# CRISPResso2

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

##### FANCF_BE1

Guardrail Warning! <=90.0% of reads were aligned. Total reads: 25000, Aligned reads: 15668.
Guardrail Warning! >=1.0% of reads have modifications at the start or end. Total reads: 15668, Irregular reads: 15668.
Guardrail Warning! >=0.2% of substitutions were outside of the quantification window. Total substitutions: 4587, Substitutions outside window: 2029.

##### 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 21:38:06

Amplicon sequence:

    CATTGCAGAGAGGCGTATCATTTCGCGGATGTTCCAATCAGTACGCAGAGAGTCGCCGTCTCCAAGGTGAAAGCGGAAGTAGGGCCTTCGCGCACCTCATGGAATCCCTTCTGCAGCACCTGGATCGCTTTTCCGAGCTTCTGGCGGTCTCAAGCACTACCTACGTCAGCACCTGGGACCCC

Guide sequence:

    GGAATCCCTTCTGCAGCACC

Command used:

    CRISPResso -o CRISPRessoBatch_on_batch --name FANCF_BE1 --min_paired_end_reads_overlap 10 --quantification_window_size 20 --base_editor_output --fastp_command fastp --flexiguide_gap_extend_penalty -2 --prime_editing_gap_extend_penalty 0 --plot_window_size 20 --exclude_bp_from_right 15 --flash_command None --exclude_bp_from_left 15 --verbosity 3 --aln_seed_len 10 --n_processes 1 --amplicon_seq CATTGCAGAGAGGCGTATCATTTCGCGGATGTTCCAATCAGTACGCAGAGAGTCGCCGTCTCCAAGGTGAAAGCGGAAGTAGGGCCTTCGCGCACCTCATGGAATCCCTTCTGCAGCACCTGGATCGCTTTTCCGAGCTTCTGGCGGTCTCAAGCACTACCTACGTCAGCACCTGGGACCCC --min_bp_quality_or_N 0 --amplicon_name Reference --flexiguide_homology 80 --needleman_wunsch_gap_extend -2 --prime_editing_pegRNA_extension_quantification_window_size 5 --min_average_read_quality 0 --needleman_wunsch_aln_matrix_loc EDNAFULL --needleman_wunsch_gap_incentive 1 --max_rows_alleles_around_cut_to_plot 50 --prime_editing_gap_open_penalty -50 --place_report_in_output_folder --quantification_window_center -10 --conversion_nuc_from C --conversion_nuc_to T --write_cleaned_report --guide_seq GGAATCCCTTCTGCAGCACC --trimmomatic_command None --prime_editing_pegRNA_scaffold_min_match_length 1 --needleman_wunsch_gap_open -20 --min_frequency_alleles_around_cut_to_plot 0.2 --default_min_aln_score 60 --config_file None --aln_seed_min 2 --max_paired_end_reads_overlap None --flexiguide_seq None --min_single_bp_quality 0 --aln_seed_count 5 --fastq_r1 SRR3305543.fastq.gz --flexiguide_gap_open_penalty -20

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: Reference
    amplicon_seq: CATTGCAGAGAGGCGTATCATTTCGCGGATGTTCCAATCAGTACGCAGAGAGTCGCCGTCTCCAAGGTGAAAGCGGAAGTAGGGCCTTCGCGCACCTCATGGAATCCCTTCTGCAGCACCTGGATCGCTTTTCCGAGCTTCTGGCGGTCTCAAGCACTACCTACGTCAGCACCTGGGACCCC
    annotate_wildtype_allele:
    assign_ambiguous_alignments_to_first_reference: False
    auto: False
    bam_chr_loc:
    bam_input:
    bam_output: False
    base_editor_output: True
    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: SRR3305543.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: GGAATCCCTTCTGCAGCACC
    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: FANCF_BE1
    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: CRISPRessoBatch_on_batch
    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: -10
    quantification_window_coordinates: None
    quantification_window_size: 20
    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

##### Nucleotide composition

Hover your mouse over the bottom image to zoom in on a specific region.
Figure 2a: Nucleotide distribution across amplicon. At each base in the reference amplicon, the percentage of each base as observed in sequencing reads is shown (A = green; C = orange; G = yellow; T = purple). Black bars show the percentage of reads for which that base was deleted. Brown bars between bases show the percentage of reads having an insertion at that position.

Data: Nucleotide frequency table

Figure 2b: Nucleotide distribution around the sgRNA GGAATCCCTTCTGCAGCACC.

Data: Nucleotide frequency in quantification window

##### Modification lengths

Figure 3a: Frequency distribution of alleles with indels (blue) and without indels (red). Note that histograms are clipped to show 99% of the data. To show all data, run using the parameter '--plot_histogram_outliers'. (Minimum -53 not shown)

Data: Indel histogram

Figure 3b: Left panel, frequency distribution of sequence modifications that increase read length with respect to the reference amplicon, classified as insertions (positive indel size). Middle panel, frequency distribution of sequence modifications that reduce read length with respect to the reference amplicon, classified as deletions (negative indel size). Right panel, frequency distribution of sequence modifications that do not alter read length with respect to the reference amplicon, which are classified as substitutions (number of substituted positions shown).

Data: Insertions frequency

Data: Deletions Frequency

Data: Substitutions Frequency

##### Indel characterization

Figure 4a: Combined frequency of any modification across the amplicon. Modifications outside of the quantification window are also shown.
Figure 4b: Frequency of insertions, deletions, and substitutions across the entire amplicon, including modifications outside of the quantification window.

Data: Modification frequency

Figure 4c: Frequency of insertions, deletions, and substitutions across the entire amplicon, considering only modifications that overlap with the quantification window.

Data: Modification frequency in quantification window

Figure 4d: Position dependent insertion size(left) and deletion size (right), including only modifications that overlap with the quantification window.

##### Allele plots

Figure 9: Visualization of the distribution of identified alleles around the cleavage site for the sgRNA GGAATCCCTTCTGCAGCACC. Nucleotides are indicated by unique colors (A = green; C = red; G = yellow; T = purple). Substitutions are shown in bold font. Red rectangles highlight inserted sequences. Horizontal dashed lines indicate deleted sequences. The vertical dashed line indicates the predicted cleavage site.

Data: Allele frequency table

##### Base editing

Figure 10a: Substitution frequencies across the amplicon.

Data: Nucleotide frequencies

Figure 10b: Substitution frequencies across the amplicon.

Data: Nucleotide frequencies

Figure 10c: Substitution frequencies in the quantification window

Data: Nucleotide frequencies in quantification window

Figure 10d: Log2 nucleotide frequencies for each position in the plotting window around the sgRNA GGAATCCCTTCTGCAGCACC. The quantification window is outlined by the dotted box.
Figure 10e: Proportion of each base at each nucleotide targeted by base editors in the plotting window around the sgRNA GGAATCCCTTCTGCAGCACC. The number of each target base is annotated on the reference sequence at the bottom of the plot.

Data: Nucleotide frequencies at Cs

Figure 10f: Non-reference base proportions. For target nucleotides in the plotting window, this plot shows the proportion of non-reference (non-C) bases as a percentage of all non-reference sequences. The number of each target base is annotated on the reference sequence at the bottom of the plot.

Data: Nucleotide frequencies at Cs

Figure 10g: Non-reference base counts. For target nucleotides in the plotting window, this plot shows the number of non-reference (non-C) bases. The number of each target base is annotated on the reference sequence at the bottom of the plot.

Data: Nucleotide frequencies at Cs