bowtie2 -t -x ref/NC_012967.1 -1 data/SRR030257_1.fastq -2 data/SRR030257_2.fastq -S data/SRR030257.sam
Time loading reference: 00:00:00
Time loading forward index: 00:00:00
Time loading mirror index: 00:00:00
Multiseed full-index search: 00:07:05
3800180 reads; of these:
  3800180 (100.00%) were paired; of these:
    207120 (5.45%) aligned concordantly 0 times
    3479207 (91.55%) aligned concordantly exactly 1 time
    113853 (3.00%) aligned concordantly >1 times
    ----
    207120 pairs aligned concordantly 0 times; of these:
      5606 (2.71%) aligned discordantly 1 time
    ----
    201514 pairs aligned 0 times concordantly or discordantly; of these:
      403028 mates make up the pairs; of these:
        371144 (92.09%) aligned 0 times
        29153 (7.23%) aligned exactly 1 time
        2731 (0.68%) aligned >1 times
95.12% overall alignment rate
Time searching: 00:07:05
Overall time: 00:07:05