Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-737.fastq.uq.polyn	RAL-737.filter	percent
uq reads:	66341966	10052104	15.1520%
   reads: 	73496220	12541778	17.0645%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-737.filter	RAL-737.nostrna	percent
uq reads:	10052104	4465459	44.4231%
   reads: 	12541778	5164854	41.1812%
----------------
TE_filter:
  reads:	RAL-737.nostrna	RAL-737.noTE	percent
uq reads:	4465459	4423358	99.0572%
   reads: 	5164854	5117401	99.0812%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-737.noGEN.front	RAL-737.noGEN.front.gen	percent
uq reads:	4423358	1458649	32.9761%
   reads: 	5117401	1626918	31.7919%
----------------
match_TE:2:
  reads:	RAL-737.noGEN.front	RAL-737.noGEN.front.TE	percent
uq reads:	4423358	164187	3.7118%
   reads: 	5117401	177373	3.4661%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-737.noGEN.end	RAL-737.noGEN.end.gen	percent
uq reads:	4423358	1165627	26.3516%
   reads: 	5117401	1330028	25.9903%
----------------
match_TE:2:
  reads:	RAL-737.noGEN.end	RAL-737.noGEN.end.TE	percent
uq reads:	4423358	157118	3.5520%
   reads: 	5117401	171050	3.3425%
----------------
Candidate insertion sites in file: RAL-737_insert.txt
  reads:	14801
  uqreads:	14388
  Number of Candidate sites:	14388

Level 1 collapse of insertion sites in file: RAL-737_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	612

Level 1 annotation file: RAL-737_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-737_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-737.noGEN.front	RAL-737.noGEN.front.gendel	percent
uq reads:	4423358	1458649	32.9761%
   reads: 	5117401	1626918	31.7919%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-737.noGEN.end	RAL-737.noGEN.end.gendel	percent
uq reads:	4423358	1165627	26.3516%
   reads: 	5117401	1330028	25.9903%
----------------
Candidate breakpoint sites in file: RAL-737_depletion.xls
  reads:	30525
  uqreads:	29357
  Number of reads supporting candidate sites:	29357

Level 1 collapse of depletion sites in file: RAL-737_depletion_level1.xls
  Number of Level 1 collapsed sites:	2536