Sample K006535_K006536_2_lane_gembs
===================================

Mapping Stats (Reads)
---------------------

+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Concept                                     |Total Reads                                 |%                                           |P1 Reads                                    |%                                           |P2 Reads                                    |%                                          |
+============================================+============================================+============================================+============================================+============================================+============================================+===========================================+
|Sequenced Reads                             |3076682210                                  |100.00 %                                    |1538341105                                  |100.00 %                                    |1538341105                                  |100.00 %                                   |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|General Reads                               |2804754427                                  |91.16 %                                     |1416223852                                  |92.06 %                                     |1388530575                                  |90.26 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Reads in Control sequences                  |0                                           |0.00 %                                      |0                                           |0.00 %                                      |0                                           |0.00 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Reads under conversion control              |169                                         |0.00 %                                      |89                                          |0.00 %                                      |80                                          |0.00 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Reads over conversion control               |0                                           |0.00 %                                      |0                                           |0.00 %                                      |0                                           |0.00 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Unmapped reads                              |271927614                                   |8.84 %                                      |122117164                                   |7.94 %                                      |149810450                                   |9.74 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Bisulfite_reads C2T                         |1463563250                                  |47.57 %                                     |738987498                                   |48.04 %                                     |724575752                                   |47.10 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Bisulfite_reads G2A                         |1341191346                                  |43.59 %                                     |677236443                                   |44.02 %                                     |663954903                                   |43.16 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+

Uniqueness (Fragments)
----------------------

+--------------------------------------------+-------------------------------------------+
|Concept                                     |Value                                      |
+============================================+===========================================+
|Unique Fragments                            |1028527295                                 |
+--------------------------------------------+-------------------------------------------+
|Average Unique                              |66.86 %                                    |
+--------------------------------------------+-------------------------------------------+

Mapping Stats (Bases)
---------------------

+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Concept                                     |Total Bases                                 |%                                           |P1 Bases                                    |%                                           |P2 Bases                                    |%                                          |
+============================================+============================================+============================================+============================================+============================================+============================================+===========================================+
|Base Counts Overall A                       |111476859981                                |36.17 %                                     |43296975844                                 |28.50 %                                     |68179884137                                 |43.62 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall C                       |40380096645                                 |13.10 %                                     |2415799642                                  |1.59 %                                      |37964297003                                 |24.29 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall G                       |41019679394                                 |13.31 %                                     |38625475654                                 |25.43 %                                     |2394203740                                  |1.53 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall T                       |110889361738                                |35.98 %                                     |65941754797                                 |43.41 %                                     |44947606941                                 |28.75 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall N                       |4446626472                                  |1.44 %                                      |1612922390                                  |1.06 %                                      |2833704082                                  |1.81 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+

Mapping Quality Histogram
-------------------------

.. image:: K006535_K006536_2_lane_gembs_mapq.png

Bisulfite Conversion Rate
-------------------------

+--------------------------------------------+-------------------------------------------+
|Bisulfite Conversion Type                   |Conversion Rate                            |
+============================================+===========================================+
|Under Conversion Rate                       |0.016957802842026446                       |
+--------------------------------------------+-------------------------------------------+
|Over Conversion Rate                        |NA                                         |
+--------------------------------------------+-------------------------------------------+

Insert Size Histogram
---------------------

.. image:: K006535_K006536_2_lane_gembs_isize.png

Correct Pairs
-------------

+--------------------------------------------+-------------------------------------------+
|Concept                                     |Total Reads                                |
+============================================+===========================================+
|Correct Pairs                               |1298602083                                 |
+--------------------------------------------+-------------------------------------------+

Sample K006535_K006536_2_lane_gembs Lane SRX259093_3_lanes
----------------------------------------------------------

Mapping Stats (Reads)
^^^^^^^^^^^^^^^^^^^^^

+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Concept                                     |Total Reads                                 |%                                           |P1 Reads                                    |%                                           |P2 Reads                                    |%                                          |
+============================================+============================================+============================================+============================================+============================================+============================================+===========================================+
|Sequenced Reads                             |1182193614                                  |100.00 %                                    |591096807                                   |100.00 %                                    |591096807                                   |100.00 %                                   |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|General Reads                               |1152680182                                  |97.50 %                                     |578546388                                   |97.88 %                                     |574133794                                   |97.13 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Reads in Control sequences                  |0                                           |0.00 %                                      |0                                           |0.00 %                                      |0                                           |0.00 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Reads under conversion control              |165                                         |0.00 %                                      |85                                          |0.00 %                                      |80                                          |0.00 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Reads over conversion control               |0                                           |0.00 %                                      |0                                           |0.00 %                                      |0                                           |0.00 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Unmapped reads                              |29513267                                    |2.50 %                                      |12550334                                    |2.12 %                                      |16962933                                    |2.87 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Bisulfite_reads C2T                         |603623302                                   |51.06 %                                     |303015589                                   |51.26 %                                     |300607713                                   |50.86 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Bisulfite_reads G2A                         |549057045                                   |46.44 %                                     |275530884                                   |46.61 %                                     |273526161                                   |46.27 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+

Uniqueness (Fragments)
^^^^^^^^^^^^^^^^^^^^^^

+--------------------------------------------+-------------------------------------------+
|Concept                                     |Value                                      |
+============================================+===========================================+
|Unique Fragments                            |390072942                                  |
+--------------------------------------------+-------------------------------------------+
|Average Unique                              |65.99 %                                    |
+--------------------------------------------+-------------------------------------------+

Mapping Stats (Bases)
^^^^^^^^^^^^^^^^^^^^^

+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Concept                                     |Total Bases                                 |%                                           |P1 Bases                                    |%                                           |P2 Bases                                    |%                                          |
+============================================+============================================+============================================+============================================+============================================+============================================+===========================================+
|Base Counts Overall A                       |44104052255                                 |36.94 %                                     |17707295687                                 |29.66 %                                     |26396756568                                 |44.22 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall C                       |15358989817                                 |12.86 %                                     |1077930190                                  |1.81 %                                      |14281059627                                 |23.92 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall G                       |15651327727                                 |13.11 %                                     |14631771311                                 |24.51 %                                     |1019556416                                  |1.71 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall T                       |43086126257                                 |36.09 %                                     |25684161683                                 |43.02 %                                     |17401964574                                 |29.15 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall N                       |1201058958                                  |1.01 %                                      |599618636                                   |1.00 %                                      |601440322                                   |1.01 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+

Bisulfite Conversion Rate
^^^^^^^^^^^^^^^^^^^^^^^^^

+--------------------------------------------+-------------------------------------------+
|Bisulfite Conversion Type                   |Conversion Rate                            |
+============================================+===========================================+
|Under Conversion Rate                       |0.016957802842026446                       |
+--------------------------------------------+-------------------------------------------+
|Over Conversion Rate                        |NA                                         |
+--------------------------------------------+-------------------------------------------+

Correct Pairs
^^^^^^^^^^^^^

+--------------------------------------------+-------------------------------------------+
|Concept                                     |Total Reads                                |
+============================================+===========================================+
|Correct Pairs                               |523684736                                  |
+--------------------------------------------+-------------------------------------------+

Mapping Quality Histogram
^^^^^^^^^^^^^^^^^^^^^^^^^

.. image:: SRX259093_3_lanes_mapq.png

Read Length
^^^^^^^^^^^

+--------------------------------------------+-------------------------------------------+
|Read Length                                 |Reads                                      |
+============================================+===========================================+
|100                                         |591096807                                  |
+--------------------------------------------+-------------------------------------------+
|100                                         |591096807                                  |
+--------------------------------------------+-------------------------------------------+

Insert Size Histogram
^^^^^^^^^^^^^^^^^^^^^

.. image:: SRX259093_3_lanes_isize.png

Sample K006535_K006536_2_lane_gembs Lane SRX142783_5_lanes
----------------------------------------------------------

Mapping Stats (Reads)
^^^^^^^^^^^^^^^^^^^^^

+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Concept                                     |Total Reads                                 |%                                           |P1 Reads                                    |%                                           |P2 Reads                                    |%                                          |
+============================================+============================================+============================================+============================================+============================================+============================================+===========================================+
|Sequenced Reads                             |1894488596                                  |100.00 %                                    |947244298                                   |100.00 %                                    |947244298                                   |100.00 %                                   |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|General Reads                               |1652074245                                  |87.20 %                                     |837677464                                   |88.43 %                                     |814396781                                   |85.98 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Reads in Control sequences                  |0                                           |0.00 %                                      |0                                           |0.00 %                                      |0                                           |0.00 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Reads under conversion control              |4                                           |0.00 %                                      |4                                           |0.00 %                                      |0                                           |0.00 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Reads over conversion control               |0                                           |0.00 %                                      |0                                           |0.00 %                                      |0                                           |0.00 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Unmapped reads                              |242414347                                   |12.80 %                                     |109566830                                   |11.57 %                                     |132847517                                   |14.02 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Bisulfite_reads C2T                         |859939948                                   |45.39 %                                     |435971909                                   |46.03 %                                     |423968039                                   |44.76 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Bisulfite_reads G2A                         |792134301                                   |41.81 %                                     |401705559                                   |42.41 %                                     |390428742                                   |41.22 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+

Uniqueness (Fragments)
^^^^^^^^^^^^^^^^^^^^^^

+--------------------------------------------+-------------------------------------------+
|Concept                                     |Value                                      |
+============================================+===========================================+
|Unique Fragments                            |638454353                                  |
+--------------------------------------------+-------------------------------------------+
|Average Unique                              |67.40 %                                    |
+--------------------------------------------+-------------------------------------------+

Mapping Stats (Bases)
^^^^^^^^^^^^^^^^^^^^^

+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Concept                                     |Total Bases                                 |%                                           |P1 Bases                                    |%                                           |P2 Bases                                    |%                                          |
+============================================+============================================+============================================+============================================+============================================+============================================+===========================================+
|Base Counts Overall A                       |67372807726                                 |35.68 %                                     |25589680157                                 |27.76 %                                     |41783127569                                 |43.25 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall C                       |25021106828                                 |13.25 %                                     |1337869452                                  |1.45 %                                      |23683237376                                 |24.51 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall G                       |25368351667                                 |13.44 %                                     |23993704343                                 |26.03 %                                     |1374647324                                  |1.42 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall T                       |67803235481                                 |35.91 %                                     |40257593114                                 |43.67 %                                     |27545642367                                 |28.51 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall N                       |3245567514                                  |1.72 %                                      |1013303754                                  |1.10 %                                      |2232263760                                  |2.31 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+

Bisulfite Conversion Rate
^^^^^^^^^^^^^^^^^^^^^^^^^

+--------------------------------------------+-------------------------------------------+
|Bisulfite Conversion Type                   |Conversion Rate                            |
+============================================+===========================================+
|Under Conversion Rate                       |NA                                         |
+--------------------------------------------+-------------------------------------------+
|Over Conversion Rate                        |NA                                         |
+--------------------------------------------+-------------------------------------------+

Correct Pairs
^^^^^^^^^^^^^

+--------------------------------------------+-------------------------------------------+
|Concept                                     |Total Reads                                |
+============================================+===========================================+
|Correct Pairs                               |774917347                                  |
+--------------------------------------------+-------------------------------------------+

Mapping Quality Histogram
^^^^^^^^^^^^^^^^^^^^^^^^^

.. image:: SRX142783_5_lanes_mapq.png

Read Length
^^^^^^^^^^^

+--------------------------------------------+-------------------------------------------+
|Read Length                                 |Reads                                      |
+============================================+===========================================+
|94                                          |506455796                                  |
+--------------------------------------------+-------------------------------------------+
|99                                          |440788502                                  |
+--------------------------------------------+-------------------------------------------+
|101                                         |947244298                                  |
+--------------------------------------------+-------------------------------------------+

Insert Size Histogram
^^^^^^^^^^^^^^^^^^^^^

.. image:: SRX142783_5_lanes_isize.png

