Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-730.fastq.uq.polyn	RAL-730.filter	percent
uq reads:	35529408	4194299	11.8051%
   reads: 	37649235	4651688	12.3553%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-730.filter	RAL-730.nostrna	percent
uq reads:	4194299	3191081	76.0814%
   reads: 	4651688	3570069	76.7478%
----------------
TE_filter:
  reads:	RAL-730.nostrna	RAL-730.noTE	percent
uq reads:	3191081	3171537	99.3875%
   reads: 	3570069	3549255	99.4170%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-730.noGEN.front	RAL-730.noGEN.front.gen	percent
uq reads:	3171537	1241982	39.1603%
   reads: 	3549255	1479615	41.6880%
----------------
match_TE:2:
  reads:	RAL-730.noGEN.front	RAL-730.noGEN.front.TE	percent
uq reads:	3171537	154262	4.8640%
   reads: 	3549255	160056	4.5096%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-730.noGEN.end	RAL-730.noGEN.end.gen	percent
uq reads:	3171537	1039263	32.7684%
   reads: 	3549255	1268895	35.7510%
----------------
match_TE:2:
  reads:	RAL-730.noGEN.end	RAL-730.noGEN.end.TE	percent
uq reads:	3171537	162573	5.1260%
   reads: 	3549255	169074	4.7636%
----------------
Candidate insertion sites in file: RAL-730_insert.txt
  reads:	20257
  uqreads:	20111
  Number of Candidate sites:	20111

Level 1 collapse of insertion sites in file: RAL-730_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	422

Level 1 annotation file: RAL-730_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-730_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-730.noGEN.front	RAL-730.noGEN.front.gendel	percent
uq reads:	3171537	1241982	39.1603%
   reads: 	3549255	1479615	41.6880%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-730.noGEN.end	RAL-730.noGEN.end.gendel	percent
uq reads:	3171537	1039263	32.7684%
   reads: 	3549255	1268895	35.7510%
----------------
Candidate breakpoint sites in file: RAL-730_depletion.xls
  reads:	37718
  uqreads:	37179
  Number of reads supporting candidate sites:	37179

Level 1 collapse of depletion sites in file: RAL-730_depletion_level1.xls
  Number of Level 1 collapsed sites:	1605