Detection of modifications

In order to detect and annotated modified positions, modPhred scans read alignments and for every position of reference genome/transcriptome it calculates

  • depth of coverage,

  • basecall accuracy,

  • modification frequency

  • and median modification probability.

Those values are reported into mod.gz file.

By default, modPhred reports only sites with modifications fulfilling following criteria:

  • minimum mapping quality of 15 - only reads with mapping quality of 15 or more are considered

  • minimum sequencing depth of 25 - at least 25 reads for given positions

  • at least 0.05 frequency of modification - at least 5% of reads being modified for this position

  • at least 0.5 modification probability - only bases with modification probability of 50% or more are considered as truly modified.

The default values can be adjusted with several parameters:

./run -h
...
-m --mapq               min mapping quality [15]
-d --minDepth           min depth of coverage [25]
--minModFreq            min modification frequency per position [0.05]
--minModProb            min modification probability per base [0.5]
...