Processing Report

HiCUP_output/Sample-1.A002.C8DRAANXX.s_2.r_1_2

17-27-31_15-03-2016


Truncating and Mapping

  Read 1 Read 2
Total Reads 28754600 28754600
Not Truncated 21205631 21308433
Truncated 7548969 7446167
Too short to map 751623 698375
Average length of truncated sequence 58.69 59.65
  Read 1 Read 2
Unique Alignments 21072845 20505141
Multiple Alignments 4475271 4336149
Failed To Align 2454861 3214935
Paired 14383198 14383198

Filtering

  Di-Tag Count
Valid Pairs 8935388
Invalid Pairs 5447810
Same Circularised 136087
Same Fragment Dangling Ends 530246
Same Fragment Internal 2442480
Re-ligation 834795
Contiguous Sequence 48328
Wrong Size 1455874
Total Pairs 14383198

Di-tag length Distribution


De-duplication

Percentage uniques: 99.21

  All Di-Tags Unique Di-Tags
Read Pairs 8935388 8864466
Cis-close (< 10Kbp) 1169666 1159324
Cis-far (> 10Kbp) 5787588 5742469
Trans 1978134 1962673