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Detailed information for vg1123361505:

Variant ID: vg1123361505 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 23361505
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.69, T: 0.31, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:


TGAAATCCGTCAGAAGGGATGAGGATTTTCCCCCCTGAATTCATCGTGTTCTTCGTCAGGATCTCCATGACACCGTGGTCCTGGCTTGCTGCACTGACCG[A/T]
AAACGCAAGGGAGAAGAGCACGGGAAGTTGGGCAATGATAAACAAAGCATCTGTGCTCAGTGATGTCAATGATAAAGTCAATTTCTCCAGGTTTTGTAGC

Reverse complement sequence

GCTACAAAACCTGGAGAAATTGACTTTATCATTGACATCACTGAGCACAGATGCTTTGTTTATCATTGCCCAACTTCCCGTGCTCTTCTCCCTTGCGTTT[T/A]
CGGTCAGTGCAGCAAGCCAGGACCACGGTGTCATGGAGATCCTGACGAAGAACACGATGAATTCAGGGGGGAAAATCCTCATCCCTTCTGACGGATTTCA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 52.90% 44.80% 0.25% 2.09% NA
All Indica  2759 47.50% 50.80% 0.25% 1.49% NA
All Japonica  1512 63.40% 36.10% 0.26% 0.26% NA
Aus  269 53.90% 45.70% 0.00% 0.37% NA
Indica I  595 72.80% 23.40% 0.50% 3.36% NA
Indica II  465 8.40% 91.40% 0.00% 0.22% NA
Indica III  913 56.70% 43.00% 0.11% 0.11% NA
Indica Intermediate  786 40.70% 56.50% 0.38% 2.42% NA
Temperate Japonica  767 72.00% 27.50% 0.52% 0.00% NA
Tropical Japonica  504 59.50% 40.30% 0.00% 0.20% NA
Japonica Intermediate  241 44.00% 54.80% 0.00% 1.24% NA
VI/Aromatic  96 43.80% 5.20% 1.04% 50.00% NA
Intermediate  90 47.80% 46.70% 0.00% 5.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1123361505 A -> T LOC_Os11g39230.1 missense_variant ; p.Ser639Thr; MODERATE nonsynonymous_codon ; S639T Average:86.568; most accessible tissue: Zhenshan97 root, score: 93.72 unknown unknown TOLERATED 0.13
vg1123361505 A -> DEL LOC_Os11g39230.1 N frameshift_variant Average:86.568; most accessible tissue: Zhenshan97 root, score: 93.72 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)
vg1123361505 A T -0.01 -0.02 -0.02 -0.01 -0.03 -0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1123361505 NA 1.85E-13 Grain_length Ind_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg1123361505 NA 8.28E-06 mr1308 Ind_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
vg1123361505 NA 4.74E-06 mr1904 Ind_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
vg1123361505 NA 2.22E-08 mr1942 Ind_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
vg1123361505 NA 5.60E-08 mr1942_2 Ind_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