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Detailed information for vg1208553492:

Variant ID: vg1208553492 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 8553492
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.68, T: 0.32, others allele: 0.00, population size: 81. )

Flanking Sequence (100 bp) in Reference Genome:


GCGGCATAATAGGCCAGCCGTGTAGGCGGAGACACCAGTCGGCGGCGGCGAAGGCAAGCCGGTCGGTGAAGATGTGGTCGCCCATGAATGGTGGTGTGAC[T/C]
AACCAACCTTATAGGCGAGGACATCAGTCGGCAACAGCAGTGCTGTGGTCATTACATATAAACAACAAAAAATACCAAGAGATTAATCAGATTTACAGAG

Reverse complement sequence

CTCTGTAAATCTGATTAATCTCTTGGTATTTTTTGTTGTTTATATGTAATGACCACAGCACTGCTGTTGCCGACTGATGTCCTCGCCTATAAGGTTGGTT[A/G]
GTCACACCACCATTCATGGGCGACCACATCTTCACCGACCGGCTTGCCTTCGCCGCCGCCGACTGGTGTCTCCGCCTACACGGCTGGCCTATTATGCCGC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 45.60% 20.30% 19.74% 14.37% NA
All Indica  2759 44.90% 9.90% 30.05% 15.22% NA
All Japonica  1512 55.80% 40.30% 0.93% 2.98% NA
Aus  269 7.40% 8.90% 26.39% 57.25% NA
Indica I  595 51.40% 15.80% 28.07% 4.71% NA
Indica II  465 28.60% 14.80% 35.05% 21.51% NA
Indica III  913 51.40% 1.80% 26.73% 20.15% NA
Indica Intermediate  786 42.00% 11.80% 32.44% 13.74% NA
Temperate Japonica  767 30.80% 63.90% 1.04% 4.30% NA
Tropical Japonica  504 86.30% 10.90% 0.79% 1.98% NA
Japonica Intermediate  241 71.40% 27.00% 0.83% 0.83% NA
VI/Aromatic  96 17.70% 25.00% 8.33% 48.96% NA
Intermediate  90 40.00% 33.30% 12.22% 14.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1208553492 T -> C LOC_Os12g14939-LOC_Os12g14960 intergenic_region ; MODIFIER silent_mutation Average:26.944; most accessible tissue: Minghui63 panicle, score: 53.77 N N N N
vg1208553492 T -> DEL N N silent_mutation Average:26.944; most accessible tissue: Minghui63 panicle, score: 53.77 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1208553492 NA 4.47E-11 Heading_date Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg1208553492 NA 7.37E-13 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
vg1208553492 NA 5.24E-13 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
vg1208553492 NA 7.19E-08 mr1013 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
vg1208553492 NA 1.25E-09 mr1031 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
vg1208553492 NA 2.25E-06 mr1034 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
vg1208553492 NA 2.26E-08 mr1056 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
vg1208553492 NA 4.20E-07 mr1163 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
vg1208553492 5.51E-09 2.02E-18 mr1002_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
vg1208553492 3.22E-10 6.97E-21 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
vg1208553492 NA 2.36E-08 mr1010_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
vg1208553492 NA 5.71E-11 mr1011_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
vg1208553492 NA 3.10E-09 mr1011_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
vg1208553492 NA 1.33E-15 mr1013_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
vg1208553492 NA 3.93E-10 mr1013_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
vg1208553492 2.80E-06 8.82E-16 mr1031_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
vg1208553492 NA 1.74E-12 mr1031_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
vg1208553492 NA 7.70E-06 mr1330_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
vg1208553492 NA 5.67E-08 mr1563_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
vg1208553492 NA 5.71E-07 mr1792_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
vg1208553492 NA 4.01E-06 mr1870_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
vg1208553492 NA 1.76E-11 mr1879_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
vg1208553492 NA 7.88E-06 mr1902_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