Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-310.fastq.uq.polyn	RAL-310.filter	percent
uq reads:	31878402	2749151	8.6239%
   reads: 	33139066	3039088	9.1707%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-310.filter	RAL-310.nostrna	percent
uq reads:	2749151	1776318	64.6133%
   reads: 	3039088	1997831	65.7378%
----------------
TE_filter:
  reads:	RAL-310.nostrna	RAL-310.noTE	percent
uq reads:	1776318	1767238	99.4888%
   reads: 	1997831	1987809	99.4984%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-310.noGEN.front	RAL-310.noGEN.front.gen	percent
uq reads:	1767238	573042	32.4259%
   reads: 	1987809	713504	35.8940%
----------------
match_TE:2:
  reads:	RAL-310.noGEN.front	RAL-310.noGEN.front.TE	percent
uq reads:	1767238	67195	3.8023%
   reads: 	1987809	69497	3.4962%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-310.noGEN.end	RAL-310.noGEN.end.gen	percent
uq reads:	1767238	505135	28.5833%
   reads: 	1987809	637938	32.0925%
----------------
match_TE:2:
  reads:	RAL-310.noGEN.end	RAL-310.noGEN.end.TE	percent
uq reads:	1767238	66180	3.7448%
   reads: 	1987809	68669	3.4545%
----------------
Candidate insertion sites in file: RAL-310_insert.txt
  reads:	5525
  uqreads:	5453
  Number of Candidate sites:	5453

Level 1 collapse of insertion sites in file: RAL-310_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	354

Level 1 annotation file: RAL-310_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-310_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-310.noGEN.front	RAL-310.noGEN.front.gendel	percent
uq reads:	1767238	573042	32.4259%
   reads: 	1987809	713504	35.8940%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-310.noGEN.end	RAL-310.noGEN.end.gendel	percent
uq reads:	1767238	505135	28.5833%
   reads: 	1987809	637938	32.0925%
----------------
Candidate breakpoint sites in file: RAL-310_depletion.xls
  reads:	12780
  uqreads:	12530
  Number of reads supporting candidate sites:	12530

Level 1 collapse of depletion sites in file: RAL-310_depletion_level1.xls
  Number of Level 1 collapsed sites:	1161