This is probably a dummy question, but I haven't found an explanation and I want to be sure. When paired-end sequencing is done, there are usually 2 fastq files generated, one with "left" mates and the other with "right" mates.

Assuming that mates in the first file are read from the forward strand, are then mates in the second file read from the reverse strand?

If so, what is exactly written in the second file? A reverse complement of the read sequence (the corresponding sequence on the forward strand) or the pure reverse-strand sequence? And in which direction?
Illumina paired-end sequencing is based on the idea that you have initial DNA fragments (longer than your actual read length) and you sequence both its ends. On the Illumina chip, both ends of each sequence are amplified prior to actual sequencing using [bridging][1]. This approach results in two reads per fragment, with the* first read in forward* orientation and the *second read in reverse-complement* orientation. Depending on the inital fragment size and read length, these fragment can either overlap or not

For example, with 100 bp reads:

```
------[f-180bp]----->
----[r1]----->
        <----[r2]----

------------------[f-350bp]----------------->
----[r1]----->
                                <----[r2]----
```

Therefore, the first fastq file will contain all "r1" reads, the second file all "r2" reads.

 [1]: http://www.illumina.com/documents/products/techspotlights/techspotlight_sequencing.pdf