[uqavarla@sandboxav smbk]$ /ebi/sw/bowtie2-2.1.0/bowtie2 -p 4 -x bt2NC_ -1 smbk2_R1.fastq -2 smbk2_R2.fastq -S smbk.sam
9475954 reads; of these:
  9475954 (100.00%) were paired; of these:
    9446283 (99.69%) aligned concordantly 0 times
    27298 (0.29%) aligned concordantly exactly 1 time
    2373 (0.03%) aligned concordantly >1 times
    ----
    9446283 pairs aligned concordantly 0 times; of these:
      63650 (0.67%) aligned discordantly 1 time
    ----
    9382633 pairs aligned 0 times concordantly or discordantly; of these:
      18765266 mates make up the pairs; of these:
        18434932 (98.24%) aligned 0 times
        302234 (1.61%) aligned exactly 1 time
        28100 (0.15%) aligned >1 times
2.73% overall alignment rate