Sample K006170_1_lane_gembs
===========================

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

+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Concept                                     |Total Reads                                 |%                                           |P1 Reads                                    |%                                           |P2 Reads                                    |%                                          |
+============================================+============================================+============================================+============================================+============================================+============================================+===========================================+
|Sequenced Reads                             |574552766                                   |100.00 %                                    |287276383                                   |100.00 %                                    |287276383                                   |100.00 %                                   |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|General Reads                               |564266041                                   |98.21 %                                     |283401368                                   |98.65 %                                     |280864673                                   |97.77 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Reads in Control sequences                  |0                                           |0.00 %                                      |0                                           |0.00 %                                      |0                                           |0.00 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Reads under conversion control              |120630                                      |0.02 %                                      |60587                                       |0.02 %                                      |60043                                       |0.02 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Reads over conversion control               |0                                           |0.00 %                                      |0                                           |0.00 %                                      |0                                           |0.00 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Unmapped reads                              |10166095                                    |1.77 %                                      |3814428                                     |1.33 %                                      |6351667                                     |2.21 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Bisulfite_reads C2T                         |287765657                                   |50.09 %                                     |144518678                                   |50.31 %                                     |143246979                                   |49.86 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Bisulfite_reads G2A                         |276621014                                   |48.15 %                                     |138943277                                   |48.37 %                                     |137677737                                   |47.93 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+

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

+--------------------------------------------+-------------------------------------------+
|Concept                                     |Value                                      |
+============================================+===========================================+
|Unique Fragments                            |239003360                                  |
+--------------------------------------------+-------------------------------------------+
|Average Unique                              |83.20 %                                    |
+--------------------------------------------+-------------------------------------------+

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

+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Concept                                     |Total Bases                                 |%                                           |P1 Bases                                    |%                                           |P2 Bases                                    |%                                          |
+============================================+============================================+============================================+============================================+============================================+============================================+===========================================+
|Base Counts Overall A                       |22844505612                                 |39.37 %                                     |9803286901                                  |33.79 %                                     |13041218711                                 |44.95 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall C                       |5993388293                                  |10.33 %                                     |308946472                                   |1.06 %                                      |5684441821                                  |19.59 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall G                       |6056410545                                  |10.44 %                                     |5741742251                                  |19.79 %                                     |314668294                                   |1.08 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall T                       |22527693127                                 |38.82 %                                     |12867608348                                 |44.35 %                                     |9660084779                                  |33.29 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall N                       |607831789                                   |1.05 %                                      |293330711                                   |1.01 %                                      |314501078                                   |1.08 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+

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

.. image:: K006170_1_lane_gembs_mapq.png

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

+--------------------------------------------+-------------------------------------------+
|Bisulfite Conversion Type                   |Conversion Rate                            |
+============================================+===========================================+
|Under Conversion Rate                       |0.9804407834821285                         |
+--------------------------------------------+-------------------------------------------+
|Over Conversion Rate                        |NA                                         |
+--------------------------------------------+-------------------------------------------+

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

.. image:: K006170_1_lane_gembs_isize.png

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

+--------------------------------------------+-------------------------------------------+
|Concept                                     |Total Reads                                |
+============================================+===========================================+
|Correct Pairs                               |273168827                                  |
+--------------------------------------------+-------------------------------------------+

Sample K006170_1_lane_gembs Lane McGill0002.Bisulfite-Seq.DNA_Methylation.EGAX00001272804.fastq_MS000205
--------------------------------------------------------------------------------------------------------

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

+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Concept                                     |Total Reads                                 |%                                           |P1 Reads                                    |%                                           |P2 Reads                                    |%                                          |
+============================================+============================================+============================================+============================================+============================================+============================================+===========================================+
|Sequenced Reads                             |574552766                                   |100.00 %                                    |287276383                                   |100.00 %                                    |287276383                                   |100.00 %                                   |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|General Reads                               |564266041                                   |98.21 %                                     |283401368                                   |98.65 %                                     |280864673                                   |97.77 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Reads in Control sequences                  |0                                           |0.00 %                                      |0                                           |0.00 %                                      |0                                           |0.00 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Reads under conversion control              |120630                                      |0.02 %                                      |60587                                       |0.02 %                                      |60043                                       |0.02 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Reads over conversion control               |0                                           |0.00 %                                      |0                                           |0.00 %                                      |0                                           |0.00 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Unmapped reads                              |10166095                                    |1.77 %                                      |3814428                                     |1.33 %                                      |6351667                                     |2.21 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Bisulfite_reads C2T                         |287765657                                   |50.09 %                                     |144518678                                   |50.31 %                                     |143246979                                   |49.86 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Bisulfite_reads G2A                         |276621014                                   |48.15 %                                     |138943277                                   |48.37 %                                     |137677737                                   |47.93 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+

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

+--------------------------------------------+-------------------------------------------+
|Concept                                     |Value                                      |
+============================================+===========================================+
|Unique Fragments                            |239003360                                  |
+--------------------------------------------+-------------------------------------------+
|Average Unique                              |83.20 %                                    |
+--------------------------------------------+-------------------------------------------+

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

+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Concept                                     |Total Bases                                 |%                                           |P1 Bases                                    |%                                           |P2 Bases                                    |%                                          |
+============================================+============================================+============================================+============================================+============================================+============================================+===========================================+
|Base Counts Overall A                       |22844505612                                 |39.37 %                                     |9803286901                                  |33.79 %                                     |13041218711                                 |44.95 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall C                       |5993388293                                  |10.33 %                                     |308946472                                   |1.06 %                                      |5684441821                                  |19.59 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall G                       |6056410545                                  |10.44 %                                     |5741742251                                  |19.79 %                                     |314668294                                   |1.08 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall T                       |22527693127                                 |38.82 %                                     |12867608348                                 |44.35 %                                     |9660084779                                  |33.29 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall N                       |607831789                                   |1.05 %                                      |293330711                                   |1.01 %                                      |314501078                                   |1.08 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+

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

+--------------------------------------------+-------------------------------------------+
|Bisulfite Conversion Type                   |Conversion Rate                            |
+============================================+===========================================+
|Under Conversion Rate                       |0.9804407834821285                         |
+--------------------------------------------+-------------------------------------------+
|Over Conversion Rate                        |NA                                         |
+--------------------------------------------+-------------------------------------------+

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

+--------------------------------------------+-------------------------------------------+
|Concept                                     |Total Reads                                |
+============================================+===========================================+
|Correct Pairs                               |273168827                                  |
+--------------------------------------------+-------------------------------------------+

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

.. image:: McGill0002.Bisulfite-Seq.DNA_Methylation.EGAX00001272804.fastq_MS000205_mapq.png

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

+--------------------------------------------+-------------------------------------------+
|Read Length                                 |Reads                                      |
+============================================+===========================================+
|100                                         |287276383                                  |
+--------------------------------------------+-------------------------------------------+
|100                                         |287276383                                  |
+--------------------------------------------+-------------------------------------------+

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

.. image:: McGill0002.Bisulfite-Seq.DNA_Methylation.EGAX00001272804.fastq_MS000205_isize.png

