Processing Report

HiCUP_output/Sample-2.A019.C8LFMANXX.s_3.r_1_2

18-19-10_14-03-2016


Truncating and Mapping

  Read 1 Read 2
Total Reads 44617077 44617077
Not Truncated 27558024 27658661
Truncated 17059053 16958416
Too short to map 603703 578991
Average length of truncated sequence 67.04 67.71
  Read 1 Read 2
Unique Alignments 34317701 34096685
Multiple Alignments 7620595 7554610
Failed To Align 2075078 2386791
Paired 27507786 27507786

Filtering

  Di-Tag Count
Valid Pairs 21592114
Invalid Pairs 5915672
Same Circularised 288201
Same Fragment Dangling Ends 502256
Same Fragment Internal 1577602
Re-ligation 2509885
Contiguous Sequence 182456
Wrong Size 855272
Total Pairs 27507786

Di-tag length Distribution


De-duplication

Percentage uniques: 87.18

  All Di-Tags Unique Di-Tags
Read Pairs 21592114 18824646
Cis-close (< 10Kbp) 4679346 4055746
Cis-far (> 10Kbp) 14807202 12927006
Trans 2105566 1841894