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  "options": {
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      "add_split_junction_sides": true,
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      "junction_minimum_side_match": 1,
      "junction_pos_hash_neg_log10_p_value_cutoff": 3.0,
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      "maximum_candidate_junctions": 5000,
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      "maximum_junction_sequence_negative_overlap_length_fraction": 0.4,
      "maximum_junction_sequence_negative_overlap_length_minimum": 12,
      "maximum_junction_sequence_overlap_length": 0,
      "maximum_junction_sequence_passed_alignment_pairs_to_consider": 100000,
      "maximum_junction_sequence_positive_overlap_length_fraction": 0.4,
      "maximum_junction_sequence_positive_overlap_length_minimum": 12,
      "minimum_candidate_junction_pos_hash_score": 2,
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      "preprocess_junction_min_indel_split_length": 3,
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      "required_both_unique_length_per_side_fraction": 0.2,
      "required_one_unique_length_per_side": 0,
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      "unmatched_end_minimum_read_length": 50
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    "mutation_identification": {
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      "consensus_frequency_cutoff": 0.8,
      "consensus_minimum_total_coverage": 0,
      "consensus_minimum_total_coverage_each_strand": 0,
      "consensus_minimum_variant_coverage": 0,
      "consensus_minimum_variant_coverage_each_strand": 0,
      "consensus_reject_indel_homopolymer_length": 372071024,
      "consensus_reject_surrounding_homopolymer_length": 32764,
      "deletion_coverage_propagation_cutoff": 0.0,
      "deletion_coverage_seed_cutoff": 0.0,
      "mixed_base_prediction": true,
      "mutation_log10_e_value_cutoff": 10.0,
      "no_indel_polymorphisms": false,
      "polymorphism_bias_p_value_cutoff": 0.0,
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      "polymorphism_log10_e_value_cutoff": 10.0,
      "polymorphism_minimum_total_coverage": 0,
      "polymorphism_minimum_total_coverage_each_strand": 0,
      "polymorphism_minimum_variant_coverage": 0,
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      "polymorphism_prediction": false,
      "polymorphism_reject_indel_homopolymer_length": 0,
      "polymorphism_reject_surrounding_homopolymer_length": 0,
      "print_mutation_identification_per_position_file": false,
      "quality_score_trim": 0,
      "targeted_sequencing": false,
      "user_evidence_genome_diff_file_name": ""
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    "mutation_prediction": {
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    "output": {
      "header_genome_diff_file_name": "",
      "hide_circular_genome_junctions": true,
      "max_displayed_reads": 100,
      "max_nucleotides_to_show_in_tables": 20,
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      "no_javascript": false
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    "read_alignment": {
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      "bowtie2_junction_maximum_alignments_to_consider_per_read": 2000,
      "bowtie2_scoring": "--ma 1 --mp 3 --np 0 --rdg 2,3 --rfg 2,3 --ignore-quals",
      "bowtie2_stage1": "--local -i S,1,0.25 --score-min L,1,0.9 -k 2000",
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      "genbank_field_for_seq_id": "AUTOMATIC",
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      "skip_missing_coverage_prediction": false,
      "skip_new_junction_prediction": false,
      "skip_read_alignment_and_missing_coverage_prediction": false,
      "skip_read_filtering": false
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  },
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        "quality_format_original": "SANGER",
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    "total_aligned_bases": 151275,
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        "coverage_nbinom_prob_parameter": 0.656532925055423,
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        "length": 33350,
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        "num_reads_mapped_to_reference": 2017.0,
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    },
    "total_features": 104,
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}