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Detailed information for vg1126921434:

Variant ID: vg1126921434 (JBrowse)Variation Type: INDEL
Chromosome: chr11Position: 26921434
Reference Allele: TAlternative Allele: G,TGGCGCAGCTGGTCGGCGCAGACG
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCTTCCCTTCTACTAGCTAGCAAGTAGCATCCACGCAGTTCTTCCGAGTTCTTTGAGATTGCCACGGCGAGATGTGGAGCGGGATGGGGCAGGCGGCGAC[T/G,TGGCGCAGCTGGTCGGCGCAGACG]
GTGGCGCAGCTGGTCGGCGCAGACGTCGGCAGGCTCATCTCCATGATCATGCAGGCGGCGTTGCCGGCTCAGCGGAACAAGAAGGAGTGCGAGCAGCTCG

Reverse complement sequence

CGAGCTGCTCGCACTCCTTCTTGTTCCGCTGAGCCGGCAACGCCGCCTGCATGATCATGGAGATGAGCCTGCCGACGTCTGCGCCGACCAGCTGCGCCAC[A/C,CGTCTGCGCCGACCAGCTGCGCCA]
GTCGCCGCCTGCCCCATCCCGCTCCACATCTCGCCGTGGCAATCTCAAAGAACTCGGAAGAACTGCGTGGATGCTACTTGCTAGCTAGTAGAAGGGAAGA

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 49.50% 28.10% 0.91% 14.73% TGGCGCAGCTGGTCGGCGCAGACG: 6.77%
All Indica  2759 63.80% 5.00% 0.69% 20.08% TGGCGCAGCTGGTCGGCGCAGACG: 10.40%
All Japonica  1512 14.50% 76.10% 1.32% 7.14% TGGCGCAGCTGGTCGGCGCAGACG: 0.93%
Aus  269 82.90% 2.20% 0.37% 8.92% TGGCGCAGCTGGTCGGCGCAGACG: 5.58%
Indica I  595 51.60% 10.90% 0.84% 34.45% TGGCGCAGCTGGTCGGCGCAGACG: 2.18%
Indica II  465 87.10% 3.20% 0.00% 3.23% TGGCGCAGCTGGTCGGCGCAGACG: 6.45%
Indica III  913 56.30% 2.00% 0.33% 24.86% TGGCGCAGCTGGTCGGCGCAGACG: 16.54%
Indica Intermediate  786 68.10% 5.10% 1.40% 13.61% TGGCGCAGCTGGTCGGCGCAGACG: 11.83%
Temperate Japonica  767 7.00% 81.50% 2.09% 7.69% TGGCGCAGCTGGTCGGCGCAGACG: 1.69%
Tropical Japonica  504 23.40% 70.80% 0.40% 5.16% TGGCGCAGCTGGTCGGCGCAGACG: 0.20%
Japonica Intermediate  241 19.50% 70.10% 0.83% 9.54% NA
VI/Aromatic  96 91.70% 6.20% 1.04% 1.04% NA
Intermediate  90 55.60% 27.80% 2.22% 10.00% TGGCGCAGCTGGTCGGCGCAGACG: 4.44%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1126921434 T -> DEL LOC_Os11g44510.1 N frameshift_variant Average:69.136; most accessible tissue: Minghui63 root, score: 93.227 N N N N
vg1126921434 T -> TGGCGCAGCTGGTCGGCGCAGACG LOC_Os11g44510.1 frameshift_variant ; p.Val7fs; HIGH frameshift_variant Average:69.136; most accessible tissue: Minghui63 root, score: 93.227 N N N N
vg1126921434 T -> G LOC_Os11g44510.1 synonymous_variant ; p.Thr6Thr; LOW synonymous_codon Average:69.136; most accessible tissue: Minghui63 root, score: 93.227 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)
vg1126921434 T G 0.02 -0.01 -0.01 -0.01 0.01 0.03
vg1126921434 T TGGCG* 0.15 0.09 0.0 -0.07 -0.18 -0.37

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1126921434 NA 2.81E-44 mr1136 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
vg1126921434 NA 7.20E-10 mr1191 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
vg1126921434 NA 2.19E-26 mr1238 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
vg1126921434 NA 5.47E-28 mr1309 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
vg1126921434 NA 1.45E-19 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
vg1126921434 NA 5.67E-23 mr1841 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
vg1126921434 NA 4.20E-13 mr1900 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
vg1126921434 NA 3.55E-10 mr1945 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
vg1126921434 NA 1.21E-27 mr1238_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
vg1126921434 NA 2.22E-07 mr1321_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
vg1126921434 NA 3.39E-20 mr1900_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
vg1126921434 NA 1.96E-18 mr1945_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