Search for Variation information by Variation ID:

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

Detailed information for vg0137829682:

Variant ID: vg0137829682 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 37829682
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.86, A: 0.14, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:


CGCGCTCTACCTGCTGGCGCTGGCGCAGGGCTTCCACAAGCCCTGCTCCGAGGCCATCGGCGCCGACCAGTTCGCCGACGACGCCGACCCCGGCGCGAAC[G/A]
CGTCGCGGAGCTCCTACTTCAACTGGTTCCACTTCTCCACATCCTGGGGCTACGCCGTCGCCACGACATTGCTGAGCTACGTCGAGGACAACGTCAGCTG

Reverse complement sequence

CAGCTGACGTTGTCCTCGACGTAGCTCAGCAATGTCGTGGCGACGGCGTAGCCCCAGGATGTGGAGAAGTGGAACCAGTTGAAGTAGGAGCTCCGCGACG[C/T]
GTTCGCGCCGGGGTCGGCGTCGTCGGCGAACTGGTCGGCGCCGATGGCCTCGGAGCAGGGCTTGTGGAAGCCCTGCGCCAGCGCCAGCAGGTAGAGCGCG

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 77.00% 22.70% 0.04% 0.32% NA
All Indica  2759 68.10% 31.30% 0.07% 0.54% NA
All Japonica  1512 99.60% 0.40% 0.00% 0.00% NA
Aus  269 29.40% 70.60% 0.00% 0.00% NA
Indica I  595 62.90% 36.30% 0.00% 0.84% NA
Indica II  465 84.70% 14.40% 0.00% 0.86% NA
Indica III  913 58.10% 41.60% 0.00% 0.33% NA
Indica Intermediate  786 73.90% 25.40% 0.25% 0.38% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 85.60% 14.40% 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
vg0137829682 G -> A LOC_Os01g65190.1 missense_variant ; p.Ala184Thr; MODERATE nonsynonymous_codon ; A184T Average:88.882; most accessible tissue: Zhenshan97 flower, score: 94.841 benign 0.864 TOLERATED 0.09
vg0137829682 G -> DEL LOC_Os01g65190.1 N frameshift_variant Average:88.882; most accessible tissue: Zhenshan97 flower, score: 94.841 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)
vg0137829682 G A -0.02 -0.01 -0.01 -0.02 -0.02 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0137829682 7.56E-06 1.07E-07 mr1375 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
vg0137829682 6.94E-09 NA mr1517 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
vg0137829682 2.51E-14 1.21E-16 mr1517 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
vg0137829682 6.14E-08 NA mr1538 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
vg0137829682 8.77E-11 3.34E-13 mr1538 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
vg0137829682 1.70E-10 NA mr1517_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
vg0137829682 9.66E-18 1.18E-17 mr1517_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
vg0137829682 3.07E-08 NA mr1538_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
vg0137829682 4.07E-13 1.31E-18 mr1538_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