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Detailed information for vg0622361473:

Variant ID: vg0622361473 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 22361473
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGACGCGGACGACGACGCTGGAGCAAGAGGACCGACCCCCATGGCGGTGGGTGACGCAGCGACGGCAGTGTCCACGCTCTCCTGTCGCGCTCCCCGTCCC[C/T]
GCCGCTCGTCGGAGGTGATGGCGCGCCATGGCGGCGTCGGGGCAGATGCTACCGCGGCCGTCGCCAGAACCACCCAGCCGACAGGCATCTCCCGTCGCAG

Reverse complement sequence

CTGCGACGGGAGATGCCTGTCGGCTGGGTGGTTCTGGCGACGGCCGCGGTAGCATCTGCCCCGACGCCGCCATGGCGCGCCATCACCTCCGACGAGCGGC[G/A]
GGGACGGGGAGCGCGACAGGAGAGCGTGGACACTGCCGTCGCTGCGTCACCCACCGCCATGGGGGTCGGTCCTCTTGCTCCAGCGTCGTCGTCCGCGTCA

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 81.20% 18.80% 0.04% 0.00% NA
All Indica  2759 97.50% 2.50% 0.00% 0.00% NA
All Japonica  1512 64.10% 35.90% 0.00% 0.00% NA
Aus  269 31.60% 68.00% 0.37% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 97.40% 2.60% 0.00% 0.00% NA
Indica III  913 96.50% 3.50% 0.00% 0.00% NA
Indica Intermediate  786 96.80% 3.20% 0.00% 0.00% NA
Temperate Japonica  767 74.60% 25.40% 0.00% 0.00% NA
Tropical Japonica  504 57.90% 42.10% 0.00% 0.00% NA
Japonica Intermediate  241 43.60% 56.40% 0.00% 0.00% NA
VI/Aromatic  96 21.90% 78.10% 0.00% 0.00% NA
Intermediate  90 80.00% 18.90% 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
vg0622361473 C -> T LOC_Os06g37770.1 missense_variant ; p.Arg81Cys; MODERATE nonsynonymous_codon ; R81C Average:92.284; most accessible tissue: Minghui63 panicle, score: 97.163 unknown unknown DELETERIOUS 0.00

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)
vg0622361473 C T -0.01 -0.01 -0.01 -0.01 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0622361473 NA 1.59E-08 mr1057 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
vg0622361473 NA 3.90E-13 mr1465 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
vg0622361473 8.30E-06 8.29E-06 mr1465 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
vg0622361473 NA 2.43E-07 mr1559 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
vg0622361473 2.90E-06 3.87E-10 mr1341_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