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Detailed information for vg0814909467:

Variant ID: vg0814909467 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 14909467
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGTTGACGACCATCTTCCTCGCGGCGGCGTCGTACCTGATCTCCGCCCGCATGACGCCGGCGAGGGTCAAGGTCGGCAGAGCGGTGAAGTTCTGGGACAC[A/G]
ATCTGGTTGACGTCGACGCCGATGTGGTCGATGACGCCGTCCTGTGGATCCCAGGGGTTCCTGCAGGTGTCGAACTCTACGCCGACGGTGCGCGGCGAGG

Reverse complement sequence

CCTCGCCGCGCACCGTCGGCGTAGAGTTCGACACCTGCAGGAACCCCTGGGATCCACAGGACGGCGTCATCGACCACATCGGCGTCGACGTCAACCAGAT[T/C]
GTGTCCCAGAACTTCACCGCTCTGCCGACCTTGACCCTCGCCGGCGTCATGCGGGCGGAGATCAGGTACGACGCCGCCGCGAGGAAGATGGTCGTCAACC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 86.00% 14.00% 0.00% 0.00% NA
All Indica  2759 99.30% 0.70% 0.00% 0.00% NA
All Japonica  1512 58.30% 41.70% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 97.20% 2.80% 0.00% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 99.50% 0.50% 0.00% 0.00% NA
Temperate Japonica  767 46.70% 53.30% 0.00% 0.00% NA
Tropical Japonica  504 71.60% 28.40% 0.00% 0.00% NA
Japonica Intermediate  241 67.60% 32.40% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 84.40% 15.60% 0.00% 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
vg0814909467 A -> G LOC_Os08g24670.1 synonymous_variant ; p.Ile167Ile; LOW synonymous_codon Average:83.467; most accessible tissue: Minghui63 flag leaf, score: 89.905 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)
vg0814909467 A G 0.03 0.02 0.02 0.0 0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0814909467 NA 6.51E-08 mr1708 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
vg0814909467 NA 1.22E-06 mr1708 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