Summary report: Single Molecule Methylation Analysis

Overview

PacBio Data Processing version {version}
Date {when}
Program name {program}
Program options {clos}
Hostname {hostname}

Result filenames

Methylation report {methylation_report}
Raw detections {raw_detections}
Joint GFFs {gff_result}

Input files

BAM File

File name {input_bam}
Size (bytes) {input_bam_size}
MD5 checksum (full) {full_md5sum}
MD5 checksum (body) {body_md5sum}

Reference

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:

Molecules/subreads

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} %)

molecule length histogram

Sequencing Position Coverage

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} %)

Sequencing positions coverage histogram

GATCs

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} %)

GATCs coverage histogram

GATC per molecule histogram

Methylations

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} %)

count of molecule types

count of methylation types