number of joined reads

[Erin]

Hello,

I used fastq to join forward and reverse reads from Illumina, below: 

# Join forward and reverse reads

$ ./fastq-join Undetermined_S0_L001_R1_001.fastq Undetermined_S0_L001_R2_001.fastq -o joined.fastq

## FASTQ JOIN STATS

## Total reads: 16009546

## Total joined: 10296305

## Average join len: 49.64

## Stdev join len: 5.43

Normally I would expect to have a total number of joined reads that is half (or less) of the original read pool.

However, I got ~60% of the total reads, joined (~10 million out of ~16 million).

Does this reflect the potentially poor quality of the reverse reads?

Or is there another explanation?

Thanks for your help!