Processing Report

HiCUP_output/Sample-2.A012.C8LFMANXX.s_3.r_1_2

18-19-10_14-03-2016


Truncating and Mapping

  Read 1 Read 2
Total Reads 43542862 43542862
Not Truncated 30710435 31083922
Truncated 12832427 12458940
Too short to map 589333 546108
Average length of truncated sequence 67.14 67.74
  Read 1 Read 2
Unique Alignments 34098328 33591997
Multiple Alignments 7182895 7071302
Failed To Align 1672306 2333455
Paired 27167640 27167640

Filtering

  Di-Tag Count
Valid Pairs 20377000
Invalid Pairs 6790640
Same Circularised 362905
Same Fragment Dangling Ends 484984
Same Fragment Internal 2016944
Re-ligation 2664241
Contiguous Sequence 184268
Wrong Size 1077298
Total Pairs 27167640

Di-tag length Distribution


De-duplication

Percentage uniques: 95.36

  All Di-Tags Unique Di-Tags
Read Pairs 20377000 19432336
Cis-close (< 10Kbp) 4281053 4073201
Cis-far (> 10Kbp) 14101172 13454368
Trans 1994775 1904767