| PacBio Data Processing version | {version} |
| Date | {when} |
| Program name | {program} |
| Program options | {clos} |
| Hostname | {hostname} |
| Methylation report | {methylation_report} |
| Raw detections | {raw_detections} |
| Joint GFFs | {gff_result} |
| File name | {input_bam} |
| Size (bytes) | {input_bam_size} |
| MD5 checksum (full) | {full_md5sum} |
| MD5 checksum (body) | {body_md5sum} |
| File name | {input_reference} |
| Reference name | {reference_reference} |
| Size (base pairs) | {reference_base_pairs} |
| MD5 checksum (fully capitalized string) | {reference_md5sum} |
The following facts were found during the analysis of the above mentioned BAM file and reference:
| number of molecules | number of subreads | |
|---|---|---|
| Initial | {mols_ini} | {subreads_ini} |
| Used in aligned CCS BAM | {mols_used_in_aligned_ccs} ({perc_mols_used_in_aligned_ccs} %) | {subreads_used_in_aligned_ccs} ({perc_subreads_used_in_aligned_ccs} %) |
| DNA mismatch discards | {mols_dna_mismatches} ({perc_mols_dna_mismatches} %) | {subreads_dna_mismatches} ({perc_subreads_dna_mismatches} %) |
| Filtered out | {filtered_out_mols} ({perc_filtered_out_mols} %) | {filtered_out_subreads} ({perc_filtered_out_subreads} %) |
| In methylation report... | {mols_in_meth_report} ({perc_mols_in_meth_report} %) | {subreads_in_meth_report} ({perc_subreads_in_meth_report} %) |
| ...only with GATCs | {mols_in_meth_report_with_gatcs} ({perc_mols_in_meth_report_with_gatcs} %) | {subreads_in_meth_report_with_gatcs} ({perc_subreads_in_meth_report_with_gatcs} %) |
| ...only without GATCs | {mols_in_meth_report_without_gatcs} ({perc_mols_in_meth_report_without_gatcs} %) | {subreads_in_meth_report_without_gatcs} ({perc_subreads_in_meth_report_without_gatcs} %) |
Note: it is understood that a position is covered if we have confidence that it has been correctly identified. The aligned CCS version of the input BAM is used for that.
| Number of base pairs in reference | {reference_base_pairs} |
| Positions covered by molecules in the BAM file | {all_positions_in_bam} ({perc_all_positions_in_bam} %) |
| Positions NOT covered by molecules in the BAM file | {all_positions_not_in_bam} ({perc_all_positions_not_in_bam} %) |
| Positions covered by molecules in the methylation report | {all_positions_in_meth} ({perc_all_positions_in_meth} %) |
| Positions NOT covered by molecules in the methylation report | {all_positions_not_in_meth} ({perc_all_positions_not_in_meth} %) |
| Total number of GATCs in reference | {total_gatcs_in_ref} |
| Number of GATCs identified in the BAM file | {all_gatcs_identified_in_bam} ({perc_all_gatcs_identified_in_bam} %) |
| Number of GATCs NOT identified in the BAM file | {all_gatcs_not_identified_in_bam} ({perc_all_gatcs_not_identified_in_bam} %) |
| Number of GATCs in methylation report | {all_gatcs_in_meth} ({perc_all_gatcs_in_meth} %) |
| Number of GATCs NOT in methylation report | {all_gatcs_not_in_meth} ({perc_all_gatcs_not_in_meth} %) |
In this section there are some global statistics concerning individual methylations.
| Total number of GATCs in all the analyzed molecules | {max_possible_methylations} |
| Fully methylated | {fully_methylated_gatcs} ({fully_methylated_gatcs_wrt_meth} %) |
| Fully unmethylated | {fully_unmethylated_gatcs} ({fully_unmethylated_gatcs_wrt_meth} %) |
| Hemi-methylated... | {hemi_methylated_gatcs} ({hemi_methylated_gatcs_wrt_meth} %) |
| ...only in '+' strand | {hemi_plus_methylated_gatcs} ({hemi_plus_methylated_gatcs_wrt_meth} %) |
| ...only in '-' strand | {hemi_minus_methylated_gatcs} ({hemi_minus_methylated_gatcs_wrt_meth} %) |