Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-195.fastq.uq.polyn	RAL-195.filter	percent
uq reads:	32567373	1798372	5.5220%
   reads: 	34743848	2404665	6.9211%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-195.filter	RAL-195.nostrna	percent
uq reads:	1798372	1750964	97.3638%
   reads: 	2404665	2351631	97.7945%
----------------
TE_filter:
  reads:	RAL-195.nostrna	RAL-195.noTE	percent
uq reads:	1750964	1737013	99.2032%
   reads: 	2351631	2335887	99.3305%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-195.noGEN.front	RAL-195.noGEN.front.gen	percent
uq reads:	1737013	499378	28.7492%
   reads: 	2335887	908982	38.9138%
----------------
match_TE:2:
  reads:	RAL-195.noGEN.front	RAL-195.noGEN.front.TE	percent
uq reads:	1737013	71047	4.0902%
   reads: 	2335887	74052	3.1702%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-195.noGEN.end	RAL-195.noGEN.end.gen	percent
uq reads:	1737013	409056	23.5494%
   reads: 	2335887	809041	34.6353%
----------------
match_TE:2:
  reads:	RAL-195.noGEN.end	RAL-195.noGEN.end.TE	percent
uq reads:	1737013	67961	3.9125%
   reads: 	2335887	71032	3.0409%
----------------
Candidate insertion sites in file: RAL-195_insert.txt
  reads:	6023
  uqreads:	5876
  Number of Candidate sites:	5876

Level 1 collapse of insertion sites in file: RAL-195_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	399

Level 1 annotation file: RAL-195_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-195_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-195.noGEN.front	RAL-195.noGEN.front.gendel	percent
uq reads:	1737013	499378	28.7492%
   reads: 	2335887	908982	38.9138%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-195.noGEN.end	RAL-195.noGEN.end.gendel	percent
uq reads:	1737013	409056	23.5494%
   reads: 	2335887	809041	34.6353%
----------------
Candidate breakpoint sites in file: RAL-195_depletion.xls
  reads:	14822
  uqreads:	14163
  Number of reads supporting candidate sites:	14163

Level 1 collapse of depletion sites in file: RAL-195_depletion_level1.xls
  Number of Level 1 collapsed sites:	1338