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Detailed information for vg1128914308:

Variant ID: vg1128914308 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 28914308
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.93, T: 0.07, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:


CTGCGCCACTATTTTTTTTTTCTTTTCCCCTTCCTTTTCTTTAGCTGCTTCTGGGCTGGGCCTTCAATTATGTACTGGGCCCGGCCCAACTCCATCTTGT[T/C]
TCTTTTCTTTTCTATATGTAACTACGCTTTTTTGCTTTGTTTGCCTGACTTAGCTGGGCTGCTCTCTGAGAGATGGGCCACTGTTGTTTCGATCTGCCCA

Reverse complement sequence

TGGGCAGATCGAAACAACAGTGGCCCATCTCTCAGAGAGCAGCCCAGCTAAGTCAGGCAAACAAAGCAAAAAAGCGTAGTTACATATAGAAAAGAAAAGA[A/G]
ACAAGATGGAGTTGGGCCGGGCCCAGTACATAATTGAAGGCCCAGCCCAGAAGCAGCTAAAGAAAAGGAAGGGGAAAAGAAAAAAAAAATAGTGGCGCAG

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 63.70% 36.10% 0.19% 0.00% NA
All Indica  2759 89.20% 10.50% 0.22% 0.00% NA
All Japonica  1512 14.90% 85.10% 0.00% 0.00% NA
Aus  269 77.70% 21.60% 0.74% 0.00% NA
Indica I  595 93.40% 6.40% 0.17% 0.00% NA
Indica II  465 94.20% 5.40% 0.43% 0.00% NA
Indica III  913 84.40% 15.60% 0.00% 0.00% NA
Indica Intermediate  786 88.70% 10.90% 0.38% 0.00% NA
Temperate Japonica  767 17.60% 82.40% 0.00% 0.00% NA
Tropical Japonica  504 11.50% 88.50% 0.00% 0.00% NA
Japonica Intermediate  241 13.30% 86.70% 0.00% 0.00% NA
VI/Aromatic  96 69.80% 29.20% 1.04% 0.00% NA
Intermediate  90 51.10% 48.90% 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
vg1128914308 T -> C LOC_Os11g47944.1 downstream_gene_variant ; 4608.0bp to feature; MODIFIER silent_mutation Average:96.671; most accessible tissue: Callus, score: 99.765 N N N N
vg1128914308 T -> C LOC_Os11g47940.1 intron_variant ; MODIFIER silent_mutation Average:96.671; most accessible tissue: Callus, score: 99.765 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)
vg1128914308 T C -0.01 0.02 0.02 0.02 0.02 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1128914308 NA 1.61E-06 mr1329_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
vg1128914308 NA 4.17E-09 mr1517_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
vg1128914308 NA 9.08E-07 mr1524_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
vg1128914308 NA 3.15E-08 mr1683_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
vg1128914308 NA 4.53E-13 mr1838_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
vg1128914308 NA 4.32E-06 mr1982_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
vg1128914308 NA 2.62E-06 mr1994_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