Insertion Pipeline
Bowtie2_wholegenome:
  reads:	pool-EU-IT-DF1.fastq.uq.polyn	pool-EU-IT-DF1.filter	percent
uq reads:	20153678	2585568	12.8293%
   reads: 	22014267	2957968	13.4366%
----------------
virus_structural_rna_repbase_filter:
  reads:	pool-EU-IT-DF1.filter	pool-EU-IT-DF1.nostrna	percent
uq reads:	2585568	2240716	86.6624%
   reads: 	2957968	2523767	85.3210%
----------------
TE_filter:
  reads:	pool-EU-IT-DF1.nostrna	pool-EU-IT-DF1.noTE	percent
uq reads:	2240716	2233874	99.6947%
   reads: 	2523767	2514722	99.6416%
----------------
match_dm6_mask_gen:1:
  reads:	pool-EU-IT-DF1.noGEN.front	pool-EU-IT-DF1.noGEN.front.gen	percent
uq reads:	2233874	301380	13.4914%
   reads: 	2514722	341164	13.5667%
----------------
match_TE:2:
  reads:	pool-EU-IT-DF1.noGEN.front	pool-EU-IT-DF1.noGEN.front.TE	percent
uq reads:	2233874	42916	1.9211%
   reads: 	2514722	45894	1.8250%
----------------
match_dm6_mask_gen:1:
  reads:	pool-EU-IT-DF1.noGEN.end	pool-EU-IT-DF1.noGEN.end.gen	percent
uq reads:	2233874	291742	13.0599%
   reads: 	2514722	331559	13.1847%
----------------
match_TE:2:
  reads:	pool-EU-IT-DF1.noGEN.end	pool-EU-IT-DF1.noGEN.end.TE	percent
uq reads:	2233874	42458	1.9006%
   reads: 	2514722	45480	1.8085%
----------------
Candidate insertion sites in file: pool-EU-IT-DF1_insert.txt
  reads:	7284
  uqreads:	6978
  Number of Candidate sites:	6978

Level 1 collapse of insertion sites in file: pool-EU-IT-DF1_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	82

Level 1 annotation file: pool-EU-IT-DF1_level1siteannotation.xls
Insertion sites in fixed bin:
pool-EU-IT-DF1_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	pool-EU-IT-DF1.noGEN.front	pool-EU-IT-DF1.noGEN.front.gendel	percent
uq reads:	2233874	305878	13.6927%
   reads: 	2514722	346394	13.7746%
----------------
match_dm6_mask_gen_del:1:
  reads:	pool-EU-IT-DF1.noGEN.end	pool-EU-IT-DF1.noGEN.end.gendel	percent
uq reads:	2233874	296082	13.2542%
   reads: 	2514722	336685	13.3886%
----------------
Candidate breakpoint sites in file: pool-EU-IT-DF1_depletion.xls
  reads:	17779
  uqreads:	16991
  Number of reads supporting candidate sites:	16991

Level 1 collapse of depletion sites in file: pool-EU-IT-DF1_depletion_level1.xls
  Number of Level 1 collapsed sites:	1050