Processing Report

HiCUP_output/Sample-2.A006.C8LFMANXX.s_3.r_1_2

18-19-10_14-03-2016


Truncating and Mapping

  Read 1 Read 2
Total Reads 52316898 52316898
Not Truncated 32192721 32433590
Truncated 20124177 19883308
Too short to map 962947 914822
Average length of truncated sequence 66.11 66.83
  Read 1 Read 2
Unique Alignments 39321762 39112933
Multiple Alignments 8818185 8749902
Failed To Align 3214004 3539241
Paired 31163044 31163044

Filtering

  Di-Tag Count
Valid Pairs 24532872
Invalid Pairs 6630172
Same Circularised 342377
Same Fragment Dangling Ends 466229
Same Fragment Internal 1777624
Re-ligation 2867016
Contiguous Sequence 207732
Wrong Size 969194
Total Pairs 31163044

Di-tag length Distribution


De-duplication

Percentage uniques: 87.14

  All Di-Tags Unique Di-Tags
Read Pairs 24532872 21378250
Cis-close (< 10Kbp) 5251509 4556068
Cis-far (> 10Kbp) 16883070 14724374
Trans 2398293 2097808