Processing Report

HiCUP_output/Sample-1.A005.C8DRAANXX.s_2.r_1_2

17-27-31_15-03-2016


Truncating and Mapping

  Read 1 Read 2
Total Reads 26780491 26780491
Not Truncated 18418678 18343710
Truncated 8361813 8436781
Too short to map 431302 407260
Average length of truncated sequence 66.22 67.02
  Read 1 Read 2
Unique Alignments 20379141 20071745
Multiple Alignments 4263954 4167422
Failed To Align 1706094 2134064
Paired 15245021 15245021

Filtering

  Di-Tag Count
Valid Pairs 11314841
Invalid Pairs 3930180
Same Circularised 187236
Same Fragment Dangling Ends 298334
Same Fragment Internal 1580105
Re-ligation 924315
Contiguous Sequence 59919
Wrong Size 880271
Total Pairs 15245021

Di-tag length Distribution


De-duplication

Percentage uniques: 99.16

  All Di-Tags Unique Di-Tags
Read Pairs 11314841 11219537
Cis-close (< 10Kbp) 1509270 1495237
Cis-far (> 10Kbp) 7304795 7243835
Trans 2500776 2480465