Processing Report

HiCUP_output/Sample-3.A012.C8H0KANXX.s_2.r_1_2

15-53-36_21-03-2016


Truncating and Mapping

  Read 1 Read 2
Total Reads 88983957 88983957
Not Truncated 77270539 77306028
Truncated 11713418 11677929
Too short to map 362269 343348
Average length of truncated sequence 68.86 69.83
  Read 1 Read 2
Unique Alignments 41016766 40669060
Multiple Alignments 10775430 10669903
Failed To Align 36829492 37301646
Paired 34359246 34359246

Filtering

  Di-Tag Count
Valid Pairs 13479427
Invalid Pairs 20879819
Same Circularised 1326386
Same Fragment Dangling Ends 4687182
Same Fragment Internal 10511940
Re-ligation 3796438
Contiguous Sequence 180685
Wrong Size 377188
Total Pairs 34359246

Di-tag length Distribution


De-duplication

Percentage uniques: 12.62

  All Di-Tags Unique Di-Tags
Read Pairs 13479427 1700554
Cis-close (< 10Kbp) 2226005 279083
Cis-far (> 10Kbp) 5286795 664459
Trans 5966627 757012