Read Me
Suffix of the file: "5mC_unphased.tsv.gz" indicates the unphased methylation. "5mC_1.tsv.gz" indicates methylation data within haplotype one. "5mC_2.tsv.gz" indicates methylation data within haplotype two.
This is the methylation output of modbam2bed.
The File format is as follows:
Column 1: reference sequence name
Column 2: 0-based start position
Column 3: 0-based exclusive end position (invariably start + 1)
Column 4: Abbreviated name of modified-base examined
Column 5: "Score" 1000 * (Nmod + Ncanon) / (Nmod + Ncanon + Nno call + Nalt mod + Nfilt + Nsub + Ndel). The quantity reflects the extent to which the calculated modification frequency in Column 11 is confounded by the alternative calls. The denominator here is the total read coverage as given in Column 10.
Column 6: Strand (of reference sequence). Forward "+", or reverse "-".
Columns 7-9: Ignore, included simply for compatibility.
Column 10: Read coverage at reference position including all canonical, modified, undecided (no calls and filtered), substitutions from reference, and deletions. Nmod + Ncanon + Nno call + Nalt mod + Nfilt + Nsub + Ndel
Column 11: Percentage of modified bases, as a proportion of canonical and modified (excluding no calls, filtered, substitutions, and deletions). 100 * Nmod / (Nmod + Nalt mod + Ncanon)
Column 12: N-can. Number of canononical bases. Number of calls passing filters were classified as the canonical base rather than modified. The exact base must be inferred by the modification code. For example, if the modification code is m (5mC) then the canonical base is cytosine. If the modification code is a, the canonical base is adenosine.
Column 13: N-mod. Number of modified bases. Number of calls passing filters that were classified as a residue with a specified base modification.
Column 14: N-filt. Those bases with a modification probability falling between given thresholds.
Column 15: N-no call. Those bases for which the query base was the correct canonical base for the modified base being considered, but no call was made (see the definition of the . and ? flags in the SAM tag specification).
Column 16: N-alt mod. Those bases for which the query base was the correct canonical base for the modified base being considered, but and alternative modification was present.