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} %) |