# CRISPResso2

### Analysis of genome editing outcomes from deep sequencing data

Guardrail Warning! Disproportionate percentages of reads were aligned to amplicon: P23H, Percent of aligned reads aligned to this amplicon: 45.21%.
Guardrail Warning! Disproportionate percentages of reads were aligned to amplicon: WT, Percent of aligned reads aligned to this amplicon: 51.0%.
Guardrail Warning! >=1.0% of reads have modifications at the start or end. Total reads: 24626, Irregular reads: 2114.
Guardrail Warning! >=0.2% of substitutions were outside of the quantification window. Total substitutions: 7154, Substitutions outside window: 6891.

##### CRISPResso2 run information

Figure 1a: The number of reads in input fastqs, after preprocessing, and after alignment to amplicons.

Data: Mapping statistics

CRISPResso version: 2.3.2

Run completed: 2025-04-25 21:35:57

Amplicon sequence:

    CGAGAGCCGCAGCCATGAACGGCACAGAGGGCCCCAATTTTTATGTGCCCTTCTCCAACGTCACAGGCGTGGTGCGGAGCCACTTCGAGCAGCCGCAGTACTACCTGGCGGAACCATGGCAGTTCTCCATGCTGGCAGCGTACATGTTCCTGCTCATCGTGCTGGG,CGAGAGCCGCAGCCATGAACGGCACAGAGGGCCCCAATTTTTATGTGCCCTTCTCCAACGTCACAGGCGTGGTGCGGAGCCCCTTCGAGCAGCCGCAGTACTACCTGGCGGAACCATGGCAGTTCTCCATGCTGGCAGCGTACATGTTCCTGCTCATCGTGCTGGG

Guide sequence:

    GTGCGGAGCCACTTCGAGCAGC

Command used:

    CRISPResso -r1 allele_specific.fastq.gz -a CGAGAGCCGCAGCCATGAACGGCACAGAGGGCCCCAATTTTTATGTGCCCTTCTCCAACGTCACAGGCGTGGTGCGGAGCCACTTCGAGCAGCCGCAGTACTACCTGGCGGAACCATGGCAGTTCTCCATGCTGGCAGCGTACATGTTCCTGCTCATCGTGCTGGG,CGAGAGCCGCAGCCATGAACGGCACAGAGGGCCCCAATTTTTATGTGCCCTTCTCCAACGTCACAGGCGTGGTGCGGAGCCCCTTCGAGCAGCCGCAGTACTACCTGGCGGAACCATGGCAGTTCTCCATGCTGGCAGCGTACATGTTCCTGCTCATCGTGCTGGG -an P23H,WT -g GTGCGGAGCCACTTCGAGCAGC --write_cleaned_report --place_report_in_output_folder

Parameters:

    allele_plot_pcts_only_for_assigned_reference: False
    aln_seed_count: 5
    aln_seed_len: 10
    aln_seed_min: 2
    amplicon_min_alignment_score:
    amplicon_name: P23H,WT
    amplicon_seq: CGAGAGCCGCAGCCATGAACGGCACAGAGGGCCCCAATTTTTATGTGCCCTTCTCCAACGTCACAGGCGTGGTGCGGAGCCACTTCGAGCAGCCGCAGTACTACCTGGCGGAACCATGGCAGTTCTCCATGCTGGCAGCGTACATGTTCCTGCTCATCGTGCTGGG,CGAGAGCCGCAGCCATGAACGGCACAGAGGGCCCCAATTTTTATGTGCCCTTCTCCAACGTCACAGGCGTGGTGCGGAGCCCCTTCGAGCAGCCGCAGTACTACCTGGCGGAACCATGGCAGTTCTCCATGCTGGCAGCGTACATGTTCCTGCTCATCGTGCTGGG
    annotate_wildtype_allele:
    assign_ambiguous_alignments_to_first_reference: False
    auto: False
    bam_chr_loc:
    bam_input:
    bam_output: False
    base_editor_output: False
    bowtie2_index:
    coding_seq:
    config_file: None
    conversion_nuc_from: C
    conversion_nuc_to: T
    crispresso1_mode: False
    debug: False
    default_min_aln_score: 60
    disable_guardrails: False
    discard_guide_positions_overhanging_amplicon_edge: False
    discard_indel_reads: False
    dsODN:
    dump: False
    exclude_bp_from_left: 15
    exclude_bp_from_right: 15
    expand_allele_plots_by_quantification: False
    expand_ambiguous_alignments: False
    expected_hdr_amplicon_seq:
    fastp_command: fastp
    fastp_options_string:
    fastq_output: False
    fastq_r1: allele_specific.fastq.gz
    fastq_r2:
    file_prefix:
    flash_command: None
    flexiguide_gap_extend_penalty: -2
    flexiguide_gap_open_penalty: -20
    flexiguide_homology: 80
    flexiguide_name:
    flexiguide_seq: None
    force_merge_pairs: False
    guide_name:
    guide_seq: GTGCGGAGCCACTTCGAGCAGC
    halt_on_plot_fail: False
    ignore_deletions: False
    ignore_insertions: False
    ignore_substitutions: False
    keep_intermediate: False
    max_paired_end_reads_overlap: None
    max_rows_alleles_around_cut_to_plot: 50
    min_average_read_quality: 0
    min_bp_quality_or_N: 0
    min_frequency_alleles_around_cut_to_plot: 0.2
    min_paired_end_reads_overlap: 10
    min_single_bp_quality: 0
    n_processes: 1
    name:
    needleman_wunsch_aln_matrix_loc: EDNAFULL
    needleman_wunsch_gap_extend: -2
    needleman_wunsch_gap_incentive: 1
    needleman_wunsch_gap_open: -20
    no_rerun: False
    output_folder:
    place_report_in_output_folder: True
    plot_histogram_outliers: False
    plot_window_size: 20
    prime_editing_gap_extend_penalty: 0
    prime_editing_gap_open_penalty: -50
    prime_editing_nicking_guide_seq:
    prime_editing_override_prime_edited_ref_seq:
    prime_editing_override_sequence_checks: False
    prime_editing_pegRNA_extension_quantification_window_size: 5
    prime_editing_pegRNA_extension_seq:
    prime_editing_pegRNA_scaffold_min_match_length: 1
    prime_editing_pegRNA_scaffold_seq:
    prime_editing_pegRNA_spacer_seq:
    quantification_window_center: -3
    quantification_window_coordinates: None
    quantification_window_size: 1
    samtools_exclude_flags: 0
    save_also_png: False
    split_interleaved_input: False
    stringent_flash_merging: False
    suppress_amplicon_name_truncation: False
    suppress_plots: False
    suppress_report: False
    trim_sequences: False
    trimmomatic_command: None
    trimmomatic_options_string:
    use_legacy_insertion_quantification: False
    use_matplotlib: False
    verbosity: 3
    write_cleaned_report: True
    write_detailed_allele_table: False
    zip_output: False

Running log

##### Allele assignments

Figure 1b: Alignment and editing frequency of reads as determined by the percentage and number of sequence reads showing unmodified and modified alleles.

Data: Quantification of editing

Figure 1c: Alignment and editing frequency of reads as determined by the percentage and number of sequence reads showing unmodified and modified alleles.

Data: Quantification of editing

Reads are aligned to each amplicon sequence separately. Quantification and visualization of these reads are shown for each amplicon below:

##### Amplicons