Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-850.fastq.uq.polyn	RAL-850.filter	percent
uq reads:	60836947	6121770	10.0626%
   reads: 	68872121	8433487	12.2451%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-850.filter	RAL-850.nostrna	percent
uq reads:	6121770	4157362	67.9111%
   reads: 	8433487	5350787	63.4469%
----------------
TE_filter:
  reads:	RAL-850.nostrna	RAL-850.noTE	percent
uq reads:	4157362	4145144	99.7061%
   reads: 	5350787	5334595	99.6974%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-850.noGEN.front	RAL-850.noGEN.front.gen	percent
uq reads:	4145144	1327385	32.0227%
   reads: 	5334595	1637304	30.6922%
----------------
match_TE:2:
  reads:	RAL-850.noGEN.front	RAL-850.noGEN.front.TE	percent
uq reads:	4145144	219587	5.2975%
   reads: 	5334595	237274	4.4478%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-850.noGEN.end	RAL-850.noGEN.end.gen	percent
uq reads:	4145144	882665	21.2940%
   reads: 	5334595	1182463	22.1659%
----------------
match_TE:2:
  reads:	RAL-850.noGEN.end	RAL-850.noGEN.end.TE	percent
uq reads:	4145144	167183	4.0332%
   reads: 	5334595	184254	3.4539%
----------------
Candidate insertion sites in file: RAL-850_insert.txt
  reads:	37258
  uqreads:	35695
  Number of Candidate sites:	35695

Level 1 collapse of insertion sites in file: RAL-850_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	621

Level 1 annotation file: RAL-850_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-850_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-850.noGEN.front	RAL-850.noGEN.front.gendel	percent
uq reads:	4145144	1327385	32.0227%
   reads: 	5334595	1637304	30.6922%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-850.noGEN.end	RAL-850.noGEN.end.gendel	percent
uq reads:	4145144	882665	21.2940%
   reads: 	5334595	1182463	22.1659%
----------------
Candidate breakpoint sites in file: RAL-850_depletion.xls
  reads:	100095
  uqreads:	94735
  Number of reads supporting candidate sites:	94735

Level 1 collapse of depletion sites in file: RAL-850_depletion_level1.xls
  Number of Level 1 collapsed sites:	4078