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@CO Testing explicit vs implicit base modifications.
@CO This covers the case where a lack of a signal could be either
@CO implicitly assumed to be no-mod (default) or assumed to be
@CO unchecked and require an explicit statement to indicate it was
@CO looked at and no base modification was observed.
@CO
@CO ATCATCATTCCTACCGCTATAGCCT r1; implicit
@CO - - .. -. - --
@CO Mm M
@CO - - .. -. - --
@CO hH h
@CO
@CO ATCATCATTCCTACCGCTATAGCCT r2; explicit to a small region
@CO - - ?? ?? ? --
@CO Mm mM m
@CO - - ?? ?? ? --
@CO hH hh h
@CO
@CO ATCATCATTCCTACCGCTATAGCCT r3; mixture
@CO - - . -. - --
@CO M M
@CO - - ?? ?? ? --
@CO hH hh h --
@CO
r1 0 * 0 0 * * 0 0 ATCATCATTCCTACCGCTATAGCCT * Mm:Z:C+mh,2,0,1; Ml:B:C,200,10,50,170,160,20
r2 0 * 0 0 * * 0 0 ATCATCATTCCTACCGCTATAGCCT * Mm:Z:C+mh?,2,0,0,0,0; Ml:B:C,200,10,50,170,10,5,160,20,10,5
r3 0 * 0 0 * * 0 0 ATCATCATTCCTACCGCTATAGCCT * Mm:Z:C+m.,2,2;C+h?,2,0,0,0,0; Ml:B:C,200,160,10,170,5,20,5
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