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Detailed information for vg1125606899:

Variant ID: vg1125606899 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 25606899
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:


ACTACACTATTAATACCTAGTCACACATGTCATACACACACTGTATCTTGAAGTCCGTGCTACAGCGCCTATAAATCTATAGCCCGCTACTCTTCTCTCT[C/T]
ATCATTTATCTCTTTAAAATATGTTTGTAGCTGGCTTATAGCCTGCTATTGTACATGCTTTTAGTAGTACCCTTGTGCTGGAGGTGCCGAAGAGGATGGA

Reverse complement sequence

TCCATCCTCTTCGGCACCTCCAGCACAAGGGTACTACTAAAAGCATGTACAATAGCAGGCTATAAGCCAGCTACAAACATATTTTAAAGAGATAAATGAT[G/A]
AGAGAGAAGAGTAGCGGGCTATAGATTTATAGGCGCTGTAGCACGGACTTCAAGATACAGTGTGTGTATGACATGTGTGACTAGGTATTAATAGTGTAGT

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 94.80% 5.20% 0.02% 0.00% NA
All Indica  2759 98.80% 1.10% 0.04% 0.00% NA
All Japonica  1512 89.00% 11.00% 0.00% 0.00% NA
Aus  269 85.10% 14.90% 0.00% 0.00% NA
Indica I  595 97.50% 2.50% 0.00% 0.00% NA
Indica II  465 99.60% 0.20% 0.22% 0.00% NA
Indica III  913 98.80% 1.20% 0.00% 0.00% NA
Indica Intermediate  786 99.50% 0.50% 0.00% 0.00% NA
Temperate Japonica  767 79.80% 20.20% 0.00% 0.00% NA
Tropical Japonica  504 99.00% 1.00% 0.00% 0.00% NA
Japonica Intermediate  241 97.50% 2.50% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 91.10% 8.90% 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
vg1125606899 C -> T LOC_Os11g42510.1 upstream_gene_variant ; 4481.0bp to feature; MODIFIER silent_mutation Average:83.479; most accessible tissue: Minghui63 root, score: 98.171 N N N N
vg1125606899 C -> T LOC_Os11g42520.1 upstream_gene_variant ; 1509.0bp to feature; MODIFIER silent_mutation Average:83.479; most accessible tissue: Minghui63 root, score: 98.171 N N N N
vg1125606899 C -> T LOC_Os11g42525.1 upstream_gene_variant ; 4886.0bp to feature; MODIFIER silent_mutation Average:83.479; most accessible tissue: Minghui63 root, score: 98.171 N N N N
vg1125606899 C -> T LOC_Os11g42510.2 upstream_gene_variant ; 3410.0bp to feature; MODIFIER silent_mutation Average:83.479; most accessible tissue: Minghui63 root, score: 98.171 N N N N
vg1125606899 C -> T LOC_Os11g42510-LOC_Os11g42520 intergenic_region ; MODIFIER silent_mutation Average:83.479; most accessible tissue: Minghui63 root, score: 98.171 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)
vg1125606899 C T 0.05 0.0 0.0 0.02 0.03 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1125606899 NA 6.77E-07 mr1229 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
vg1125606899 1.01E-06 NA mr1549 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
vg1125606899 NA 8.53E-06 mr1354_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