Download Next Generation Sequencing So ware User`s Manual Version 1.5

The first way is to ignore mismatches occurring on read positions with low quality scores during
the mapping process.
A low confidence score denotes low sequencing quality at that position in the read. Therefore,
mismatches occurring at positions with low quality scores are more likely due to sequencing
error. Thus mismatches on positions with high quality scores are more meaningful than those at
low quality score positions. Use the following combo box or enter some value to assign the
threshold of high quality score.
The second way is to utilize quality scores to rank several possible mapping results of each read
and choose the best position as the mapping results. Since the process happens after all mapping
positions have been found, this way will be described in part “5. Collecting Results”.
In our experiments, we observed that more reads were uniquely mapped when quality scores
were included to help mapping.
Mapping Criteria
Mismatches and insertion/deletion
The following is an example that a read is mapped to the reference sequence with only
mismatches. The four red characters in the alignment are the mismatches between the read and
its target region on the reference sequence.
The following is an example that a read is mapped to the reference sequence with a deletion on
the read. The read deletes an “A” nucleotide. There is one deletion of length one.
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