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Detailed information for vg1100141300:

Variant ID: vg1100141300 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 141300
Reference Allele: CAlternative Allele: A
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, A: 0.03, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:


GGGGAAAAAAATAATAGGAGATGGGCAGCAGCGCCAAGCTTCCTTTGGTGGATATTGGGGAGGAGGAGGAGGCGTTGGTGTTTGAAGATGAGGAGAAGAC[C/A]
GAGCTGATTAGGGTGCAAGACTTCCGTCGCGTCTGGGAACATCGCTTTAACAGCTAAGGGCATCCACAATGCTATTATTTGGTAATAAGTAATGCTACTA

Reverse complement sequence

TAGTAGCATTACTTATTACCAAATAATAGCATTGTGGATGCCCTTAGCTGTTAAAGCGATGTTCCCAGACGCGACGGAAGTCTTGCACCCTAATCAGCTC[G/T]
GTCTTCTCCTCATCTTCAAACACCAACGCCTCCTCCTCCTCCCCAATATCCACCAAAGGAAGCTTGGCGCTGCTGCCCATCTCCTATTATTTTTTTCCCC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 52.20% 47.40% 0.19% 0.19% NA
All Indica  2759 84.80% 14.60% 0.29% 0.29% NA
All Japonica  1512 1.50% 98.50% 0.00% 0.00% NA
Aus  269 29.40% 70.60% 0.00% 0.00% NA
Indica I  595 97.50% 1.80% 0.50% 0.17% NA
Indica II  465 53.80% 45.60% 0.00% 0.65% NA
Indica III  913 92.40% 7.30% 0.11% 0.11% NA
Indica Intermediate  786 84.60% 14.50% 0.51% 0.38% NA
Temperate Japonica  767 1.30% 98.70% 0.00% 0.00% NA
Tropical Japonica  504 1.20% 98.80% 0.00% 0.00% NA
Japonica Intermediate  241 2.50% 97.50% 0.00% 0.00% NA
VI/Aromatic  96 9.40% 90.60% 0.00% 0.00% NA
Intermediate  90 22.20% 75.60% 1.11% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1100141300 C -> A LOC_Os11g01260.1 synonymous_variant ; p.Thr27Thr; LOW synonymous_codon Average:67.811; most accessible tissue: Callus, score: 88.234 N N N N
vg1100141300 C -> DEL LOC_Os11g01260.1 N frameshift_variant Average:67.811; most accessible tissue: Callus, score: 88.234 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)
vg1100141300 C A 0.11 0.01 0.0 0.03 0.06 0.06

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1100141300 NA 5.89E-19 mr1598 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
vg1100141300 NA 3.85E-12 mr1609 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
vg1100141300 NA 4.62E-10 mr1889 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
vg1100141300 NA 4.07E-08 mr1896 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
vg1100141300 NA 1.10E-08 mr1903 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
vg1100141300 NA 2.01E-14 mr1907 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
vg1100141300 NA 2.43E-10 mr1934 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
vg1100141300 NA 4.31E-09 mr1935 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
vg1100141300 NA 5.69E-09 mr1835_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
vg1100141300 NA 6.21E-16 mr1836_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
vg1100141300 NA 3.73E-13 mr1889_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
vg1100141300 NA 1.49E-07 mr1896_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
vg1100141300 NA 1.88E-13 mr1907_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
vg1100141300 NA 4.23E-10 mr1934_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