Table 2

Syndromes for ECC generator
Error Interpretation Position Equivalence
Type p c1 c2 c3 c4 c5 p + classes
+ β Complement β0 0β α1 α1 0β ββ 0β {c5}
+ α Transition α0 0α 1β 1β 0α αα 0α {c2,c3}
+1 Transcomplement 10 01 βα βα 01 11 01 {c1,c4,p + }

All syndromes caused by a single error in a block of five code letters (c1c2c3c4c5) and two parity letters (pp + ) of the SOLiD ECC code. Each row in the table corresponds to a specific type of error at the given position of the code word, with the ‘interpretation’ of an error type being the effect it would have when considered as a nucleotide substitution. The table entries are the values of the relevant elements of the syndrome, corresponding to the upstream and downstream parity checks for the block for each error type. The error type +0 is not shown since it represents no error; its syndromes would be 00 at all positions. The equivalence classes are listed separately and do not correspond to specific error types. Note that pis also p + for the preceding block.

Massingham and Goldman

Massingham and Goldman BMC Bioinformatics 2012 13:145   doi:10.1186/1471-2105-13-145

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