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Table 2 Summary of a subset of results found in this analysis

From: Evaluation of whole-genome DNA methylation sequencing library preparation protocols

Short Name Kapa NEB PBAT Swift Low NEB Low Swift
Sample A B A B A B A B A B A B
# Sequenced Reads (Millions) 347.5 607.9 355.6 389.9 127.9 124.1 395.8 368.2 453.7 408.6 392.7 449.8
Low Quality Bases Trimmed (R1) 2.3 1.8 1.0 1.0 0.9 0.9 0.6 0.6 1.2 1.1 1.1 0.8
Low Quality Bases Trimmed (R2) 2.0 1.7 1.1 1.0 5.9 3.4 0.7 0.7 1.2 1.2 1.0 0.8
Insert Size 208.1 228.0 285.4 297.8 299.3 300.6 222.1 225.0 291.4 290.8 217.9 223.8
Duplicate Rate 27.5 32.4 9.5 9.9 13.5 11.0 12.8 12.1 18.0 16.2 30.7 26.9
% CpGs Covered 74.0 72.3 87.5 87.6 81.8 82.6 85.6 85.2 87.6 87.6 85.5 85.3
% CpG Retention 81.6 79.0 78.5 75.6 74.0 71.1 80.3 77.5 77.8 74.8 79.4 76.9
  1. All values shown are averaged across the two technical replicates, with the exception of PBAT, which only had one technical replicate. The first four rows are taken from the raw data, while the last three rows are taken from the subsampled data, where the BAMs were downsampled to be comparable to PBAT