This is done for compression and in order to make the file there

no basically in order to make the file size smaller.

So in order to do any real computation on qualities

you have to convert them into integers.

You can actually see what happens, and

you can do that by coalescing the quality scores into a matrix.

So here I coalesce a matrix, and I show the first two reads and

the first ten pages of the first two reads.

So we can see here by comparing to the thing upstairs that 8 gets translated

to 39 and I get's translated to 40.

So first scale qualities are numbers between 0 and 40 and

they're supposed to have a probabilistic interpretation

giving you some idea of the chance that the reported base is correct.

Or in other words the chance of getting a sequencing arrow.