Sample PX0821_GATCAG_6_lane_gembs
=================================

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

+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Concept                                     |Total Reads                                 |%                                           |P1 Reads                                    |%                                           |P2 Reads                                    |%                                          |
+============================================+============================================+============================================+============================================+============================================+============================================+===========================================+
|Sequenced Reads                             |1789876858                                  |100.00 %                                    |894938429                                   |100.00 %                                    |894938429                                   |100.00 %                                   |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|General Reads                               |1721967858                                  |96.21 %                                     |870061762                                   |97.22 %                                     |851906096                                   |95.19 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Reads in Control sequences                  |0                                           |0.00 %                                      |0                                           |0.00 %                                      |0                                           |0.00 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Reads under conversion control              |23634883                                    |1.32 %                                      |11970889                                    |1.34 %                                      |11663994                                    |1.30 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Reads over conversion control               |0                                           |0.00 %                                      |0                                           |0.00 %                                      |0                                           |0.00 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Unmapped reads                              |44274117                                    |2.47 %                                      |12905778                                    |1.44 %                                      |31368339                                    |3.51 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Bisulfite_reads C2T                         |888002315                                   |49.61 %                                     |448650623                                   |50.13 %                                     |439351692                                   |49.09 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Bisulfite_reads G2A                         |857600426                                   |47.91 %                                     |433382028                                   |48.43 %                                     |424218398                                   |47.40 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+

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

+--------------------------------------------+-------------------------------------------+
|Concept                                     |Value                                      |
+============================================+===========================================+
|Unique Fragments                            |382954067                                  |
+--------------------------------------------+-------------------------------------------+
|Average Unique                              |42.79 %                                    |
+--------------------------------------------+-------------------------------------------+

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

+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Concept                                     |Total Bases                                 |%                                           |P1 Bases                                    |%                                           |P2 Bases                                    |%                                          |
+============================================+============================================+============================================+============================================+============================================+============================================+===========================================+
|Base Counts Overall A                       |97439123812                                 |36.05 %                                     |50330726843                                 |37.24 %                                     |47108396969                                 |34.86 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall C                       |37814326918                                 |13.99 %                                     |20285381213                                 |15.01 %                                     |17528945705                                 |12.97 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall G                       |40210889111                                 |14.88 %                                     |18428949086                                 |13.64 %                                     |21781940025                                 |16.12 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall T                       |92991356164                                 |34.41 %                                     |45187384927                                 |33.44 %                                     |47803971237                                 |35.37 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall N                       |1815709553                                  |0.67 %                                      |903260710                                   |0.67 %                                      |912448843                                   |0.68 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+

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

.. image:: PX0821_GATCAG_6_lane_gembs_mapq.png

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

+--------------------------------------------+-------------------------------------------+
|Bisulfite Conversion Type                   |Conversion Rate                            |
+============================================+===========================================+
|Under Conversion Rate                       |0.9690276694440193                         |
+--------------------------------------------+-------------------------------------------+
|Over Conversion Rate                        |NA                                         |
+--------------------------------------------+-------------------------------------------+

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

.. image:: PX0821_GATCAG_6_lane_gembs_isize.png

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

+--------------------------------------------+-------------------------------------------+
|Concept                                     |Total Reads                                |
+============================================+===========================================+
|Correct Pairs                               |596518655                                  |
+--------------------------------------------+-------------------------------------------+

Sample PX0821_GATCAG_6_lane_gembs Lane HJ353CCXY_8_2
----------------------------------------------------

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

+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Concept                                     |Total Reads                                 |%                                           |P1 Reads                                    |%                                           |P2 Reads                                    |%                                          |
+============================================+============================================+============================================+============================================+============================================+============================================+===========================================+
|Sequenced Reads                             |327606782                                   |100.00 %                                    |163803391                                   |100.00 %                                    |163803391                                   |100.00 %                                   |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|General Reads                               |315478015                                   |96.30 %                                     |159381094                                   |97.30 %                                     |156096921                                   |95.30 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Reads in Control sequences                  |0                                           |0.00 %                                      |0                                           |0.00 %                                      |0                                           |0.00 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Reads under conversion control              |4321128                                     |1.32 %                                      |2189561                                     |1.34 %                                      |2131567                                     |1.30 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Reads over conversion control               |0                                           |0.00 %                                      |0                                           |0.00 %                                      |0                                           |0.00 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Unmapped reads                              |7807639                                     |2.38 %                                      |2232736                                     |1.36 %                                      |5574903                                     |3.40 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Bisulfite_reads C2T                         |162691019                                   |49.66 %                                     |82184478                                    |50.17 %                                     |80506541                                    |49.15 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Bisulfite_reads G2A                         |157108124                                   |47.96 %                                     |79386177                                    |48.46 %                                     |77721947                                    |47.45 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+

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

+--------------------------------------------+-------------------------------------------+
|Concept                                     |Value                                      |
+============================================+===========================================+
|Unique Fragments                            |69258673                                   |
+--------------------------------------------+-------------------------------------------+
|Average Unique                              |42.28 %                                    |
+--------------------------------------------+-------------------------------------------+

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

+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Concept                                     |Total Bases                                 |%                                           |P1 Bases                                    |%                                           |P2 Bases                                    |%                                          |
+============================================+============================================+============================================+============================================+============================================+============================================+===========================================+
|Base Counts Overall A                       |17834922263                                 |36.05 %                                     |9218775000                                  |37.27 %                                     |8616147263                                  |34.83 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall C                       |6932699758                                  |14.01 %                                     |3726890839                                  |15.07 %                                     |3205808919                                  |12.96 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall G                       |7443229036                                  |15.05 %                                     |3389233867                                  |13.70 %                                     |4053995169                                  |16.39 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall T                       |16925202073                                 |34.21 %                                     |8233533979                                  |33.29 %                                     |8691668094                                  |35.14 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall N                       |332570952                                   |0.67 %                                      |165878356                                   |0.67 %                                      |166692596                                   |0.67 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+

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

+--------------------------------------------+-------------------------------------------+
|Bisulfite Conversion Type                   |Conversion Rate                            |
+============================================+===========================================+
|Under Conversion Rate                       |0.9679110338642172                         |
+--------------------------------------------+-------------------------------------------+
|Over Conversion Rate                        |NA                                         |
+--------------------------------------------+-------------------------------------------+

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

+--------------------------------------------+-------------------------------------------+
|Concept                                     |Total Reads                                |
+============================================+===========================================+
|Correct Pairs                               |108162368                                  |
+--------------------------------------------+-------------------------------------------+

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

.. image:: HJ353CCXY_8_2_mapq.png

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

+--------------------------------------------+-------------------------------------------+
|Read Length                                 |Reads                                      |
+============================================+===========================================+
|150                                         |163803391                                  |
+--------------------------------------------+-------------------------------------------+
|150                                         |163803391                                  |
+--------------------------------------------+-------------------------------------------+

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

.. image:: HJ353CCXY_8_2_isize.png

Sample PX0821_GATCAG_6_lane_gembs Lane HL2VKCCXY_6_2
----------------------------------------------------

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

+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Concept                                     |Total Reads                                 |%                                           |P1 Reads                                    |%                                           |P2 Reads                                    |%                                          |
+============================================+============================================+============================================+============================================+============================================+============================================+===========================================+
|Sequenced Reads                             |294236138                                   |100.00 %                                    |147118069                                   |100.00 %                                    |147118069                                   |100.00 %                                   |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|General Reads                               |283111817                                   |96.22 %                                     |143025700                                   |97.22 %                                     |140086117                                   |95.22 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Reads in Control sequences                  |0                                           |0.00 %                                      |0                                           |0.00 %                                      |0                                           |0.00 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Reads under conversion control              |3890762                                     |1.32 %                                      |1970506                                     |1.34 %                                      |1920256                                     |1.31 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Reads over conversion control               |0                                           |0.00 %                                      |0                                           |0.00 %                                      |0                                           |0.00 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Unmapped reads                              |7233559                                     |2.46 %                                      |2121863                                     |1.44 %                                      |5111696                                     |3.47 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Bisulfite_reads C2T                         |145992385                                   |49.62 %                                     |73750823                                    |50.13 %                                     |72241562                                    |49.10 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Bisulfite_reads G2A                         |141010194                                   |47.92 %                                     |71245383                                    |48.43 %                                     |69764811                                    |47.42 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+

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

+--------------------------------------------+-------------------------------------------+
|Concept                                     |Value                                      |
+============================================+===========================================+
|Unique Fragments                            |63106061                                   |
+--------------------------------------------+-------------------------------------------+
|Average Unique                              |42.89 %                                    |
+--------------------------------------------+-------------------------------------------+

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

+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Concept                                     |Total Bases                                 |%                                           |P1 Bases                                    |%                                           |P2 Bases                                    |%                                          |
+============================================+============================================+============================================+============================================+============================================+============================================+===========================================+
|Base Counts Overall A                       |16021585015                                 |36.06 %                                     |8274008513                                  |37.25 %                                     |7747576502                                  |34.88 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall C                       |6213276034                                  |13.98 %                                     |3331173268                                  |15.00 %                                     |2882102766                                  |12.97 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall G                       |6587738065                                  |14.83 %                                     |3024893195                                  |13.62 %                                     |3562844870                                  |16.04 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall T                       |15308985421                                 |34.46 %                                     |7436285202                                  |33.47 %                                     |7872700219                                  |35.44 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall N                       |298072303                                   |0.67 %                                      |148468241                                   |0.67 %                                      |149604062                                   |0.67 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+

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

+--------------------------------------------+-------------------------------------------+
|Bisulfite Conversion Type                   |Conversion Rate                            |
+============================================+===========================================+
|Under Conversion Rate                       |0.9691934335969773                         |
+--------------------------------------------+-------------------------------------------+
|Over Conversion Rate                        |NA                                         |
+--------------------------------------------+-------------------------------------------+

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

+--------------------------------------------+-------------------------------------------+
|Concept                                     |Total Reads                                |
+============================================+===========================================+
|Correct Pairs                               |98259218                                   |
+--------------------------------------------+-------------------------------------------+

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

.. image:: HL2VKCCXY_6_2_mapq.png

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

+--------------------------------------------+-------------------------------------------+
|Read Length                                 |Reads                                      |
+============================================+===========================================+
|150                                         |147118069                                  |
+--------------------------------------------+-------------------------------------------+
|150                                         |147118069                                  |
+--------------------------------------------+-------------------------------------------+

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

.. image:: HL2VKCCXY_6_2_isize.png

Sample PX0821_GATCAG_6_lane_gembs Lane HL2VKCCXY_7_2
----------------------------------------------------

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

+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Concept                                     |Total Reads                                 |%                                           |P1 Reads                                    |%                                           |P2 Reads                                    |%                                          |
+============================================+============================================+============================================+============================================+============================================+============================================+===========================================+
|Sequenced Reads                             |294128702                                   |100.00 %                                    |147064351                                   |100.00 %                                    |147064351                                   |100.00 %                                   |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|General Reads                               |282902069                                   |96.18 %                                     |142940374                                   |97.20 %                                     |139961695                                   |95.17 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Reads in Control sequences                  |0                                           |0.00 %                                      |0                                           |0.00 %                                      |0                                           |0.00 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Reads under conversion control              |3879926                                     |1.32 %                                      |1964785                                     |1.34 %                                      |1915141                                     |1.30 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Reads over conversion control               |0                                           |0.00 %                                      |0                                           |0.00 %                                      |0                                           |0.00 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Unmapped reads                              |7346707                                     |2.50 %                                      |2159192                                     |1.47 %                                      |5187515                                     |3.53 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Bisulfite_reads C2T                         |145902637                                   |49.61 %                                     |73715776                                    |50.12 %                                     |72186861                                    |49.09 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Bisulfite_reads G2A                         |140879358                                   |47.90 %                                     |71189383                                    |48.41 %                                     |69689975                                    |47.39 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+

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

+--------------------------------------------+-------------------------------------------+
|Concept                                     |Value                                      |
+============================================+===========================================+
|Unique Fragments                            |63154921                                   |
+--------------------------------------------+-------------------------------------------+
|Average Unique                              |42.94 %                                    |
+--------------------------------------------+-------------------------------------------+

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

+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Concept                                     |Total Bases                                 |%                                           |P1 Bases                                    |%                                           |P2 Bases                                    |%                                          |
+============================================+============================================+============================================+============================================+============================================+============================================+===========================================+
|Base Counts Overall A                       |16011460271                                 |36.05 %                                     |8265246677                                  |37.22 %                                     |7746213594                                  |34.88 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall C                       |6215463890                                  |13.99 %                                     |3328879883                                  |14.99 %                                     |2886584007                                  |13.00 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall G                       |6587493573                                  |14.83 %                                     |3028029807                                  |13.64 %                                     |3559463766                                  |16.03 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall T                       |15301568443                                 |34.45 %                                     |7436537636                                  |33.49 %                                     |7865030807                                  |35.42 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall N                       |297447825                                   |0.67 %                                      |148022998                                   |0.67 %                                      |149424827                                   |0.67 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+

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

+--------------------------------------------+-------------------------------------------+
|Bisulfite Conversion Type                   |Conversion Rate                            |
+============================================+===========================================+
|Under Conversion Rate                       |0.9691063111983416                         |
+--------------------------------------------+-------------------------------------------+
|Over Conversion Rate                        |NA                                         |
+--------------------------------------------+-------------------------------------------+

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

+--------------------------------------------+-------------------------------------------+
|Concept                                     |Total Reads                                |
+============================================+===========================================+
|Correct Pairs                               |98312021                                   |
+--------------------------------------------+-------------------------------------------+

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

.. image:: HL2VKCCXY_7_2_mapq.png

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

+--------------------------------------------+-------------------------------------------+
|Read Length                                 |Reads                                      |
+============================================+===========================================+
|150                                         |147064351                                  |
+--------------------------------------------+-------------------------------------------+
|150                                         |147064351                                  |
+--------------------------------------------+-------------------------------------------+

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

.. image:: HL2VKCCXY_7_2_isize.png

Sample PX0821_GATCAG_6_lane_gembs Lane HL2VKCCXY_4_2
----------------------------------------------------

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

+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Concept                                     |Total Reads                                 |%                                           |P1 Reads                                    |%                                           |P2 Reads                                    |%                                          |
+============================================+============================================+============================================+============================================+============================================+============================================+===========================================+
|Sequenced Reads                             |291964890                                   |100.00 %                                    |145982445                                   |100.00 %                                    |145982445                                   |100.00 %                                   |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|General Reads                               |280905173                                   |96.21 %                                     |141884274                                   |97.19 %                                     |139020899                                   |95.23 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Reads in Control sequences                  |0                                           |0.00 %                                      |0                                           |0.00 %                                      |0                                           |0.00 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Reads under conversion control              |3845406                                     |1.32 %                                      |1946410                                     |1.33 %                                      |1898996                                     |1.30 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Reads over conversion control               |0                                           |0.00 %                                      |0                                           |0.00 %                                      |0                                           |0.00 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Unmapped reads                              |7214311                                     |2.47 %                                      |2151761                                     |1.47 %                                      |5062550                                     |3.47 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Bisulfite_reads C2T                         |144839881                                   |49.61 %                                     |73153357                                    |50.11 %                                     |71686524                                    |49.11 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Bisulfite_reads G2A                         |139910698                                   |47.92 %                                     |70677327                                    |48.41 %                                     |69233371                                    |47.43 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+

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

+--------------------------------------------+-------------------------------------------+
|Concept                                     |Value                                      |
+============================================+===========================================+
|Unique Fragments                            |62740296                                   |
+--------------------------------------------+-------------------------------------------+
|Average Unique                              |42.98 %                                    |
+--------------------------------------------+-------------------------------------------+

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

+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Concept                                     |Total Bases                                 |%                                           |P1 Bases                                    |%                                           |P2 Bases                                    |%                                          |
+============================================+============================================+============================================+============================================+============================================+============================================+===========================================+
|Base Counts Overall A                       |15887148338                                 |36.04 %                                     |8203498385                                  |37.22 %                                     |7683649953                                  |34.86 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall C                       |6162535738                                  |13.98 %                                     |3303092026                                  |14.98 %                                     |2859443712                                  |12.97 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall G                       |6554063120                                  |14.87 %                                     |3008781495                                  |13.65 %                                     |3545281625                                  |16.08 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall T                       |15187984780                                 |34.45 %                                     |7380761705                                  |33.48 %                                     |7807223075                                  |35.42 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall N                       |294966414                                   |0.67 %                                      |147215584                                   |0.67 %                                      |147750830                                   |0.67 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+

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

+--------------------------------------------+-------------------------------------------+
|Bisulfite Conversion Type                   |Conversion Rate                            |
+============================================+===========================================+
|Under Conversion Rate                       |0.9692839916110536                         |
+--------------------------------------------+-------------------------------------------+
|Over Conversion Rate                        |NA                                         |
+--------------------------------------------+-------------------------------------------+

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

+--------------------------------------------+-------------------------------------------+
|Concept                                     |Total Reads                                |
+============================================+===========================================+
|Correct Pairs                               |97705652                                   |
+--------------------------------------------+-------------------------------------------+

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

.. image:: HL2VKCCXY_4_2_mapq.png

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

+--------------------------------------------+-------------------------------------------+
|Read Length                                 |Reads                                      |
+============================================+===========================================+
|150                                         |145982445                                  |
+--------------------------------------------+-------------------------------------------+
|150                                         |145982445                                  |
+--------------------------------------------+-------------------------------------------+

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

.. image:: HL2VKCCXY_4_2_isize.png

Sample PX0821_GATCAG_6_lane_gembs Lane HL2VKCCXY_5_2
----------------------------------------------------

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

+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Concept                                     |Total Reads                                 |%                                           |P1 Reads                                    |%                                           |P2 Reads                                    |%                                          |
+============================================+============================================+============================================+============================================+============================================+============================================+===========================================+
|Sequenced Reads                             |285847292                                   |100.00 %                                    |142923646                                   |100.00 %                                    |142923646                                   |100.00 %                                   |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|General Reads                               |274737598                                   |96.11 %                                     |138944093                                   |97.22 %                                     |135793505                                   |95.01 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Reads in Control sequences                  |0                                           |0.00 %                                      |0                                           |0.00 %                                      |0                                           |0.00 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Reads under conversion control              |3772727                                     |1.32 %                                      |1912222                                     |1.34 %                                      |1860505                                     |1.30 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Reads over conversion control               |0                                           |0.00 %                                      |0                                           |0.00 %                                      |0                                           |0.00 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Unmapped reads                              |7336967                                     |2.57 %                                      |2067331                                     |1.45 %                                      |5269636                                     |3.69 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Bisulfite_reads C2T                         |141680291                                   |49.57 %                                     |71645833                                    |50.13 %                                     |70034458                                    |49.00 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Bisulfite_reads G2A                         |136830034                                   |47.87 %                                     |69210482                                    |48.42 %                                     |67619552                                    |47.31 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+

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

+--------------------------------------------+-------------------------------------------+
|Concept                                     |Value                                      |
+============================================+===========================================+
|Unique Fragments                            |61374078                                   |
+--------------------------------------------+-------------------------------------------+
|Average Unique                              |42.94 %                                    |
+--------------------------------------------+-------------------------------------------+

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

+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Concept                                     |Total Bases                                 |%                                           |P1 Bases                                    |%                                           |P2 Bases                                    |%                                          |
+============================================+============================================+============================================+============================================+============================================+============================================+===========================================+
|Base Counts Overall A                       |15562558040                                 |36.06 %                                     |8040181346                                  |37.26 %                                     |7522376694                                  |34.86 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall C                       |6028643398                                  |13.97 %                                     |3233598254                                  |14.98 %                                     |2795045144                                  |12.95 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall G                       |6407133008                                  |14.84 %                                     |2936766242                                  |13.61 %                                     |3470366766                                  |16.08 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall T                       |14873016798                                 |34.46 %                                     |7226809495                                  |33.49 %                                     |7646207303                                  |35.43 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall N                       |291589848                                   |0.68 %                                      |144115209                                   |0.67 %                                      |147474639                                   |0.68 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+

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

+--------------------------------------------+-------------------------------------------+
|Bisulfite Conversion Type                   |Conversion Rate                            |
+============================================+===========================================+
|Under Conversion Rate                       |0.9696675558345442                         |
+--------------------------------------------+-------------------------------------------+
|Over Conversion Rate                        |NA                                         |
+--------------------------------------------+-------------------------------------------+

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

+--------------------------------------------+-------------------------------------------+
|Concept                                     |Total Reads                                |
+============================================+===========================================+
|Correct Pairs                               |95430371                                   |
+--------------------------------------------+-------------------------------------------+

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

.. image:: HL2VKCCXY_5_2_mapq.png

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

+--------------------------------------------+-------------------------------------------+
|Read Length                                 |Reads                                      |
+============================================+===========================================+
|150                                         |142923646                                  |
+--------------------------------------------+-------------------------------------------+
|150                                         |142923646                                  |
+--------------------------------------------+-------------------------------------------+

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

.. image:: HL2VKCCXY_5_2_isize.png

Sample PX0821_GATCAG_6_lane_gembs Lane HL2VKCCXY_8_2
----------------------------------------------------

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

+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Concept                                     |Total Reads                                 |%                                           |P1 Reads                                    |%                                           |P2 Reads                                    |%                                          |
+============================================+============================================+============================================+============================================+============================================+============================================+===========================================+
|Sequenced Reads                             |296093054                                   |100.00 %                                    |148046527                                   |100.00 %                                    |148046527                                   |100.00 %                                   |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|General Reads                               |284833186                                   |96.20 %                                     |143886227                                   |97.19 %                                     |140946959                                   |95.20 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Reads in Control sequences                  |0                                           |0.00 %                                      |0                                           |0.00 %                                      |0                                           |0.00 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Reads under conversion control              |3924934                                     |1.33 %                                      |1987405                                     |1.34 %                                      |1937529                                     |1.31 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Reads over conversion control               |0                                           |0.00 %                                      |0                                           |0.00 %                                      |0                                           |0.00 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Unmapped reads                              |7334934                                     |2.48 %                                      |2172895                                     |1.47 %                                      |5162039                                     |3.49 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Bisulfite_reads C2T                         |146896102                                   |49.61 %                                     |74200356                                    |50.12 %                                     |72695746                                    |49.10 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Bisulfite_reads G2A                         |141862018                                   |47.91 %                                     |71673276                                    |48.41 %                                     |70188742                                    |47.41 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+

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

+--------------------------------------------+-------------------------------------------+
|Concept                                     |Value                                      |
+============================================+===========================================+
|Unique Fragments                            |63320038                                   |
+--------------------------------------------+-------------------------------------------+
|Average Unique                              |42.77 %                                    |
+--------------------------------------------+-------------------------------------------+

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

+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Concept                                     |Total Bases                                 |%                                           |P1 Bases                                    |%                                           |P2 Bases                                    |%                                          |
+============================================+============================================+============================================+============================================+============================================+============================================+===========================================+
|Base Counts Overall A                       |16121449885                                 |36.06 %                                     |8329016922                                  |37.26 %                                     |7792432963                                  |34.86 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall C                       |6261708100                                  |14.01 %                                     |3361746943                                  |15.04 %                                     |2899961157                                  |12.97 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall G                       |6631232309                                  |14.83 %                                     |3041244480                                  |13.60 %                                     |3589987829                                  |16.06 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall T                       |15394598649                                 |34.43 %                                     |7473456910                                  |33.43 %                                     |7921141739                                  |35.43 %                                    |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+
|Base Counts Overall N                       |301062211                                   |0.67 %                                      |149560322                                   |0.67 %                                      |151501889                                   |0.68 %                                     |
+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+--------------------------------------------+-------------------------------------------+

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

+--------------------------------------------+-------------------------------------------+
|Bisulfite Conversion Type                   |Conversion Rate                            |
+============================================+===========================================+
|Under Conversion Rate                       |0.9691299511058831                         |
+--------------------------------------------+-------------------------------------------+
|Over Conversion Rate                        |NA                                         |
+--------------------------------------------+-------------------------------------------+

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

+--------------------------------------------+-------------------------------------------+
|Concept                                     |Total Reads                                |
+============================================+===========================================+
|Correct Pairs                               |98649025                                   |
+--------------------------------------------+-------------------------------------------+

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

.. image:: HL2VKCCXY_8_2_mapq.png

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

+--------------------------------------------+-------------------------------------------+
|Read Length                                 |Reads                                      |
+============================================+===========================================+
|150                                         |148046527                                  |
+--------------------------------------------+-------------------------------------------+
|150                                         |148046527                                  |
+--------------------------------------------+-------------------------------------------+

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

.. image:: HL2VKCCXY_8_2_isize.png

