Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-761.fastq.uq.polyn	RAL-761.filter	percent
uq reads:	37657716	4604745	12.2279%
   reads: 	40128330	5409808	13.4813%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-761.filter	RAL-761.nostrna	percent
uq reads:	4604745	2527509	54.8892%
   reads: 	5409808	2796717	51.6972%
----------------
TE_filter:
  reads:	RAL-761.nostrna	RAL-761.noTE	percent
uq reads:	2527509	2507818	99.2209%
   reads: 	2796717	2773078	99.1548%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-761.noGEN.front	RAL-761.noGEN.front.gen	percent
uq reads:	2507818	815854	32.5324%
   reads: 	2773078	961680	34.6792%
----------------
match_TE:2:
  reads:	RAL-761.noGEN.front	RAL-761.noGEN.front.TE	percent
uq reads:	2507818	107990	4.3061%
   reads: 	2773078	110866	3.9979%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-761.noGEN.end	RAL-761.noGEN.end.gen	percent
uq reads:	2507818	659583	26.3011%
   reads: 	2773078	795297	28.6792%
----------------
match_TE:2:
  reads:	RAL-761.noGEN.end	RAL-761.noGEN.end.TE	percent
uq reads:	2507818	101919	4.0641%
   reads: 	2773078	105647	3.8097%
----------------
Candidate insertion sites in file: RAL-761_insert.txt
  reads:	11699
  uqreads:	11501
  Number of Candidate sites:	11501

Level 1 collapse of insertion sites in file: RAL-761_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	512

Level 1 annotation file: RAL-761_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-761_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-761.noGEN.front	RAL-761.noGEN.front.gendel	percent
uq reads:	2507818	815854	32.5324%
   reads: 	2773078	961680	34.6792%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-761.noGEN.end	RAL-761.noGEN.end.gendel	percent
uq reads:	2507818	659583	26.3011%
   reads: 	2773078	795297	28.6792%
----------------
Candidate breakpoint sites in file: RAL-761_depletion.xls
  reads:	22006
  uqreads:	21372
  Number of reads supporting candidate sites:	21372

Level 1 collapse of depletion sites in file: RAL-761_depletion_level1.xls
  Number of Level 1 collapsed sites:	1640