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Detailed information for vg0101342775:

Variant ID: vg0101342775 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 1342775
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAATAGCATTTGTTGTCTAGCATAAACTGAGATATCACGAGGATATATGCGTGCATATATTTTGGTATATCCGAGAGGATTGAATATCAGGTGAAAACAG[A/T]
TAAATAAGTAAAAATTCATTAAAATCGGACTTTTTCTTTTTGAAAAATAAAGTATAAACGTATATGCTCATAACATGCGTGCACACTCATGCTATGAACT

Reverse complement sequence

AGTTCATAGCATGAGTGTGCACGCATGTTATGAGCATATACGTTTATACTTTATTTTTCAAAAAGAAAAAGTCCGATTTTAATGAATTTTTACTTATTTA[T/A]
CTGTTTTCACCTGATATTCAATCCTCTCGGATATACCAAAATATATGCACGCATATATCCTCGTGATATCTCAGTTTATGCTAGACAACAAATGCTATTT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 90.50% 8.70% 0.04% 0.76% NA
All Indica  2759 95.10% 4.90% 0.04% 0.04% NA
All Japonica  1512 97.40% 0.30% 0.00% 2.31% NA
Aus  269 10.80% 88.80% 0.37% 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 92.00% 7.80% 0.11% 0.11% NA
Indica Intermediate  786 92.10% 7.90% 0.00% 0.00% NA
Temperate Japonica  767 99.60% 0.10% 0.00% 0.26% NA
Tropical Japonica  504 99.00% 0.60% 0.00% 0.40% NA
Japonica Intermediate  241 87.10% 0.00% 0.00% 12.86% NA
VI/Aromatic  96 80.20% 19.80% 0.00% 0.00% NA
Intermediate  90 83.30% 16.70% 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
vg0101342775 A -> T LOC_Os01g03310.1 upstream_gene_variant ; 3636.0bp to feature; MODIFIER silent_mutation Average:78.438; most accessible tissue: Minghui63 young leaf, score: 96.033 N N N N
vg0101342775 A -> T LOC_Os01g03320.1 upstream_gene_variant ; 498.0bp to feature; MODIFIER silent_mutation Average:78.438; most accessible tissue: Minghui63 young leaf, score: 96.033 N N N N
vg0101342775 A -> T LOC_Os01g03330.1 downstream_gene_variant ; 1782.0bp to feature; MODIFIER silent_mutation Average:78.438; most accessible tissue: Minghui63 young leaf, score: 96.033 N N N N
vg0101342775 A -> T LOC_Os01g03340.1 downstream_gene_variant ; 4792.0bp to feature; MODIFIER silent_mutation Average:78.438; most accessible tissue: Minghui63 young leaf, score: 96.033 N N N N
vg0101342775 A -> T LOC_Os01g03320-LOC_Os01g03330 intergenic_region ; MODIFIER silent_mutation Average:78.438; most accessible tissue: Minghui63 young leaf, score: 96.033 N N N N
vg0101342775 A -> DEL N N silent_mutation Average:78.438; most accessible tissue: Minghui63 young leaf, score: 96.033 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)
vg0101342775 A T 0.01 -0.02 -0.02 0.01 -0.01 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0101342775 NA 3.66E-06 mr1029 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
vg0101342775 NA 3.57E-19 mr1117 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
vg0101342775 NA 3.16E-18 mr1119 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
vg0101342775 NA 3.18E-21 mr1247 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
vg0101342775 NA 5.03E-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
vg0101342775 NA 1.08E-11 mr1471 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
vg0101342775 NA 5.03E-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
vg0101342775 3.98E-06 NA mr1682 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
vg0101342775 NA 4.41E-06 mr1684 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
vg0101342775 NA 7.44E-07 mr1706 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
vg0101342775 NA 3.11E-10 mr1722 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
vg0101342775 5.43E-06 NA mr1754 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
vg0101342775 NA 4.05E-10 mr1047_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
vg0101342775 NA 1.03E-17 mr1113_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
vg0101342775 NA 9.77E-17 mr1114_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
vg0101342775 NA 2.81E-21 mr1117_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
vg0101342775 NA 2.59E-20 mr1119_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
vg0101342775 NA 3.34E-24 mr1120_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
vg0101342775 3.49E-06 NA mr1134_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
vg0101342775 NA 7.77E-09 mr1166_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
vg0101342775 NA 1.31E-18 mr1240_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
vg0101342775 NA 2.53E-24 mr1247_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
vg0101342775 NA 2.85E-21 mr1305_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
vg0101342775 NA 2.09E-06 mr1344_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
vg0101342775 NA 6.04E-16 mr1530_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
vg0101342775 NA 2.73E-08 mr1582_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
vg0101342775 NA 1.15E-17 mr1587_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
vg0101342775 NA 6.84E-14 mr1803_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
vg0101342775 NA 7.64E-18 mr1961_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