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Detailed information for vg0225759132:

Variant ID: vg0225759132 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 25759132
Reference Allele: TAlternative Allele: G
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, T: 0.03, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:


GCTTCTGCCACAAGTCACAAGGCCTCCTTTTTCTCCTATATATGGAGAAAAAAGCGCAAATAAATATTTTCCGCTTTTTAGACTCTGCTGCGCTTTGGGA[T/G]
AAAAACAAGTGAGGAAAATATGCAAAAGAAGGAAGAGTTAATTAATTAATCAACGCTACGTATATGCGCGCCGTGTTACGTATCTCTTGCTGACTTTATA

Reverse complement sequence

TATAAAGTCAGCAAGAGATACGTAACACGGCGCGCATATACGTAGCGTTGATTAATTAATTAACTCTTCCTTCTTTTGCATATTTTCCTCACTTGTTTTT[A/C]
TCCCAAAGCGCAGCAGAGTCTAAAAAGCGGAAAATATTTATTTGCGCTTTTTTCTCCATATATAGGAGAAAAAGGAGGCCTTGTGACTTGTGGCAGAAGC

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 68.10% 31.80% 0.08% 0.00% NA
All Indica  2759 96.70% 3.20% 0.07% 0.00% NA
All Japonica  1512 16.30% 83.50% 0.13% 0.00% NA
Aus  269 94.10% 5.90% 0.00% 0.00% NA
Indica I  595 99.20% 0.70% 0.17% 0.00% NA
Indica II  465 98.30% 1.50% 0.22% 0.00% NA
Indica III  913 96.30% 3.70% 0.00% 0.00% NA
Indica Intermediate  786 94.40% 5.60% 0.00% 0.00% NA
Temperate Japonica  767 20.30% 79.40% 0.26% 0.00% NA
Tropical Japonica  504 12.70% 87.30% 0.00% 0.00% NA
Japonica Intermediate  241 11.20% 88.80% 0.00% 0.00% NA
VI/Aromatic  96 4.20% 95.80% 0.00% 0.00% NA
Intermediate  90 53.30% 46.70% 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
vg0225759132 T -> G LOC_Os02g42850.2 upstream_gene_variant ; 707.0bp to feature; MODIFIER silent_mutation Average:84.825; most accessible tissue: Minghui63 root, score: 97.393 N N N N
vg0225759132 T -> G LOC_Os02g42850.1 upstream_gene_variant ; 708.0bp to feature; MODIFIER silent_mutation Average:84.825; most accessible tissue: Minghui63 root, score: 97.393 N N N N
vg0225759132 T -> G LOC_Os02g42840-LOC_Os02g42850 intergenic_region ; MODIFIER silent_mutation Average:84.825; most accessible tissue: Minghui63 root, score: 97.393 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)
vg0225759132 T G -0.03 -0.04 -0.03 -0.05 -0.03 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0225759132 NA 6.50E-07 mr1220 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
vg0225759132 NA 3.01E-15 mr1324 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
vg0225759132 NA 1.34E-12 mr1335 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
vg0225759132 9.06E-06 NA mr1480 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
vg0225759132 9.34E-08 9.34E-08 mr1480 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
vg0225759132 NA 1.61E-07 mr1604 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
vg0225759132 NA 8.50E-06 mr1692 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
vg0225759132 NA 2.91E-11 mr1751 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
vg0225759132 NA 4.15E-07 mr1824 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
vg0225759132 NA 1.44E-08 mr1986 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
vg0225759132 NA 1.27E-14 mr1324_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