samtools flagstat统计bam文件比对结果

$ samtools flagstat
Usage: samtools flagstat [options] <in.bam>
      --input-fmt-option OPT[=VAL]
               Specify a single input file format option in the form
               of OPTION or OPTION=VALUE
  -@, --threads INT
               Number of additional threads to use [0]

$ samtools flagstat -@ 8 EV-1_HISAT2.bam
59306432 + 0 in total (QC-passed reads + QC-failed reads)
4546096 + 0 secondary 
0 + 0 supplementary
0 + 0 duplicates
55162761 + 0 mapped (93.01% : N/A) #匹配到reference的reads百分比（55162761/59306432）
54760336 + 0 paired in sequencing #pair数目
27380168 + 0 read1
27380168 + 0 read2
48652166 + 0 properly paired (88.85% : N/A)
49197764 + 0 with itself and mate mapped #pair reads都成功匹配到reference sequence的对数
1418901 + 0 singletons (2.59% : N/A) #pair reads只有一条匹配到reference sequence的条数
106592 + 0 with mate mapped to a different chr #paired reads分别匹配到不同染色体
82634 + 0 with mate mapped to a different chr (mapQ>=5)