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fiberhmm-qc grades DddA against a somatic DddA control. The packaged
DddA reference was built from a sperm DAF-seq sample (0.7% median
deamination, no nucleosome phasing), so normal DddA libraries failed the
signal rate and the periodicity grade compared them with a flat curve. The
rate, phasogram, footprint-size and example-molecule references now come
from the NAPA and UBA1 DddA amplicons (14.6% median deamination, NRL 202
bp). DddA periodicity allows 15 bp around the reference NRL, since amplicon
loci differ in repeat length. Re-run fiberhmm-qc on DddA BAMs; calls are
unchanged, and DddB and Hia5 grades are unchanged.
The nucleosome-size legend no longer covers the long-span note in QC plots.