The unique reads of the basic concept of Sheng Xin-multi-mapping reads

Unique reads: There is only one match point on the reference group

Multi-mapping reads: There are multiple matching points on the reference group

Here is a result case for tophat:

Reads:          Input     :  26140314           Mapped   :  25159791 (96.2% of Input) of            these:   10276914.1%) has multiple alignments (1832 has >)96.2% overall read mapping rate.

The quantity of unique reads:25159791-1027691=

The quantity of multi-mapping reads:1027691

How many alignment did the 1,027,691 multi-mapping reads produce? or mention unique reads for next step analysis?

$samtools View accepted.bam| grep ' nh:i:1 '| WC -L
$samtolls view Accepted.bam|grep ' \bnh:i:1\b ' >accepted_unique.sam

The unique reads of the basic concept of Sheng Xin-multi-mapping reads