Visualization of CRISPR-Cas9 mutant clones. A) Coverage across the barcoded amplicon in a variety of different ‘knockout’ CRISPR-Cas9 clones. The wildtype clone has full coverage over the whole amplicon, while the mutant clones have variable indels around the targeted site. Deletions are represented by a gap in the coverage, insertions are shown as black bars, while substitutions are shown in red. Blue bars represent mismatched mapped reads, due to a large deletion. Brown bars show presumed sequencing errors, which each have significant strand bias and commonly occur at the same position in multiple samples. B) The sequencing reads and coverage for clone A6, which is a compound heterozygote with a 1 bp deletion on one allele and a 13 bp deletion on the other allele. The deletions at the targeted site are present at equal proportion on both strands (blue and red), whereas the sequencing error upstream is present only on the red strand.