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Align columns of the first tabular #74

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Align columns of the first tabular #74

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12 changes: 6 additions & 6 deletions doc/manual.rst
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Expand Up @@ -112,19 +112,19 @@ The modifications.gff file will not work directly with most genome browsers. Yo

The auxiliary data column of the GFF file contains other statistics which may be useful downstream analysis or filtering. In particular the coverage level of the reads used to make the call, and +/- 20bp sequence context surrounding the site.

================ ===========
Column Description
================ ===========
seqid Fasta contig name
source Name of tool -- 'kinModCall'
================ ===========
Column Description
================ ===========
seqid Fasta contig name
source Name of tool -- 'kinModCall'
type Modification type -- in identification mode this will be m6A, m4C, or m5C for identified bases, or the generic tag 'modified_base' if a kinetic event was detected that does not match a known modification signature
start Modification position on contig
end Modification position on contig
score Phred transformed p-value of detection - this is the single-site detection p-value
strand Sample strand containing modification
phase Not applicable
attributes Extra fields relevant to base mods. IPDRatio is traditional IPDRatio, context is the reference sequence -20bp to +20bp around the modification, and coverage level is the number of IPD observations used after Mapping QV filtering and accuracy filtering. If the row results from an identified modification we also include an identificationQv tag with the from the modification identification procedure. identificationQv is the phred-transformed probability of an incorrect identification, for bases that were identified as having a particular modification. frac, fracLow, fracUp are the estimated fraction of molecules carrying the modification, and the 5% confidence intervals of the estimate. The methylated fraction estimation is a beta-level feature, and should only be used for exploratory purposes.
================ ===========
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modifications.csv
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