Processing Report

HiCUP_output/Sample-3.A006.C8H0KANXX.s_2.r_1_2

15-53-36_21-03-2016


Truncating and Mapping

  Read 1 Read 2
Total Reads 70954559 70954559
Not Truncated 58000756 57958038
Truncated 12953803 12996521
Too short to map 445321 422309
Average length of truncated sequence 68.33 69.35
  Read 1 Read 2
Unique Alignments 52564749 52344645
Multiple Alignments 12979739 12908077
Failed To Align 4964750 5279528
Paired 44061736 44061736

Filtering

  Di-Tag Count
Valid Pairs 16389479
Invalid Pairs 27672257
Same Circularised 1414759
Same Fragment Dangling Ends 8148030
Same Fragment Internal 12729367
Re-ligation 4166946
Contiguous Sequence 222556
Wrong Size 990599
Total Pairs 44061736

Di-tag length Distribution


De-duplication

Percentage uniques: 29.97

  All Di-Tags Unique Di-Tags
Read Pairs 16389479 4912154
Cis-close (< 10Kbp) 2798506 838257
Cis-far (> 10Kbp) 8277453 2480624
Trans 5313520 1593273