical Japonica  504 92.50% 0.80% 0.99% 5.75% NA
Japonica Intermediate  241 97.50% 0.40% 0.41% 1.66% NA
VI/Aromatic  96 88.50% 10.40% 1.04% 0.00% NA
Intermediate  90 44.40% 15.60% 13.33% 26.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1112946292 G -> DEL N N silent_mutation Average:15.903; most accessible tissue: Callus, score: 46.294 N N N N
vg1112946292 G -> C LOC_Os11g22510.1 downstream_gene_variant ; 4927.0bp to feature; MODIFIER silent_mutation Average:15.903; most accessible tissue: Callus, score: 46.294 N N N N
vg1112946292 G -> C LOC_Os11g22530.1 intron_variant ; MODIFIER silent_mutation Average:15.903; most accessible tissue: Callus, score: 46.294 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1112946292 NA 1.24E-07 mr1028 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
vg1112946292 NA 1.45E-06 mr1073 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
vg1112946292 NA 1.97E-10 mr1232 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
vg1112946292 NA 1.38E-06 mr1245 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
vg1112946292 NA 4.33E-10 mr1307 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
vg1112946292 NA 6.25E-07 mr1369 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
vg1112946292 NA 2.24E-07 mr1373 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
vg1112946292 NA 4.35E-07 mr1392 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
vg1112946292 NA 2.70E-07 mr1420 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
vg1112946292 NA 4.93E-07 mr1445 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
vg1112946292 NA 2.85E-09 mr1453 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
vg1112946292 NA 1.95E-06 mr1523 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
vg1112946292 NA 2.49E-08 mr1545 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
vg1112946292 NA 3.39E-08 mr1652 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
vg1112946292 NA 6.62E-06 mr1681 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
vg1112946292 NA 1.76E-07 mr1764 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