CRISPResso version 2.3.2
[Command used]:
/opt/conda/bin/CRISPResso --fastq_r1 base_editor.fastq.gz --amplicon_seq GGCCCCAGTGGCTGCTCTGGGGGCCTCCTGAGTTTCTCATCTGTGCCCCTCCCTCCCTGGCCCAGGTGAAGGTGTGGTTCCAGAACCGGAGGACAAAGTACAAACGGCAGAAGCTGGAGGAGGAAGGGCCTGAGTCCGAGCAGAAGAAGAAGGGCTCCCATCACATCAACCGGTGGCGCATTGCCACGAAGCAGGCCAATGGGGAGGACATCGATGTCACCTCCAATGACTAGGGTGG --guide_seq GAGTCCGAGCAGAAGAAGAA --quantification_window_size 20 --quantification_window_center -10 --base_editor_output --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: []
Aligning sequences...
Finished reading fastq file; 3939 unique reads found of 25000 total reads found 
Processing Reads; 0 Completed out of 3939 Unique Reads
Finished reads; N_TOT_READS: 25000 N_COMPUTED_ALN: 3909 N_CACHED_ALN: 21061 N_COMPUTED_NOTALN: 30 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 GAGTCCGAGCAGAAGAAGAA 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 substitutions across reference for Reference
Plotting substitution frequency barplot for Reference
Plotting substitution frequency barplot in quantification window for Reference
Plotting allele distribution around cut for Reference
Plotting log2 nucleotide frequency for Reference
Plotting conversion at Cs around the sgRNA GAGTCCGAGCAGAAGAAGAA for Reference
Plotting non-reference conversion at Cs around the sgRNA GAGTCCGAGCAGAAGAAGAA for Reference
Plotting scaled non-reference conversion at Cs around the sgRNA GAGTCCGAGCAGAAGAAGAA for Reference
Done!
Done!
Removing Intermediate files...
 >=1.0% of reads have modifications at the start or end. Total reads: 24970, Irregular reads: 24970.
 >=0.2% of substitutions were outside of the quantification window. Total substitutions: 17498, Substitutions outside window: 4061.
Analysis Complete!
                                                                               
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