CRISPResso version 2.3.2 [Command used]: /opt/conda/bin/CRISPResso -r1 hdr.fastq.gz -a acatttgcttctgacacaactgtgttcactagcaacctcaaacagacaccatggtgcatctgactcctgTggagaagtctgccgttactgccctgtggggcaaggtgaacgtggatgaagttggtggtgaggccctgggcaggttggtatcaaggtta -e acatttgcttctgacacaactgtgttcactagcaacctcaaacagacaccatggtgcaCctgactccGgaggagaagtctgccgttactgcGctgtggggcaaggtgaacgtggatgaagttggtggtgaggccctgggcaggttggtatcaaggtta -c atggtgcatctgactcctgTggagaagtctgccgttactgccctgtggggcaaggtgaacgtggatgaagttggtggtgaggccctgggcag -g TGCACCATGGTGTCTGTTTG --write_cleaned_report --place_report_in_output_folder [Execution log]: CRISPRessoPro not installed Computing quantification windows Added 0 guides with flexible matching Original flexiguides: ['None'] Found guides: [] Mismatch locations: [] Added 0 guides with flexible matching Original flexiguides: ['None'] Found guides: [] Mismatch locations: [] Aligning sequences... Finished reading fastq file; 1107 unique reads found of 25000 total reads found Processing Reads; 0 Completed out of 1107 Unique Reads Finished reads; N_TOT_READS: 25000 N_COMPUTED_ALN: 1107 N_CACHED_ALN: 23893 N_COMPUTED_NOTALN: 0 N_CACHED_NOTALN: 0 Done! Quantifying indels/substitutions... Done! Calculating allele frequencies... Done! Saving processed data... Making Plots... Plotting read bar plot Plotting read class pie chart and bar plot Begin processing plots for amplicon Reference Plotting nucleotide quilt across amplicon Plotting nucleotide distribuition around sgRNA TGCACCATGGTGTCTGTTTG for Reference Plotting indel size distribution for Reference Plotting frequency deletions/insertions for Reference Plotting amplication modifications for Reference Plotting modification frequency for Reference Plotting quantification window locations for Reference Plotting position dependent indel for Reference Plotting global modifications with respect to reference Plotting HDR nucleotide quilt Plotting frameshift analysis for Reference Plotting frameshift frequency for Reference Plotting non-coding mutation positions for Reference Plotting potential splice sites Plotting allele distribution around cut for Reference Done! Begin processing plots for amplicon HDR Plotting nucleotide quilt across amplicon Plotting nucleotide distribuition around sgRNA TGCACCATGGTGTCTGTTTG for HDR Plotting indel size distribution for HDR Plotting frequency deletions/insertions for HDR Plotting amplication modifications for HDR Plotting modification frequency for HDR Plotting quantification window locations for HDR Plotting position dependent indel for HDR Plotting global modifications with respect to reference Plotting frameshift analysis for HDR Plotting frameshift frequency for HDR Plotting non-coding mutation positions for HDR Plotting potential splice sites Plotting allele distribution around cut for HDR Done! Plotting global frameshift in-frame mutations pie chart Plotting global frameshift in-frame mutation profiles Plotting global potential splice sites pie chart Done! Removing Intermediate files... Disproportionate percentages of reads were aligned to amplicon: Reference, Percent of aligned reads aligned to this amplicon: 93.66%. Disproportionate percentages of reads were aligned to amplicon: HDR, Percent of aligned reads aligned to this amplicon: 6.31%. >=0.2% of substitutions were outside of the quantification window. Total substitutions: 3649, Substitutions outside window: 3500. Analysis Complete! _ ' ) .-' (____ C)| \ \ / \___/