Newbler GSmapper output numMappedReads 2 results

[pepperoni]

Hello, I am wondering why I get two very different results in the metrics of the Newbler GSmapper
numMappedReads = 362295, 96.47%, 48.20%;
numMappedBases = 51845395, 92.31%, 91.33%;
which is the right percentage? the second one does not make any sense to me, does not coincide with the trimmed reads result or anything.
thank you very much

[sklages]

Have a look at the sourrounding block. numMappedReads appears in different contexts.

best, Sven

[pepperoni]

Have a look at the sourrounding block. numMappedReads appears in different contexts.

best, Sven

Sorry, I still don't get it, which sourrounding block? which contexts?

thanks

[sklages]

Roche manual states:

Percentage metrics are calculated in two distinct ways, with the first percentage
value of each pair calculated based on the number of reads (or bases) used in the
mapping computation, and the second percentage value calculated from the total
number of physical reads (i.e. number of sequences in the read files).

hth, Sven

[pepperoni]

Thanks Sven, I just checked and my first reads in the metrics file coincide with what you told me

first = percentage of total second = percentage of trimmed reads

But then I have miseq paired data and in those the numbers didn't fit but now I've realized they are:

first = percentage of trimmed reads second = half of it (one pair)

I also noticed that for the number of bases is the other way round

first = percentage of trimmed second = percentage of total