CRISPResso version 2.3.2
[Command used]:
/opt/conda/bin/CRISPResso -r1 allele_specific.fastq.gz -a CGAGAGCCGCAGCCATGAACGGCACAGAGGGCCCCAATTTTTATGTGCCCTTCTCCAACGTCACAGGCGTGGTGCGGAGCCACTTCGAGCAGCCGCAGTACTACCTGGCGGAACCATGGCAGTTCTCCATGCTGGCAGCGTACATGTTCCTGCTCATCGTGCTGGG,CGAGAGCCGCAGCCATGAACGGCACAGAGGGCCCCAATTTTTATGTGCCCTTCTCCAACGTCACAGGCGTGGTGCGGAGCCCCTTCGAGCAGCCGCAGTACTACCTGGCGGAACCATGGCAGTTCTCCATGCTGGCAGCGTACATGTTCCTGCTCATCGTGCTGGG -an P23H,WT -g GTGCGGAGCCACTTCGAGCAGC --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; 4387 unique reads found of 25000 total reads found 
Processing Reads; 0 Completed out of 4387 Unique Reads
Finished reads; N_TOT_READS: 25000 N_COMPUTED_ALN: 4219 N_CACHED_ALN: 20407 N_COMPUTED_NOTALN: 168 N_CACHED_NOTALN: 206
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 P23H
Plotting nucleotide quilt across amplicon
Plotting nucleotide distribuition around sgRNA GTGCGGAGCCACTTCGAGCAGC for P23H
Plotting indel size distribution for P23H
Plotting frequency deletions/insertions for P23H
Plotting amplication modifications for P23H
Plotting modification frequency for P23H
Plotting quantification window locations for P23H
Plotting position dependent indel for P23H
Plotting allele distribution around cut for P23H
Done!
Begin processing plots for amplicon WT
Plotting nucleotide quilt across amplicon
Plotting nucleotide distribuition around sgRNA GTGCGGAGCCACTTCGAGCAGC for WT
Plotting indel size distribution for WT
Plotting frequency deletions/insertions for WT
Plotting amplication modifications for WT
Plotting modification frequency for WT
Plotting quantification window locations for WT
Plotting position dependent indel for WT
Plotting allele distribution around cut for WT
Done!
Done!
Removing Intermediate files...
 Disproportionate percentages of reads were aligned to amplicon: P23H, Percent of aligned reads aligned to this amplicon: 45.21%.
 Disproportionate percentages of reads were aligned to amplicon: WT, Percent of aligned reads aligned to this amplicon: 51.0%.
 >=1.0% of reads have modifications at the start or end. Total reads: 24626, Irregular reads: 2114.
 >=0.2% of substitutions were outside of the quantification window. Total substitutions: 7154, Substitutions outside window: 6891.
Analysis Complete!
                                                                               
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