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Table 5 Notation table

From: An effective method to resolve ambiguous bisulfite-treated reads

Symbol Definition
M One of the multireads
G The reference genome
\({M}_{k}\) The k-th base of the multiread M
\({G}_{s}\) The s-th base of the reference genome G
\({U}_{lt}\) The t-th base on the l-th overlapped unique reads
\({S}_{j}\) Probability of M aligned to the j-th position of G
\({{\varepsilon }_{k}}\) Probability of sequencing errors in \({M}_{k}\)
\({{\varepsilon }_{lt}}\) Probability of sequencing errors in \({U}_{lt}\)
loss A global loss function
WinLen The certain length we defined
a[i] Actual coverage of every locus in WinLen
\(\overline{x}\) The average depth of coverage from 0 to \(WinLen-1\)
\({S}_{{{M}_{k}}{{G}_{s}}}\) Probability of aligning \({M}_{k}\) to \({G}_{s}\), related to the base \({M}_{k}\) and \({G}_{s}\)
\(P({{M}_{k}},{{G}_{s}})\) Part of \({S}_{{{M}_{k}}{{G}_{s}}}\). The probability of observing \({M}_{k}\) for a given base \({G}_{s}\)
\(Score({{M}_{k}},{{G}_{s}})\) Part of \({S}_{{{M}_{k}}{{G}_{s}}}\). A similar score between \({M}_{k}\) and \({G}_{s}\)
\(S[{{G}_{s}}]\) Total similar score when the base of the reference genome is \({G}_{s}\)
\({S}_{{{M}_{k}}{{U}_{t}}}\) Probability of aligning \({M}_{k}\) to the l-th overlapping unique reads \({{U}_{t}}\)
\({S}_{{{M}_{k}}{{U}_{lt}}}\) Probability of aligning \({M}_{k}\) to all overlapping unique reads \({{U}_{lt}}\)
\(P({{M}_{k}} \rightarrow {{U}_{lt}})\) Probability of no sequencing errors occurring in both \({M}_{k}\) and \({{U}_{lt}}\)
\(Score({{M}_{k}},{{U}_{lt}})\) Part of \(P({{M}_{k}} \rightarrow {{U}_{lt}})\). A similar score between \({M}_{k}\) and \({{U}_{lt}}\)