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Detailed information for vg0137958805:

Variant ID: vg0137958805 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 37958805
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTTGACGTCGAGGAAGAACACCCGAGGTTTCGCGGGCTTCGCGGGGGCGCCGTCCCTGCCCACCAGCTGCTTGCGGGAATGCCTCGCTGGAGGCGGCGGT[G/A]
GGATGGAGACGGCGAAGGTGGAAGGGGAGGACGACGAGGATACGGAGGCGTACGGGGTCACGCGGAGGCGGAGCGAGCGAGGTCTACGGGGCGCCGCCGC

Reverse complement sequence

GCGGCGGCGCCCCGTAGACCTCGCTCGCTCCGCCTCCGCGTGACCCCGTACGCCTCCGTATCCTCGTCGTCCTCCCCTTCCACCTTCGCCGTCTCCATCC[C/T]
ACCGCCGCCTCCAGCGAGGCATTCCCGCAAGCAGCTGGTGGGCAGGGACGGCGCCCCCGCGAAGCCCGCGAAACCTCGGGTGTTCTTCCTCGACGTCAAC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.60% 5.40% 0.00% 0.00% NA
All Indica  2759 97.90% 2.10% 0.00% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 29.00% 71.00% 0.00% 0.00% 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 96.60% 3.40% 0.00% 0.00% NA
Indica Intermediate  786 96.80% 3.20% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 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
vg0137958805 G -> A LOC_Os01g65400.2 missense_variant ; p.Pro56Leu; MODERATE nonsynonymous_codon ; P56L Average:97.527; most accessible tissue: Zhenshan97 flag leaf, score: 99.049 possibly damaging 1.728 TOLERATED 0.39
vg0137958805 G -> A LOC_Os01g65400.4 missense_variant ; p.Pro56Leu; MODERATE nonsynonymous_codon ; P56L Average:97.527; most accessible tissue: Zhenshan97 flag leaf, score: 99.049 possibly damaging 1.728 TOLERATED 0.41
vg0137958805 G -> A LOC_Os01g65400.5 missense_variant ; p.Pro56Leu; MODERATE nonsynonymous_codon ; P56L Average:97.527; most accessible tissue: Zhenshan97 flag leaf, score: 99.049 possibly damaging 1.728 TOLERATED 0.42
vg0137958805 G -> A LOC_Os01g65400.3 missense_variant ; p.Pro56Leu; MODERATE nonsynonymous_codon ; P56L Average:97.527; most accessible tissue: Zhenshan97 flag leaf, score: 99.049 possibly damaging 1.728 TOLERATED 0.41
vg0137958805 G -> A LOC_Os01g65400.1 missense_variant ; p.Pro56Leu; MODERATE nonsynonymous_codon ; P56L Average:97.527; most accessible tissue: Zhenshan97 flag leaf, score: 99.049 possibly damaging 1.728 TOLERATED 0.39

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)
vg0137958805 G A 0.01 0.01 0.01 0.0 0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0137958805 NA 9.27E-09 mr1317 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
vg0137958805 NA 2.87E-08 mr1348 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
vg0137958805 NA 7.70E-07 mr1415 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
vg0137958805 NA 5.40E-08 mr1446 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
vg0137958805 8.52E-06 NA mr1504 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
vg0137958805 NA 7.70E-07 mr1567 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
vg0137958805 NA 1.36E-09 mr1608 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
vg0137958805 NA 5.99E-13 mr1612 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
vg0137958805 NA 8.18E-22 mr1855_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