text: user1008: Below are the statistics for RNA-seq mapped and unmapped paired-end reads to rice genome using reformat.sh from bbtools on bam files. It gives 77% mapped and 5% unmapped, what about the remaining 18% reads? How I can get information for all reads?
  Command;
  reformat.sh in=Leaf_T1_F_R10_S1_L001.bam out=Leaf_T1_F_R10_S1_L001.mapped.bam, mappedonly
  
  
  Unspecified format for output Leaf_T1_F_R10_S1_L001.mapped.bam,; defaulting to fastq.
  Found sambamba.
  Input is being processed as unpaired
  Input:                   67471075 reads           9312399845 bases
  Output:                 52020538 reads (77.10%) 7208830835 bases (77.41%)
  
  Time:                         171.212 seconds.
  Reads Processed:      67471k 394.08k reads/sec
  Bases Processed:       9312m 54.39m bases/sec
  
  For unmapped read;
  Command;
  reformat.sh in=Leaf_T1_F_R10_S1_L001.bam out=Leaf_T1_F_R10_S1_L001.unmapped.bam, unmappedonly
  
  Unspecified format for output Leaf_T1_F_R10_S1_L001.unmapped.bam,; defaulting to fastq.
  Found sambamba.
  Input is being processed as unpaired
  Input:                   67471075 reads           9312399845 bases
  Output:                 3435326 reads (5.09%) 465456267 bases (5.00%)
  
  Time:                         142.978 seconds.
  Reads Processed:      67471k 471.90k reads/sec
  Bases Processed:       9312m 65.13m bases/sec
  
  With sambamba; Can I say 94.91% reads are mapped and 5.09% are unmapped?
  67471075 + 0 in total (QC-passed reads + QC-failed reads)
  12015211 + 0 secondary
  0 + 0 supplementary
  0 + 0 duplicates
  64035749 + 0 mapped (94.91%:N/A)
  55455864 + 0 paired in sequencing
  27727932 + 0 read1
  27727932 + 0 read2
  51006046 + 0 properly paired (91.98%:N/A)
  51419222 + 0 with itself and mate mapped
  601316 + 0 singletons (1.08%:N/A)
  263816 + 0 with mate mapped to a different chr
  237111 + 0 with mate mapped to a different chr (mapQ>=5)
  
  
  user6251: Try samtools flagstat or sambamba flagstat to get similar type of information about your bam file. It may be easier to interpret. Both of these tools can be installed using conda if needed.
  EDIT:
  Yes, the results of sambamba flagstat you showed in your edited post indicate exactly what you said: 94.91% mapped and 100% - 94.91% = 5.09% unmapped:
  64035749 + 0 mapped (94.91%:N/A)
  
  
original_text: 1008: <p>Below are the statistics for RNA-seq mapped and unmapped paired-end reads to rice genome using reformat.sh from bbtools on bam files. It gives 77% mapped and 5% unmapped, what about the remaining 18% reads? How I can get information for all reads?</p>
  <pre><code>Command;
  reformat.sh in=Leaf_T1_F_R10_S1_L001.bam out=Leaf_T1_F_R10_S1_L001.mapped.bam, mappedonly
  
  
  Unspecified format for output Leaf_T1_F_R10_S1_L001.mapped.bam,; defaulting to fastq.
  Found sambamba.
  Input is being processed as unpaired
  Input:                   67471075 reads           9312399845 bases
  Output:                 52020538 reads (77.10%) 7208830835 bases (77.41%)
  
  Time:                         171.212 seconds.
  Reads Processed:      67471k 394.08k reads/sec
  Bases Processed:       9312m 54.39m bases/sec
  
  For unmapped read;
  Command;
  reformat.sh in=Leaf_T1_F_R10_S1_L001.bam out=Leaf_T1_F_R10_S1_L001.unmapped.bam, unmappedonly
  
  Unspecified format for output Leaf_T1_F_R10_S1_L001.unmapped.bam,; defaulting to fastq.
  Found sambamba.
  Input is being processed as unpaired
  Input:                   67471075 reads           9312399845 bases
  Output:                 3435326 reads (5.09%) 465456267 bases (5.00%)
  
  Time:                         142.978 seconds.
  Reads Processed:      67471k 471.90k reads/sec
  Bases Processed:       9312m 65.13m bases/sec
  </code></pre>
  <p>With sambamba; Can I say 94.91% reads are mapped and 5.09% are unmapped?</p>
  <pre><code>67471075 + 0 in total (QC-passed reads + QC-failed reads)
  12015211 + 0 secondary
  0 + 0 supplementary
  0 + 0 duplicates
  64035749 + 0 mapped (94.91%:N/A)
  55455864 + 0 paired in sequencing
  27727932 + 0 read1
  27727932 + 0 read2
  51006046 + 0 properly paired (91.98%:N/A)
  51419222 + 0 with itself and mate mapped
  601316 + 0 singletons (1.08%:N/A)
  263816 + 0 with mate mapped to a different chr
  237111 + 0 with mate mapped to a different chr (mapQ&gt;=5)
  </code></pre>
   6251: <p>Try <code>samtools flagstat</code> or <code>sambamba flagstat</code> to get similar type of information about your bam file. It may be easier to interpret. Both of these tools can be installed using <code>conda</code> if needed.</p>
  <p><strong>EDIT:</strong></p>
  <p>Yes, the results of <code>sambamba flagstat</code> you showed in your edited post indicate exactly what you said: <code>94.91%</code> mapped and <code>100% - 94.91% = 5.09%</code> unmapped:</p>
  <pre><code>64035749 + 0 mapped (94.91%:N/A)
  </code></pre>
  