The reads directory contains a single dataset of paired end reads: reads_R1.fq and reads_R2.fq contains the forward and reverse reads, respectively.

The dataset is composed by the following read pairs:

Both reads mapped against the reference in a proper pair:

• proper.1: forward fragment on the + strand, reverse fragment on the - strand
• revcompl.1: forward fragment on the - strand, reverse fragment on the + strand

One reads not aligned:

• proper-1na.1: first reads is not mapped (second is on the - strand)
• proper-2na.1: second read is not mapped (first is on the + strand)
• revcompl-1na.1: first reads is not mapped (second is on the + strand)
• revcompl-2na.1: second read is not mapped (first is on the - strand)

Both reads are not mapped:

• unmap.1

Schematic representation (coordinates not to scale, overlapping reads are spread apart to simplify the picture) of the read pairs

Here we report the truncated SAM output