The main result of the new strategy is that far fewer disagreements between data are brought to the attention of the user and fewer traces have to be inspected by eye, and so the whole process is faster. Another consequence of the new strategy is that, as fewer bases need changing to produce the correct consensus, most of what appears on the screen will be the original base calls. Indeed we have taken this a step further and suggest that if a base needs changing because it has a high accuracy estimate, and is conflicting with other good data, then rather than change the character shown on the screen, the user should lower its accuracy value. By so doing more of the original base calls are left unchanged and hence are visible to the user. There is a function within the contig editor to reset the accuracy value for the current base to 0. Alternatively the accuracy value for the base that is thought to be correct can be set within the contig editor to 100.
A natural and important outcome of the new strategy, though one which may necessitate more, rather than less, work is that the find next problem function will not only find places where there are disagreements between good readings, but also places where there is no data of sufficient accuracy to be included in the consensus. Previously some groups may have overlooked such regions if they relied only on locating regions of conflict and were satisfied if the sequence was covered by data on both strands.