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Detailed information for vg0808042725:

Variant ID: vg0808042725 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 8042725
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCCCCCTCTCCCTCCCTTCTCTCTTGTCTTGCTCTCTTCAATCTCTCTCTCTCTCTCTCCATCTCCTTCCTCTTCCGCGCGCTGCCACGGAGGCGGCGAC[T/C]
GCTCCCTCGGCGAGAGGAGAGGTGGCGGTGGCAGGAGCTGGAGGGGAGCCCGCGGAGGCCTGGCGGCTAGAGGGGATCCCGCGGCGGCCCAACGGATGGA

Reverse complement sequence

TCCATCCGTTGGGCCGCCGCGGGATCCCCTCTAGCCGCCAGGCCTCCGCGGGCTCCCCTCCAGCTCCTGCCACCGCCACCTCTCCTCTCGCCGAGGGAGC[A/G]
GTCGCCGCCTCCGTGGCAGCGCGCGGAAGAGGAAGGAGATGGAGAGAGAGAGAGAGAGATTGAAGAGAGCAAGACAAGAGAGAAGGGAGGGAGAGGGGGA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 65.60% 32.20% 0.04% 2.14% NA
All Indica  2759 95.90% 4.10% 0.04% 0.00% NA
All Japonica  1512 11.50% 81.90% 0.00% 6.61% NA
Aus  269 52.40% 47.60% 0.00% 0.00% NA
Indica I  595 93.80% 6.20% 0.00% 0.00% NA
Indica II  465 97.00% 3.00% 0.00% 0.00% NA
Indica III  913 98.60% 1.30% 0.11% 0.00% NA
Indica Intermediate  786 93.60% 6.40% 0.00% 0.00% NA
Temperate Japonica  767 2.90% 94.10% 0.00% 3.00% NA
Tropical Japonica  504 22.00% 75.20% 0.00% 2.78% NA
Japonica Intermediate  241 17.00% 56.80% 0.00% 26.14% NA
VI/Aromatic  96 85.40% 14.60% 0.00% 0.00% NA
Intermediate  90 63.30% 34.40% 1.11% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0808042725 T -> C LOC_Os08g13510.1 upstream_gene_variant ; 4333.0bp to feature; MODIFIER silent_mutation Average:74.922; most accessible tissue: Zhenshan97 young leaf, score: 89.112 N N N N
vg0808042725 T -> C LOC_Os08g13520.1 upstream_gene_variant ; 2018.0bp to feature; MODIFIER silent_mutation Average:74.922; most accessible tissue: Zhenshan97 young leaf, score: 89.112 N N N N
vg0808042725 T -> C LOC_Os08g13530.1 downstream_gene_variant ; 4236.0bp to feature; MODIFIER silent_mutation Average:74.922; most accessible tissue: Zhenshan97 young leaf, score: 89.112 N N N N
vg0808042725 T -> C LOC_Os08g13520-LOC_Os08g13530 intergenic_region ; MODIFIER silent_mutation Average:74.922; most accessible tissue: Zhenshan97 young leaf, score: 89.112 N N N N
vg0808042725 T -> DEL N N silent_mutation Average:74.922; most accessible tissue: Zhenshan97 young leaf, score: 89.112 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)
vg0808042725 T C 0.0 0.0 0.0 0.0 0.0 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0808042725 NA 4.39E-06 mr1219 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
vg0808042725 NA 4.40E-06 mr1317 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
vg0808042725 NA 3.03E-06 mr1881 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
vg0808042725 NA 1.05E-15 mr1968 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
vg0808042725 NA 5.25E-06 mr1201_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
vg0808042725 NA 3.67E-07 mr1205_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
vg0808042725 NA 5.87E-09 mr1219_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
vg0808042725 NA 2.59E-10 mr1228_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
vg0808042725 NA 2.56E-12 mr1258_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
vg0808042725 NA 1.76E-06 mr1274_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
vg0808042725 NA 7.79E-07 mr1275_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
vg0808042725 1.24E-06 2.37E-09 mr1334_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
vg0808042725 NA 3.31E-07 mr1376_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
vg0808042725 NA 7.79E-07 mr1407_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
vg0808042725 NA 1.41E-07 mr1431_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
vg0808042725 5.81E-08 NA mr1480_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
vg0808042725 NA 1.16E-13 mr1714_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
vg0808042725 NA 6.48E-09 mr1751_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
vg0808042725 NA 1.07E-11 mr1830_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
vg0808042725 NA 6.41E-08 mr1855_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
vg0808042725 NA 2.86E-06 mr1869_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
vg0808042725 NA 6.41E-09 mr1909_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
vg0808042725 NA 1.43E-06 mr1914_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
vg0808042725 NA 4.08E-08 mr1921_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
vg0808042725 1.32E-08 2.14E-27 mr1968_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
vg0808042725 NA 1.18E-07 mr1968_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