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

Detailed information for vg0105807534:

Variant ID: vg0105807534 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 5807534
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCCCGCCGTCCCTCCGCCCGCCGCCCCGCCGACGCTCCGTTTCCACCCGTCGCCCCTCTGCTCCGCCCGGCGCTTGGCGCCCGCCATCGCTCTGCCCACC[A/G]
CTCTGCGCCGCCCCACCGTCGCTTGCCCTTTTGCAGTGTAGGGGAGAGAGAGAGAGAGTGGGGTAGAGGGATGACATGTGGGACCACATGGGCCCCGCTT

Reverse complement sequence

AAGCGGGGCCCATGTGGTCCCACATGTCATCCCTCTACCCCACTCTCTCTCTCTCTCCCCTACACTGCAAAAGGGCAAGCGACGGTGGGGCGGCGCAGAG[T/C]
GGTGGGCAGAGCGATGGCGGGCGCCAAGCGCCGGGCGGAGCAGAGGGGCGACGGGTGGAAACGGAGCGTCGGCGGGGCGGCGGGCGGAGGGACGGCGGGC

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 78.20% 16.10% 0.40% 5.29% NA
All Indica  2759 84.20% 11.40% 0.29% 4.10% NA
All Japonica  1512 79.40% 20.20% 0.00% 0.33% NA
Aus  269 6.30% 46.80% 3.72% 43.12% NA
Indica I  595 91.60% 8.40% 0.00% 0.00% NA
Indica II  465 78.50% 6.00% 1.08% 14.41% NA
Indica III  913 92.90% 5.80% 0.11% 1.20% NA
Indica Intermediate  786 72.00% 23.30% 0.25% 4.45% NA
Temperate Japonica  767 95.70% 4.20% 0.00% 0.13% NA
Tropical Japonica  504 70.60% 29.00% 0.00% 0.40% NA
Japonica Intermediate  241 46.10% 53.10% 0.00% 0.83% NA
VI/Aromatic  96 83.30% 5.20% 1.04% 10.42% NA
Intermediate  90 83.30% 10.00% 0.00% 6.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0105807534 A -> G LOC_Os01g10880.1 upstream_gene_variant ; 511.0bp to feature; MODIFIER silent_mutation Average:94.573; most accessible tissue: Minghui63 young leaf, score: 99.275 N N N N
vg0105807534 A -> G LOC_Os01g10890.1 downstream_gene_variant ; 2023.0bp to feature; MODIFIER silent_mutation Average:94.573; most accessible tissue: Minghui63 young leaf, score: 99.275 N N N N
vg0105807534 A -> G LOC_Os01g10870-LOC_Os01g10880 intergenic_region ; MODIFIER silent_mutation Average:94.573; most accessible tissue: Minghui63 young leaf, score: 99.275 N N N N
vg0105807534 A -> DEL N N silent_mutation Average:94.573; most accessible tissue: Minghui63 young leaf, score: 99.275 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)
vg0105807534 A G 0.0 0.0 0.0 0.0 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0105807534 NA 9.93E-07 mr1207 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
vg0105807534 1.08E-06 NA mr1498 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
vg0105807534 1.27E-06 1.18E-10 mr1769 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
vg0105807534 1.50E-06 NA mr1951 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
vg0105807534 NA 6.52E-06 mr1155_2 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
vg0105807534 NA 5.45E-07 mr1180_2 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
vg0105807534 NA 1.42E-06 mr1183_2 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
vg0105807534 NA 6.21E-10 mr1310_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
vg0105807534 NA 5.57E-08 mr1498_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
vg0105807534 NA 5.87E-06 mr1740_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
vg0105807534 2.79E-08 2.66E-13 mr1769_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
vg0105807534 8.53E-06 5.78E-12 mr1769_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
vg0105807534 NA 8.33E-07 mr1792_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
vg0105807534 NA 1.10E-08 mr1829_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
vg0105807534 NA 3.22E-06 mr1924_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
vg0105807534 NA 7.64E-09 mr1943_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