[uqavarla@sandboxav smbk]$ /ebi/sw/bowtie2-2.1.0/bowtie2 -p 4 -x bt2NC_ -1 trimmed30_pe_1.fq -2 trimmed30_pe_2.fq -S trimmed30.sam
9475012 reads; of these:
  9475012 (100.00%) were paired; of these:
    9441420 (99.65%) aligned concordantly 0 times
    30914 (0.33%) aligned concordantly exactly 1 time
    2678 (0.03%) aligned concordantly >1 times
    ----
    9441420 pairs aligned concordantly 0 times; of these:
      73873 (0.78%) aligned discordantly 1 time
    ----
    9367547 pairs aligned 0 times concordantly or discordantly; of these:
      18735094 mates make up the pairs; of these:
        18406652 (98.25%) aligned 0 times
        298884 (1.60%) aligned exactly 1 time
        29558 (0.16%) aligned >1 times
2.87% overall alignment rate