Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-105.fastq.uq.polyn	RAL-105.filter	percent
uq reads:	29643991	1341627	4.5258%
   reads: 	31610042	1766109	5.5872%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-105.filter	RAL-105.nostrna	percent
uq reads:	1341627	1298684	96.7992%
   reads: 	1766109	1715982	97.1617%
----------------
TE_filter:
  reads:	RAL-105.nostrna	RAL-105.noTE	percent
uq reads:	1298684	1292069	99.4906%
   reads: 	1715982	1708000	99.5348%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-105.noGEN.front	RAL-105.noGEN.front.gen	percent
uq reads:	1292069	425040	32.8961%
   reads: 	1708000	703307	41.1772%
----------------
match_TE:2:
  reads:	RAL-105.noGEN.front	RAL-105.noGEN.front.TE	percent
uq reads:	1292069	68121	5.2722%
   reads: 	1708000	72025	4.2169%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-105.noGEN.end	RAL-105.noGEN.end.gen	percent
uq reads:	1292069	333867	25.8397%
   reads: 	1708000	609187	35.6667%
----------------
match_TE:2:
  reads:	RAL-105.noGEN.end	RAL-105.noGEN.end.TE	percent
uq reads:	1292069	57609	4.4587%
   reads: 	1708000	61469	3.5989%
----------------
Candidate insertion sites in file: RAL-105_insert.txt
  reads:	5427
  uqreads:	5305
  Number of Candidate sites:	5305

Level 1 collapse of insertion sites in file: RAL-105_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	372

Level 1 annotation file: RAL-105_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-105_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-105.noGEN.front	RAL-105.noGEN.front.gendel	percent
uq reads:	1292069	425040	32.8961%
   reads: 	1708000	703307	41.1772%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-105.noGEN.end	RAL-105.noGEN.end.gendel	percent
uq reads:	1292069	333867	25.8397%
   reads: 	1708000	609187	35.6667%
----------------
Candidate breakpoint sites in file: RAL-105_depletion.xls
  reads:	14240
  uqreads:	13779
  Number of reads supporting candidate sites:	13779

Level 1 collapse of depletion sites in file: RAL-105_depletion_level1.xls
  Number of Level 1 collapsed sites:	1401