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Table 1 Bisulfite matching table after bitwise masking

From: BSMAP: whole genome bisulfite sequence MAPping program

Reference   A (00) C (01) G (10) T (11)
Mask   11 (inactive) 01 (active) 11 (inactive) 11 (inactive)
Bisulfite Read A(00) 00 (match) 01 10 11
  C(01) 10 00 (match) 11 10
  G(10) => A(00) if reference is C 10 01 00 (match) 01
  T(11) => C(01) if reference is C 11 00 (match) 01 00 (match)