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  "options": {
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      "junction_minimum_side_match": 1,
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      "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,
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    "mutation_identification": {
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      "consensus_minimum_total_coverage_each_strand": 0,
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      "consensus_minimum_variant_coverage_each_strand": 0,
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      "no_indel_polymorphisms": false,
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      "polymorphism_prediction": false,
      "polymorphism_reject_indel_homopolymer_length": 0,
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      "print_mutation_identification_per_position_file": false,
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      "user_evidence_genome_diff_file_name": ""
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      "hide_circular_genome_junctions": true,
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      "no_javascript": false
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