Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-707.fastq.uq.polyn	RAL-707.filter	percent
uq reads:	42376627	6825216	16.1061%
   reads: 	45289473	7596271	16.7727%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-707.filter	RAL-707.nostrna	percent
uq reads:	6825216	5609915	82.1940%
   reads: 	7596271	6209007	81.7376%
----------------
TE_filter:
  reads:	RAL-707.nostrna	RAL-707.noTE	percent
uq reads:	5609915	5602792	99.8730%
   reads: 	6209007	6200358	99.8607%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-707.noGEN.front	RAL-707.noGEN.front.gen	percent
uq reads:	5602792	2206644	39.3847%
   reads: 	6200358	2577396	41.5685%
----------------
match_TE:2:
  reads:	RAL-707.noGEN.front	RAL-707.noGEN.front.TE	percent
uq reads:	5602792	309731	5.5282%
   reads: 	6200358	314118	5.0661%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-707.noGEN.end	RAL-707.noGEN.end.gen	percent
uq reads:	5602792	598193	10.6767%
   reads: 	6200358	933851	15.0612%
----------------
match_TE:2:
  reads:	RAL-707.noGEN.end	RAL-707.noGEN.end.TE	percent
uq reads:	5602792	136940	2.4441%
   reads: 	6200358	142971	2.3059%
----------------
Candidate insertion sites in file: RAL-707_insert.txt
  reads:	11200
  uqreads:	10888
  Number of Candidate sites:	10888

Level 1 collapse of insertion sites in file: RAL-707_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	499

Level 1 annotation file: RAL-707_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-707_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-707.noGEN.front	RAL-707.noGEN.front.gendel	percent
uq reads:	5602792	2206644	39.3847%
   reads: 	6200358	2577396	41.5685%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-707.noGEN.end	RAL-707.noGEN.end.gendel	percent
uq reads:	5602792	598193	10.6767%
   reads: 	6200358	933851	15.0612%
----------------
Candidate breakpoint sites in file: RAL-707_depletion.xls
  reads:	23325
  uqreads:	21489
  Number of reads supporting candidate sites:	21489

Level 1 collapse of depletion sites in file: RAL-707_depletion_level1.xls
  Number of Level 1 collapsed sites:	2141