Sample A83594_2_lane_gembs
==========================

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

+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Concept                                     |Total Reads                                 |%                                           |P1 Reads                                    |%                                           |P2 Reads                                    |%                                          |
+============================================+============================================+============================================+============================================+============================================+============================================+===========================================+
|Sequenced Reads                             |1107708196                                  |100.00 %                                    |553854098                                   |100.00 %                                    |553854098                                   |100.00 %                                   |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|General Reads                               |987562434                                   |89.15 %                                     |496593765                                   |89.66 %                                     |490968669                                   |88.65 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Reads in Control sequences                  |0                                           |0.00 %                                      |0                                           |0.00 %                                      |0                                           |0.00 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Reads under conversion control              |285841                                      |0.03 %                                      |143437                                      |0.03 %                                      |142404                                      |0.03 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Reads over conversion control               |0                                           |0.00 %                                      |0                                           |0.00 %                                      |0                                           |0.00 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Unmapped reads                              |119859921                                   |10.82 %                                     |57116896                                    |10.31 %                                     |62743025                                    |11.33 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Bisulfite_reads C2T                         |505600444                                   |45.64 %                                     |254137336                                   |45.89 %                                     |251463108                                   |45.40 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Bisulfite_reads G2A                         |482247831                                   |43.54 %                                     |242599866                                   |43.80 %                                     |239647965                                   |43.27 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+

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

+--------------------------------------------+-------------------------------------------+
|Concept                                     |Value                                      |
+============================================+===========================================+
|Unique Fragments                            |424585371                                  |
+--------------------------------------------+-------------------------------------------+
|Average Unique                              |76.66 %                                    |
+--------------------------------------------+-------------------------------------------+

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

+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Concept                                     |Total Bases                                 |%                                           |P1 Bases                                    |%                                           |P2 Bases                                    |%                                          |
+============================================+============================================+============================================+============================================+============================================+============================================+===========================================+
|Base Counts Overall A                       |63233027691                                 |37.80 %                                     |28165403374                                 |33.68 %                                     |35067624317                                 |41.93 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall C                       |19654172074                                 |11.75 %                                     |2529656563                                  |3.02 %                                      |17124515511                                 |20.48 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall G                       |19774119573                                 |11.82 %                                     |17080099122                                 |20.42 %                                     |2694020451                                  |3.22 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall T                       |63473310319                                 |37.95 %                                     |35294921326                                 |42.20 %                                     |28178388993                                 |33.69 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall N                       |1129307939                                  |0.68 %                                      |561888413                                   |0.67 %                                      |567419526                                   |0.68 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+

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

.. image:: A83594_2_lane_gembs_mapq.png

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

+--------------------------------------------+-------------------------------------------+
|Bisulfite Conversion Type                   |Conversion Rate                            |
+============================================+===========================================+
|Under Conversion Rate                       |0.8874714157225182                         |
+--------------------------------------------+-------------------------------------------+
|Over Conversion Rate                        |NA                                         |
+--------------------------------------------+-------------------------------------------+

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

.. image:: A83594_2_lane_gembs_isize.png

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

+--------------------------------------------+-------------------------------------------+
|Concept                                     |Total Reads                                |
+============================================+===========================================+
|Correct Pairs                               |475468777                                  |
+--------------------------------------------+-------------------------------------------+

Sample A83594_2_lane_gembs Lane HGCV2CCXY_5_2
---------------------------------------------

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

+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Concept                                     |Total Reads                                 |%                                           |P1 Reads                                    |%                                           |P2 Reads                                    |%                                          |
+============================================+============================================+============================================+============================================+============================================+============================================+===========================================+
|Sequenced Reads                             |155119702                                   |100.00 %                                    |77559851                                    |100.00 %                                    |77559851                                    |100.00 %                                   |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|General Reads                               |152890904                                   |98.56 %                                     |77009033                                    |99.29 %                                     |75881871                                    |97.84 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Reads in Control sequences                  |0                                           |0.00 %                                      |0                                           |0.00 %                                      |0                                           |0.00 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Reads under conversion control              |41106                                       |0.03 %                                      |20648                                       |0.03 %                                      |20458                                       |0.03 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Reads over conversion control               |0                                           |0.00 %                                      |0                                           |0.00 %                                      |0                                           |0.00 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Unmapped reads                              |2187692                                     |1.41 %                                      |530170                                      |0.68 %                                      |1657522                                     |2.14 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Bisulfite_reads C2T                         |78230203                                    |50.43 %                                     |39385185                                    |50.78 %                                     |38845018                                    |50.08 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Bisulfite_reads G2A                         |74701807                                    |48.16 %                                     |37644496                                    |48.54 %                                     |37057311                                    |47.78 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+

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

+--------------------------------------------+-------------------------------------------+
|Concept                                     |Value                                      |
+============================================+===========================================+
|Unique Fragments                            |65471952                                   |
+--------------------------------------------+-------------------------------------------+
|Average Unique                              |84.41 %                                    |
+--------------------------------------------+-------------------------------------------+

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

+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Concept                                     |Total Bases                                 |%                                           |P1 Bases                                    |%                                           |P2 Bases                                    |%                                          |
+============================================+============================================+============================================+============================================+============================================+============================================+===========================================+
|Base Counts Overall A                       |9156008146                                  |39.09 %                                     |4010449404                                  |34.24 %                                     |5145558742                                  |43.94 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall C                       |2471329715                                  |10.55 %                                     |110264756                                   |0.94 %                                      |2361064959                                  |20.16 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall G                       |2488762428                                  |10.63 %                                     |2361655876                                  |20.17 %                                     |127106552                                   |1.09 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall T                       |9150149525                                  |39.06 %                                     |5151203940                                  |43.98 %                                     |3998945585                                  |34.15 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall N                       |156825188                                   |0.67 %                                      |77963525                                    |0.67 %                                      |78861663                                    |0.67 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+

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

+--------------------------------------------+-------------------------------------------+
|Bisulfite Conversion Type                   |Conversion Rate                            |
+============================================+===========================================+
|Under Conversion Rate                       |0.9942709671390411                         |
+--------------------------------------------+-------------------------------------------+
|Over Conversion Rate                        |NA                                         |
+--------------------------------------------+-------------------------------------------+

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

+--------------------------------------------+-------------------------------------------+
|Concept                                     |Total Reads                                |
+============================================+===========================================+
|Correct Pairs                               |73479892                                   |
+--------------------------------------------+-------------------------------------------+

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

.. image:: HGCV2CCXY_5_2_mapq.png

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

+--------------------------------------------+-------------------------------------------+
|Read Length                                 |Reads                                      |
+============================================+===========================================+
|150                                         |77559851                                   |
+--------------------------------------------+-------------------------------------------+
|150                                         |77559851                                   |
+--------------------------------------------+-------------------------------------------+

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

.. image:: HGCV2CCXY_5_2_isize.png

Sample A83594_2_lane_gembs Lane HFJM5CCXY_4_2
---------------------------------------------

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

+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Concept                                     |Total Reads                                 |%                                           |P1 Reads                                    |%                                           |P2 Reads                                    |%                                          |
+============================================+============================================+============================================+============================================+============================================+============================================+===========================================+
|Sequenced Reads                             |952588494                                   |100.00 %                                    |476294247                                   |100.00 %                                    |476294247                                   |100.00 %                                   |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|General Reads                               |834671530                                   |87.62 %                                     |419584732                                   |88.09 %                                     |415086798                                   |87.15 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Reads in Control sequences                  |0                                           |0.00 %                                      |0                                           |0.00 %                                      |0                                           |0.00 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Reads under conversion control              |244735                                      |0.03 %                                      |122789                                      |0.03 %                                      |121946                                      |0.03 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Reads over conversion control               |0                                           |0.00 %                                      |0                                           |0.00 %                                      |0                                           |0.00 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Unmapped reads                              |117672229                                   |12.35 %                                     |56586726                                    |11.88 %                                     |61085503                                    |12.83 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Bisulfite_reads C2T                         |427370241                                   |44.86 %                                     |214752151                                   |45.09 %                                     |212618090                                   |44.64 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Bisulfite_reads G2A                         |407546024                                   |42.78 %                                     |204955370                                   |43.03 %                                     |202590654                                   |42.53 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+

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

+--------------------------------------------+-------------------------------------------+
|Concept                                     |Value                                      |
+============================================+===========================================+
|Unique Fragments                            |359113419                                  |
+--------------------------------------------+-------------------------------------------+
|Average Unique                              |75.40 %                                    |
+--------------------------------------------+-------------------------------------------+

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

+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Concept                                     |Total Bases                                 |%                                           |P1 Bases                                    |%                                           |P2 Bases                                    |%                                          |
+============================================+============================================+============================================+============================================+============================================+============================================+===========================================+
|Base Counts Overall A                       |54077019545                                 |37.60 %                                     |24154953970                                 |33.59 %                                     |29922065575                                 |41.60 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall C                       |17182842359                                 |11.95 %                                     |2419391807                                  |3.36 %                                      |14763450552                                 |20.53 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall G                       |17285357145                                 |12.02 %                                     |14718443246                                 |20.46 %                                     |2566913899                                  |3.57 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall T                       |54323160794                                 |37.77 %                                     |30143717386                                 |41.91 %                                     |24179443408                                 |33.62 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall N                       |972482751                                   |0.68 %                                      |483924888                                   |0.67 %                                      |488557863                                   |0.68 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+

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

+--------------------------------------------+-------------------------------------------+
|Bisulfite Conversion Type                   |Conversion Rate                            |
+============================================+===========================================+
|Under Conversion Rate                       |0.8702133790556316                         |
+--------------------------------------------+-------------------------------------------+
|Over Conversion Rate                        |NA                                         |
+--------------------------------------------+-------------------------------------------+

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

+--------------------------------------------+-------------------------------------------+
|Concept                                     |Total Reads                                |
+============================================+===========================================+
|Correct Pairs                               |401988885                                  |
+--------------------------------------------+-------------------------------------------+

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

.. image:: HFJM5CCXY_4_2_mapq.png

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

+--------------------------------------------+-------------------------------------------+
|Read Length                                 |Reads                                      |
+============================================+===========================================+
|150                                         |476294247                                  |
+--------------------------------------------+-------------------------------------------+
|150                                         |476294247                                  |
+--------------------------------------------+-------------------------------------------+

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

.. image:: HFJM5CCXY_4_2_isize.png

