[uqavarla@sandboxav smbk]$ /ebi/sw/bowtie2-2.1.0/bowtie2 -p 4 -x bt2NC_ -1 trimmed_pe_1.fq -2 trimmed_pe_2.fq -S trimmed.sam
9475726 reads; of these:
  9475726 (100.00%) were paired; of these:
    9442045 (99.64%) aligned concordantly 0 times
    31090 (0.33%) aligned concordantly exactly 1 time
    2591 (0.03%) aligned concordantly >1 times
    ----
    9442045 pairs aligned concordantly 0 times; of these:
      73318 (0.78%) aligned discordantly 1 time
    ----
    9368727 pairs aligned 0 times concordantly or discordantly; of these:
      18737454 mates make up the pairs; of these:
        18411554 (98.26%) aligned 0 times
        296730 (1.58%) aligned exactly 1 time
        29170 (0.16%) aligned >1 times
2.85% overall alignment rate