| exampleBAM | An example BAM file. | 
| exampleMutation | An example mutation file. | 
| exampleMutCall | An example mutated read ID file. | 
| fun_analysis | Analyzing function. | 
| fun_convert | Mutation data file converter | 
| fun_hairpin_check | Hairpin-structure sequence check function | 
| fun_hairpin_trimming | Adapter sequence trimming function | 
| fun_homology | Homology check function. | 
| fun_insert_length | Insert length checker for BAM file | 
| fun_load_bam | BAM file loader | 
| fun_load_chr_no | Chromosome number loading function. | 
| fun_load_genome | Genome loading function. | 
| fun_load_id | Mutation-supporting read ID files loader | 
| fun_load_mutation | Mutation data file loader | 
| fun_load_mutation_gz | Mutation data file loader | 
| fun_read_check | Read check function. | 
| fun_repeat_check | Repeat check function. | 
| fun_save | Save function. | 
| fun_save_gz | Save function. | 
| fun_setting | Mutated position search function. | 
| fun_summary | Summarizing function. | 
| fun_support | Supporting length calculation function. | 
| fun_zero | Devide function without 0/0 errors | 
| homology_searched | An example sequence infromation file. | 
| msec_analyzed | An example mutation file. | 
| msec_homology_searched | An example mutation file. | 
| msec_read_checked | An example mutation file. | 
| msec_summarized | An example mutation file. | 
| mut_depth_checked | An example sequence infromation file. |