Sample K006142_1_lane_gembs
===========================

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

+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Concept                                     |Total Reads                                 |%                                           |P1 Reads                                    |%                                           |P2 Reads                                    |%                                          |
+============================================+============================================+============================================+============================================+============================================+============================================+===========================================+
|Sequenced Reads                             |737480676                                   |100.00 %                                    |368740338                                   |100.00 %                                    |368740338                                   |100.00 %                                   |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|General Reads                               |709476845                                   |96.20 %                                     |356207803                                   |96.60 %                                     |353269042                                   |95.80 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Reads in Control sequences                  |0                                           |0.00 %                                      |0                                           |0.00 %                                      |0                                           |0.00 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Reads under conversion control              |776334                                      |0.11 %                                      |390502                                      |0.11 %                                      |385832                                      |0.10 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Reads over conversion control               |0                                           |0.00 %                                      |0                                           |0.00 %                                      |0                                           |0.00 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Unmapped reads                              |27227497                                    |3.69 %                                      |12142033                                    |3.29 %                                      |15085464                                    |4.09 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Bisulfite_reads C2T                         |364225400                                   |49.39 %                                     |182873260                                   |49.59 %                                     |181352140                                   |49.18 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Bisulfite_reads G2A                         |346027779                                   |46.92 %                                     |173725045                                   |47.11 %                                     |172302734                                   |46.73 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+

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

+--------------------------------------------+-------------------------------------------+
|Concept                                     |Value                                      |
+============================================+===========================================+
|Unique Fragments                            |293079809                                  |
+--------------------------------------------+-------------------------------------------+
|Average Unique                              |79.48 %                                    |
+--------------------------------------------+-------------------------------------------+

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

+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Concept                                     |Total Bases                                 |%                                           |P1 Bases                                    |%                                           |P2 Bases                                    |%                                          |
+============================================+============================================+============================================+============================================+============================================+============================================+===========================================+
|Base Counts Overall A                       |28926539435                                 |38.84 %                                     |11643433769                                 |31.26 %                                     |17283105666                                 |46.41 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall C                       |8111195844                                  |10.89 %                                     |580292683                                   |1.56 %                                      |7530903161                                  |20.22 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall G                       |8232442712                                  |11.05 %                                     |7594972352                                  |20.39 %                                     |637470360                                   |1.71 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall T                       |28402869952                                 |38.13 %                                     |17036840489                                 |45.75 %                                     |11366029463                                 |30.52 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall N                       |812500333                                   |1.09 %                                      |387234845                                   |1.04 %                                      |425265488                                   |1.14 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+

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

.. image:: K006142_1_lane_gembs_mapq.png

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

+--------------------------------------------+-------------------------------------------+
|Bisulfite Conversion Type                   |Conversion Rate                            |
+============================================+===========================================+
|Under Conversion Rate                       |0.9809725138011384                         |
+--------------------------------------------+-------------------------------------------+
|Over Conversion Rate                        |NA                                         |
+--------------------------------------------+-------------------------------------------+

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

.. image:: K006142_1_lane_gembs_isize.png

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

+--------------------------------------------+-------------------------------------------+
|Concept                                     |Total Reads                                |
+============================================+===========================================+
|Correct Pairs                               |338234252                                  |
+--------------------------------------------+-------------------------------------------+

Sample K006142_1_lane_gembs Lane McGill0027.Bisulfite-Seq.DNA_Methylation.EGAX00001425129.release_6
---------------------------------------------------------------------------------------------------

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

+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Concept                                     |Total Reads                                 |%                                           |P1 Reads                                    |%                                           |P2 Reads                                    |%                                          |
+============================================+============================================+============================================+============================================+============================================+============================================+===========================================+
|Sequenced Reads                             |737480676                                   |100.00 %                                    |368740338                                   |100.00 %                                    |368740338                                   |100.00 %                                   |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|General Reads                               |709476845                                   |96.20 %                                     |356207803                                   |96.60 %                                     |353269042                                   |95.80 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Reads in Control sequences                  |0                                           |0.00 %                                      |0                                           |0.00 %                                      |0                                           |0.00 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Reads under conversion control              |776334                                      |0.11 %                                      |390502                                      |0.11 %                                      |385832                                      |0.10 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Reads over conversion control               |0                                           |0.00 %                                      |0                                           |0.00 %                                      |0                                           |0.00 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Unmapped reads                              |27227497                                    |3.69 %                                      |12142033                                    |3.29 %                                      |15085464                                    |4.09 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Bisulfite_reads C2T                         |364225400                                   |49.39 %                                     |182873260                                   |49.59 %                                     |181352140                                   |49.18 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Bisulfite_reads G2A                         |346027779                                   |46.92 %                                     |173725045                                   |47.11 %                                     |172302734                                   |46.73 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+

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

+--------------------------------------------+-------------------------------------------+
|Concept                                     |Value                                      |
+============================================+===========================================+
|Unique Fragments                            |293079809                                  |
+--------------------------------------------+-------------------------------------------+
|Average Unique                              |79.48 %                                    |
+--------------------------------------------+-------------------------------------------+

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

+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Concept                                     |Total Bases                                 |%                                           |P1 Bases                                    |%                                           |P2 Bases                                    |%                                          |
+============================================+============================================+============================================+============================================+============================================+============================================+===========================================+
|Base Counts Overall A                       |28926539435                                 |38.84 %                                     |11643433769                                 |31.26 %                                     |17283105666                                 |46.41 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall C                       |8111195844                                  |10.89 %                                     |580292683                                   |1.56 %                                      |7530903161                                  |20.22 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall G                       |8232442712                                  |11.05 %                                     |7594972352                                  |20.39 %                                     |637470360                                   |1.71 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall T                       |28402869952                                 |38.13 %                                     |17036840489                                 |45.75 %                                     |11366029463                                 |30.52 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall N                       |812500333                                   |1.09 %                                      |387234845                                   |1.04 %                                      |425265488                                   |1.14 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+

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

+--------------------------------------------+-------------------------------------------+
|Bisulfite Conversion Type                   |Conversion Rate                            |
+============================================+===========================================+
|Under Conversion Rate                       |0.9809725138011384                         |
+--------------------------------------------+-------------------------------------------+
|Over Conversion Rate                        |NA                                         |
+--------------------------------------------+-------------------------------------------+

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

+--------------------------------------------+-------------------------------------------+
|Concept                                     |Total Reads                                |
+============================================+===========================================+
|Correct Pairs                               |338234252                                  |
+--------------------------------------------+-------------------------------------------+

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

.. image:: McGill0027.Bisulfite-Seq.DNA_Methylation.EGAX00001425129.release_6_mapq.png

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

+--------------------------------------------+-------------------------------------------+
|Read Length                                 |Reads                                      |
+============================================+===========================================+
|100                                         |368740338                                  |
+--------------------------------------------+-------------------------------------------+
|100                                         |368740338                                  |
+--------------------------------------------+-------------------------------------------+

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

.. image:: McGill0027.Bisulfite-Seq.DNA_Methylation.EGAX00001425129.release_6_isize.png

