Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0101338524:

Variant ID: vg0101338524 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 1338524
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CATGTTCAAGCTAGCAGAGAATACGTACGATGAGCCTCTCTGCTTGTTATACAGAGAAGTAGTTCTCTTCTTAGTTGTGCATTTCAGGTGTGCACCTGGG[G/C]
CCTGGGTCCCCGGTGAAGGAGTCACGGCAGACGAAGAGAGGGCGCCACGACCACGAGTCCACCATCTCGCACTGCCCGCACGCGGCGGCGCACGACTCCA

Reverse complement sequence

TGGAGTCGTGCGCCGCCGCGTGCGGGCAGTGCGAGATGGTGGACTCGTGGTCGTGGCGCCCTCTCTTCGTCTGCCGTGACTCCTTCACCGGGGACCCAGG[C/G]
CCCAGGTGCACACCTGAAATGCACAACTAAGAAGAGAACTACTTCTCTGTATAACAAGCAGAGAGGCTCATCGTACGTATTCTCTGCTAGCTTGAACATG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 78.00% 20.60% 0.28% 1.18% NA
All Indica  2759 68.90% 30.10% 0.36% 0.65% NA
All Japonica  1512 89.00% 8.30% 0.20% 2.45% NA
Aus  269 98.10% 1.90% 0.00% 0.00% NA
Indica I  595 69.60% 28.10% 0.50% 1.85% NA
Indica II  465 94.40% 5.40% 0.22% 0.00% NA
Indica III  913 54.80% 44.90% 0.00% 0.33% NA
Indica Intermediate  786 69.60% 29.10% 0.76% 0.51% NA
Temperate Japonica  767 84.20% 15.00% 0.39% 0.39% NA
Tropical Japonica  504 97.80% 1.80% 0.00% 0.40% NA
Japonica Intermediate  241 85.90% 0.80% 0.00% 13.28% NA
VI/Aromatic  96 96.90% 2.10% 0.00% 1.04% NA
Intermediate  90 90.00% 10.00% 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
vg0101338524 G -> DEL LOC_Os01g03310.1 N frameshift_variant Average:84.33; most accessible tissue: Minghui63 young leaf, score: 92.775 N N N N
vg0101338524 G -> C LOC_Os01g03310.1 synonymous_variant ; p.Gly184Gly; LOW synonymous_codon Average:84.33; most accessible tissue: Minghui63 young leaf, score: 92.775 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)
vg0101338524 G C 0.05 0.04 0.0 0.06 0.04 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0101338524 NA 9.07E-06 mr1536 Ind_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
vg0101338524 NA 4.24E-06 mr1660 Ind_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
vg0101338524 NA 3.88E-06 mr1667 Ind_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
vg0101338524 NA 1.03E-09 mr1707 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
vg0101338524 NA 5.54E-06 mr1707 Ind_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
vg0101338524 1.98E-06 2.47E-10 mr1728 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
vg0101338524 2.64E-07 1.79E-07 mr1728 Ind_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
vg0101338524 NA 6.16E-06 mr1742 Ind_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
vg0101338524 NA 2.96E-07 mr1798 Ind_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
vg0101338524 NA 5.54E-06 mr1860 Ind_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
vg0101338524 NA 8.98E-06 mr1566_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
vg0101338524 NA 2.52E-06 mr1566_2 Ind_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
vg0101338524 NA 1.36E-08 mr1860_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
vg0101338524 NA 2.48E-06 mr1860_2 Ind_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
vg0101338524 NA 2.35E-06 mr1954_2 Ind_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