Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-796.fastq.uq.polyn	RAL-796.filter	percent
uq reads:	34941242	3610001	10.3316%
   reads: 	38350706	5097466	13.2917%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-796.filter	RAL-796.nostrna	percent
uq reads:	3610001	1544718	42.7900%
   reads: 	5097466	1918289	37.6322%
----------------
TE_filter:
  reads:	RAL-796.nostrna	RAL-796.noTE	percent
uq reads:	1544718	1531683	99.1562%
   reads: 	1918289	1901337	99.1163%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-796.noGEN.front	RAL-796.noGEN.front.gen	percent
uq reads:	1531683	573085	37.4154%
   reads: 	1901337	786717	41.3770%
----------------
match_TE:2:
  reads:	RAL-796.noGEN.front	RAL-796.noGEN.front.TE	percent
uq reads:	1531683	77031	5.0292%
   reads: 	1901337	80496	4.2337%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-796.noGEN.end	RAL-796.noGEN.end.gen	percent
uq reads:	1531683	535320	34.9498%
   reads: 	1901337	742327	39.0424%
----------------
match_TE:2:
  reads:	RAL-796.noGEN.end	RAL-796.noGEN.end.TE	percent
uq reads:	1531683	75955	4.9589%
   reads: 	1901337	80013	4.2082%
----------------
Candidate insertion sites in file: RAL-796_insert.txt
  reads:	8875
  uqreads:	8629
  Number of Candidate sites:	8629

Level 1 collapse of insertion sites in file: RAL-796_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	516

Level 1 annotation file: RAL-796_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-796_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-796.noGEN.front	RAL-796.noGEN.front.gendel	percent
uq reads:	1531683	573085	37.4154%
   reads: 	1901337	786717	41.3770%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-796.noGEN.end	RAL-796.noGEN.end.gendel	percent
uq reads:	1531683	535320	34.9498%
   reads: 	1901337	742327	39.0424%
----------------
Candidate breakpoint sites in file: RAL-796_depletion.xls
  reads:	21514
  uqreads:	20709
  Number of reads supporting candidate sites:	20709

Level 1 collapse of depletion sites in file: RAL-796_depletion_level1.xls
  Number of Level 1 collapsed sites:	1939