Search for Variation information by Variation ID:

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

Detailed information for vg0907968670:

Variant ID: vg0907968670 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 7968670
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, T: 0.00, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:


ATGGAAAAACCATAAATCAAACATTGCAAGGCAGATATAGCAACCTGGATGGAATATATTATATCTCTGTATGTGTGATGTGTTAGTGCCAAATATATTT[G/T]
ATGTAAAGGGGTAGGCTAGCTTGGATGGATGGACTATTATTAGGTAGGCGTGCCACGTCGCTATCAGGTTAAAAGCTTGTTATTCCAAATGTACGCAGCG

Reverse complement sequence

CGCTGCGTACATTTGGAATAACAAGCTTTTAACCTGATAGCGACGTGGCACGCCTACCTAATAATAGTCCATCCATCCAAGCTAGCCTACCCCTTTACAT[C/A]
AAATATATTTGGCACTAACACATCACACATACAGAGATATAATATATTCCATCCAGGTTGCTATATCTGCCTTGCAATGTTTGATTTATGGTTTTTCCAT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 75.50% 24.30% 0.17% 0.00% NA
All Indica  2759 89.30% 10.70% 0.04% 0.00% NA
All Japonica  1512 55.60% 44.00% 0.33% 0.00% NA
Aus  269 72.10% 27.90% 0.00% 0.00% NA
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 85.60% 14.40% 0.00% 0.00% NA
Indica III  913 81.40% 18.50% 0.11% 0.00% NA
Indica Intermediate  786 92.70% 7.30% 0.00% 0.00% NA
Temperate Japonica  767 70.10% 29.20% 0.65% 0.00% NA
Tropical Japonica  504 25.00% 75.00% 0.00% 0.00% NA
Japonica Intermediate  241 73.40% 26.60% 0.00% 0.00% NA
VI/Aromatic  96 6.20% 92.70% 1.04% 0.00% NA
Intermediate  90 71.10% 27.80% 1.11% 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
vg0907968670 G -> T LOC_Os09g13650.1 downstream_gene_variant ; 751.0bp to feature; MODIFIER silent_mutation Average:66.063; most accessible tissue: Minghui63 root, score: 93.274 N N N N
vg0907968670 G -> T LOC_Os09g13650.2 downstream_gene_variant ; 751.0bp to feature; MODIFIER silent_mutation Average:66.063; most accessible tissue: Minghui63 root, score: 93.274 N N N N
vg0907968670 G -> T LOC_Os09g13650.3 downstream_gene_variant ; 751.0bp to feature; MODIFIER silent_mutation Average:66.063; most accessible tissue: Minghui63 root, score: 93.274 N N N N
vg0907968670 G -> T LOC_Os09g13650-LOC_Os09g13660 intergenic_region ; MODIFIER silent_mutation Average:66.063; most accessible tissue: Minghui63 root, score: 93.274 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)
vg0907968670 G T 0.25 -0.08 -0.05 -0.04 -0.12 -0.08

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0907968670 NA 2.75E-13 mr1002 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
vg0907968670 3.29E-06 NA mr1305 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
vg0907968670 NA 3.99E-10 mr1002_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
vg0907968670 NA 1.96E-06 mr1011_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
vg0907968670 NA 4.79E-08 mr1057_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
vg0907968670 NA 7.49E-06 mr1092_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
vg0907968670 NA 5.05E-06 mr1154_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
vg0907968670 NA 2.31E-06 mr1330_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
vg0907968670 NA 1.38E-06 mr1379_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
vg0907968670 NA 1.33E-08 mr1709_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
vg0907968670 NA 3.54E-12 mr1805_2 Jap_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