16 months ago by

Danmarks Tekniske Universitet

The rgqual refers to the Z_0 score. Z_0 is the likelihood for the top (most likely) read group on a PHRED scale. Considering the sequence of this read group as the template to sequence and using the principle of independence between bases, this likelihood is computed as:

```
Z_0= -10 * log_10{ PROD_{1...length indices} P(base read i|base template i) }
```

The higher the probability of assignment, the lower this score becomes. If say the probability is almost 1 (perfect), the score Z_0 will be around 0. Conversely, if the probability of assignment is dismal around 0, the score will be 200 or 300. To compute this, we use quality scores but the correspondence is not 1 to 1, it depends on the template and sequenced bases.

I think the confusion stems from the use of the PHRED scale. PHRED is a mathematical formula and does not always refer to quality scores. Mapping quality is computed on a PHRED scale for instance.