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Detailed information for vg0812629955:

Variant ID: vg0812629955 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 12629955
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:


GGATTGTATTACCAGTAGGAAGTTGAATCTGTTTCTCCCGAAGTAACAAATCAAAAATCTTATCAGCCTTGATGATATCAAAGTCATACCTCTCTTCTTT[T/C]
CCAGAACTCTTCACCCATTGGCATGGTATAACCTTCTTGTTTCTAACCCATTCGGCTGCTGCTATTTCGGAGTCGTCATCATCATCATCATCATCTGATC

Reverse complement sequence

GATCAGATGATGATGATGATGATGACGACTCCGAAATAGCAGCAGCCGAATGGGTTAGAAACAAGAAGGTTATACCATGCCAATGGGTGAAGAGTTCTGG[A/G]
AAAGAAGAGAGGTATGACTTTGATATCATCAAGGCTGATAAGATTTTTGATTTGTTACTTCGGGAGAAACAGATTCAACTTCCTACTGGTAATACAATCC

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 96.70% 0.90% 1.63% 0.83% NA
All Indica  2759 99.80% 0.00% 0.11% 0.04% NA
All Japonica  1512 90.40% 2.50% 4.70% 2.38% NA
Aus  269 98.50% 0.40% 0.74% 0.37% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.90% 0.00% 0.11% 0.00% NA
Indica Intermediate  786 99.60% 0.00% 0.25% 0.13% NA
Temperate Japonica  767 99.30% 0.40% 0.13% 0.13% NA
Tropical Japonica  504 76.40% 5.80% 11.11% 6.75% NA
Japonica Intermediate  241 91.30% 2.50% 5.81% 0.41% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 97.80% 0.00% 1.11% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0812629955 T -> C LOC_Os08g21124.1 synonymous_variant ; p.Gly292Gly; LOW synonymous_codon Average:48.222; most accessible tissue: Minghui63 young leaf, score: 67.374 N N N N
vg0812629955 T -> DEL LOC_Os08g21124.1 N frameshift_variant Average:48.222; most accessible tissue: Minghui63 young leaf, score: 67.374 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0812629955 8.05E-07 2.69E-11 Grain_weight 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
vg0812629955 NA 1.86E-07 mr1951 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
vg0812629955 NA 2.41E-06 mr1557_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
vg0812629955 NA 5.30E-07 mr1562_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
vg0812629955 NA 2.22E-07 mr1696_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
vg0812629955 NA 8.20E-11 mr1769_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
vg0812629955 NA 3.39E-08 mr1819_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
vg0812629955 NA 7.74E-07 mr1849_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
vg0812629955 4.11E-06 6.65E-13 mr1905_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
vg0812629955 NA 3.41E-07 mr1905_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
vg0812629955 NA 9.36E-10 mr1916_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
vg0812629955 NA 5.69E-06 mr1944_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