001、命令
samtools flagstat sample_name.sorted.bam > sample_name.flagstat.txt ## 基本命令
a、生成的文件是一个包含16行的文本文件：
002、
(base) [b20223040323@admin2 workdir]$ cat Asiatic1.flagstat.txt ## 查看统计结果 622520785 + 0 in total (QC-passed reads + QC-failed reads) ## 总的reads 620876200 + 0 primary ## 初级 reads？ 1644585 + 0 secondary ## 次级 secondary？ 0 + 0 supplementary ## ？？ 0 + 0 duplicates ## ？？ 0 + 0 primary duplicates ## ？？ 621864067 + 0 mapped (99.89% : N/A) ## ？？ 620219482 + 0 primary mapped (99.89% : N/A) ## ？？ 620876200 + 0 paired in sequencing ## ？？ 310438100 + 0 read1 310438100 + 0 read2 612737342 + 0 properly paired (98.69% : N/A) ## ？？ 620022610 + 0 with itself and mate mapped 196872 + 0 singletons (0.03% : N/A) 5577184 + 0 with mate mapped to a different chr 2767972 + 0 with mate mapped to a different chr (mapQ>=5)
。
003、
标签：flagstat,samtools,##,primary,reads,mapped,bam From： https://www.cnblogs.com/liujiaxin2018/p/18504221