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!
                                                                               
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