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Detailed information for vg1224718310:

Variant ID: vg1224718310 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 24718310
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CACCGACATGGCCAGCGGCAGCGACGACGACTCCGCCACCGCGCTCTGACGACGCCCCGCACGAACTGTTCATCTTCTCCACGTCTCGCCGGCGGACGAC[G/T]
ACTTCGCCTCCGCGCTCCGACGACGCCTTGCCGGTGGAGCCAGAGCGGGAGGCGGCGAGCGAGGTTGGGGAGCACGAGCGGCTCGGCGAGCGATGCGCGC

Reverse complement sequence

GCGCGCATCGCTCGCCGAGCCGCTCGTGCTCCCCAACCTCGCTCGCCGCCTCCCGCTCTGGCTCCACCGGCAAGGCGTCGTCGGAGCGCGGAGGCGAAGT[C/A]
GTCGTCCGCCGGCGAGACGTGGAGAAGATGAACAGTTCGTGCGGGGCGTCGTCAGAGCGCGGTGGCGGAGTCGTCGTCGCTGCCGCTGGCCATGTCGGTG

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 90.20% 9.60% 0.15% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 75.10% 24.60% 0.26% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 86.60% 13.00% 0.39% 0.00% NA
Tropical Japonica  504 71.80% 28.20% 0.00% 0.00% NA
Japonica Intermediate  241 45.60% 53.90% 0.41% 0.00% NA
VI/Aromatic  96 20.80% 77.10% 2.08% 0.00% NA
Intermediate  90 92.20% 6.70% 1.11% 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
vg1224718310 G -> T LOC_Os12g39980.1 intron_variant ; MODIFIER silent_mutation Average:80.45; most accessible tissue: Zhenshan97 panicle, score: 92.904 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)
vg1224718310 G T 0.04 0.02 0.05 0.01 0.05 0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1224718310 5.59E-07 NA Grain_thickness All YES 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