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Detailed information for vg1125369517:

Variant ID: vg1125369517 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 25369517
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 124. )

Flanking Sequence (100 bp) in Reference Genome:


AAAAACACGTATATGAACTTTATATATGTGTATATAAACTTTGTATACGTGTATATAAAATTGGTATACATACGTATAAAAACCCAAAAATACACATATA[C/T]
AAACTTTATATATGTGTATACAAACTTTATATATGTGTATACAAACTTTGTATACATGTATACAAAATTGGTATACGTACATATAAAAACCTAAAAATAC

Reverse complement sequence

GTATTTTTAGGTTTTTATATGTACGTATACCAATTTTGTATACATGTATACAAAGTTTGTATACACATATATAAAGTTTGTATACACATATATAAAGTTT[G/A]
TATATGTGTATTTTTGGGTTTTTATACGTATGTATACCAATTTTATATACACGTATACAAAGTTTATATACACATATATAAAGTTCATATACGTGTTTTT

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 71.80% 7.50% 13.61% 7.13% NA
All Indica  2759 72.00% 1.20% 16.96% 9.86% NA
All Japonica  1512 75.60% 12.40% 8.27% 3.70% NA
Aus  269 52.80% 33.80% 12.27% 1.12% NA
Indica I  595 72.10% 0.80% 20.67% 6.39% NA
Indica II  465 87.10% 0.60% 7.31% 4.95% NA
Indica III  913 68.10% 1.50% 14.13% 16.21% NA
Indica Intermediate  786 67.40% 1.40% 23.16% 8.02% NA
Temperate Japonica  767 96.00% 1.30% 2.48% 0.26% NA
Tropical Japonica  504 39.90% 32.10% 17.46% 10.52% NA
Japonica Intermediate  241 85.50% 6.60% 7.47% 0.41% NA
VI/Aromatic  96 55.20% 35.40% 7.29% 2.08% NA
Intermediate  90 76.70% 7.80% 11.11% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1125369517 C -> T LOC_Os11g42120.1 upstream_gene_variant ; 849.0bp to feature; MODIFIER silent_mutation Average:82.933; most accessible tissue: Minghui63 flower, score: 97.363 N N N N
vg1125369517 C -> T LOC_Os11g42130.1 upstream_gene_variant ; 2422.0bp to feature; MODIFIER silent_mutation Average:82.933; most accessible tissue: Minghui63 flower, score: 97.363 N N N N
vg1125369517 C -> T LOC_Os11g42120-LOC_Os11g42130 intergenic_region ; MODIFIER silent_mutation Average:82.933; most accessible tissue: Minghui63 flower, score: 97.363 N N N N
vg1125369517 C -> DEL N N silent_mutation Average:82.933; most accessible tissue: Minghui63 flower, score: 97.363 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)
vg1125369517 C T 0.0 -0.01 -0.01 -0.01 -0.01 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1125369517 9.25E-06 3.35E-06 mr1238 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
vg1125369517 6.12E-06 NA mr1484 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
vg1125369517 1.38E-07 3.45E-10 mr1662 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
vg1125369517 NA 3.72E-06 mr1662 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
vg1125369517 NA 6.57E-07 mr1723 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
vg1125369517 NA 8.31E-06 mr1238_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
vg1125369517 8.84E-07 7.66E-10 mr1662_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
vg1125369517 NA 7.61E-06 mr1662_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