title: determining the percentage of the coverage of reads against reference genome
body: <p>Hello Biostar I hope you're doing well i mapped my reads against the reference genome to get an idea about the coverage , what i want to know is the percentage of the coverage , but i don't know how to obtain this information using the diffrent tools i know , in qualimap , i just found <strong>the mean coverage and std coverage data</strong> also lines like this</p>
  
  <pre><code> T
  
       There is a 99.59% of reference with a coverageData &gt;= 1X
       There is a 99.56% of reference with a coverageData &gt;= 2X
       There is a 99.53% of reference with a coverageData &gt;= 3X
       There is a 99.49% of reference with a coverageData &gt;= 4X
       There is a 99.45% of reference with a coverageData &gt;= 5X
       There is a 99.42% of reference with a coverageData &gt;= 6X
       There is a 99.39% of reference with a coverageData &gt;= 7X
       There is a 99.37% of reference with a coverageData &gt;= 8X
       There is a 99.34% of reference with a coverageData &gt;= 9X
       There is a 99.31% of reference with a coverageData &gt;= 10X
       There is a 99.3% of reference with a coverageData &gt;= 11X
       There is a 99.27% of reference with a coverageData &gt;= 12X
  </code></pre>
  
  <p>..</p>
  
  <p>i don't know if it s possible to obtain the percentage of the coverage using this informations and how , Also i used bamtools stats , and obtained these informations</p>
  
  <pre><code>Total reads:       6158542
  Mapped reads:      5749217  (93.3535%)
  Forward strand:    3286294  (53.3616%)
  Reverse strand:    2872248  (46.6384%)
  Failed QC:         0    (0%)
  Duplicates:        0    (0%)
  Paired-end reads:  6158542  (100%)
  'Proper-pairs':    4667096  (75.7825%)
  Both pairs mapped: 5730384  (93.0477%)
  Read 1:            3079271
  Read 2:            3079271
  Singletons:        18833    (0.305803%)
  </code></pre>
  
  <p>and the same thing i didn't get the percentage of coverage and the same thing with samtools flagstat</p>
  
  <pre><code>6158542 + 0 in total (QC-passed reads + QC-failed reads)
  0 + 0 secondary
  0 + 0 supplementary
  0 + 0 duplicates
  5749217 + 0 mapped (93.35% : N/A)
  6158542 + 0 paired in sequencing
  3079271 + 0 read1
  3079271 + 0 read2
  4667096 + 0 properly paired (75.78% : N/A)
  5730384 + 0 with itself and mate mapped
  18833 + 0 singletons (0.31% : N/A)
  83794 + 0 with mate mapped to a different chr
  12721 + 0 with mate mapped to a different chr (mapQ&gt;=
  </code></pre>
  
  <p>5)</p>
  
  <p>and samtools idxstatsNZ_</p>
  
  <pre><code>ALWU01000001.1  581415  2031429 6451
  NZ_ALWU01000002.1   43553   76489   678
  NZ_ALWU01000003.1   29286   117672  342
  NZ_ALWU01000004.1   37537   144448  440
  NZ_ALWU01000005.1   217837  789901  2467
  NZ_ALWU01000006.1   38235   103338  325
  NZ_ALWU01000007.1   9944    45471   292
  NZ_ALWU01000008.1   178611  651422  2190
  NZ_ALWU01000009.1   17047   6352    42
  NZ_ALWU01000010.1   510276  1782695 5606
  *   0   0   390492
  </code></pre>
  
  <p>can you tell me please how to get the percentage of the coverage ? Thank you very much</p>