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Detailed information for vg1105911245:

Variant ID: vg1105911245 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 5911245
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, T: 0.08, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:


GTTTTGCAAGGCCATCTAAAGCTTCTGACAAATCTTTAACACAATTACAGCATGACAGATCCAGATGCACCAAATTTTTTAGCTGCTGAAATGATTTCGG[T/C]
AATTCTTTTATCCCAAAACAACCTGATAGGTTCAAATACTTAAGTTCTGTGAGGCTGCCCAATGTTCTCGGTAGAAATCCAATTTTACGGCACACTGATA

Reverse complement sequence

TATCAGTGTGCCGTAAAATTGGATTTCTACCGAGAACATTGGGCAGCCTCACAGAACTTAAGTATTTGAACCTATCAGGTTGTTTTGGGATAAAAGAATT[A/G]
CCGAAATCATTTCAGCAGCTAAAAAATTTGGTGCATCTGGATCTGTCATGCTGTAATTGTGTTAAAGATTTGTCAGAAGCTTTAGATGGCCTTGCAAAAC

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 68.50% 31.40% 0.11% 0.00% NA
All Indica  2759 92.10% 7.80% 0.07% 0.00% NA
All Japonica  1512 25.20% 74.70% 0.13% 0.00% NA
Aus  269 94.40% 5.60% 0.00% 0.00% NA
Indica I  595 97.00% 2.90% 0.17% 0.00% NA
Indica II  465 95.10% 4.70% 0.22% 0.00% NA
Indica III  913 89.70% 10.30% 0.00% 0.00% NA
Indica Intermediate  786 89.40% 10.60% 0.00% 0.00% NA
Temperate Japonica  767 35.20% 64.70% 0.13% 0.00% NA
Tropical Japonica  504 13.50% 86.50% 0.00% 0.00% NA
Japonica Intermediate  241 17.80% 81.70% 0.41% 0.00% NA
VI/Aromatic  96 11.50% 88.50% 0.00% 0.00% NA
Intermediate  90 53.30% 45.60% 1.11% 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
vg1105911245 T -> C LOC_Os11g10760.1 synonymous_variant ; p.Leu233Leu; LOW synonymous_codon Average:68.425; most accessible tissue: Zhenshan97 root, score: 91.389 N N N N

Effects Predicted by Deep Convolutional Neural Networks

For each variant, we constructed two sequences that contain the variation site and the sequence around it, differing only in the variation site. We then used Basenji to predict the chromatin accessibility of each tissue for the two sequences, respectively, and scored the effect of the variant by comparing the changes in chromatin accessibility corresponding to the two genotypes in the 1 kb region around the variation site. The effect score was defined as the logarithmic ratio of the predicted chromatin accessibility of the alternative genotype to the value of the reference genotype.

Var ID Ref Alt Root (RT) Young Leaf (YL) Flag Leaf (FL) Young Panicle (YP) Lemma & Palea (LP) Stamen & Pistil (SP)
vg1105911245 T C 0.01 0.02 0.01 0.0 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1105911245 NA 1.49E-06 mr1171 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
vg1105911245 NA 4.20E-20 mr1580 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
vg1105911245 NA 1.65E-06 mr1740 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
vg1105911245 NA 3.09E-06 mr1748 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
vg1105911245 NA 7.25E-07 mr1797 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
vg1105911245 NA 7.25E-07 mr1801 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
vg1105911245 NA 1.09E-06 mr1851 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
vg1105911245 3.20E-06 3.20E-06 mr1972 Jap_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