转录有参、医口流程hisat2 mapping命令如下：

hisat2 -x <hisat2 index> -p 4 --dta -t --phred33 -1 sample_1.clean.fq.gz -2 sample_2.clean.fq.gz --un-conc-gz sample.unmap.fq.gz 2> sample_align.log | samtools sort -O BAM --threads 4 -o sample.bam -

均为默认参数，hisat2版本version 2.0.5

Time loading forward index: 00:00:31
Time loading reference: 00:00:06
Multiseed full-index search: 00:13:05
21501684 reads; of these:
  21501684 (100.00%) were paired; of these:
    2675430 (12.44%) aligned concordantly 0 times
    15080209 (70.14%) aligned concordantly exactly 1 time
    3746045 (17.42%) aligned concordantly >1 times
    ----
    2675430 pairs aligned concordantly 0 times; of these:
      234828 (8.78%) aligned discordantly 1 time
    ----
    2440602 pairs aligned 0 times concordantly or discordantly; of these:
      4881204 mates make up the pairs; of these:
        3031909 (62.11%) aligned 0 times
        1359660 (27.86%) aligned exactly 1 time
        489635 (10.03%) aligned >1 times
92.95% overall alignment rate
Time searching: 00:13:12
Overall time: 00:13:43

总的mapping计算如下
  92.95% =((15080209+3746045)*2 + 234828*2 + 1359660 + 489635)/(21501684*2)
软件输出的unmap reads为 2675430 (12.44%) aligned concordantly 0 times