2、Tophat align_summary.txt and samtools flagstat accepted_hits.bam disagree

###https://www.biostars.org/p/195758/

Left reads:
          Input     :  49801387
           Mapped   :  46258301 (92.9% of input)
            of these:   1703360 ( 3.7%) have multiple alignments (103886 have >20)
Right reads:
          Input     :  49801387
           Mapped   :  45542088 (91.4% of input)
            of these:   1680180 ( 3.7%) have multiple alignments (103887 have >20)
92.2% overall read mapping rate.

Aligned pairs:  44100265
     of these:   1622622 ( 3.7%) have multiple alignments
                  261400 ( 0.6%) are discordant alignments
88.0% concordant pair alignment rate.
1、解释计算原理：(44100265 - 261400) / 49801387 = 88%` ；1622622/1622622 = 3.7% ；
2、If I needed to report a number, I'd report the 92.2% overall alignment rate. You can probably get something similar with samtools view -c -F 260 accepted_hits.bam.（得到输入left和\
right的比对数目）/49801387 *2 

3、samtools flagstat accepted_hits.bam