Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-73.fastq.uq.polyn	RAL-73.filter	percent
uq reads:	30704168	1760991	5.7353%
   reads: 	32949070	2210312	6.7083%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-73.filter	RAL-73.nostrna	percent
uq reads:	1760991	1339818	76.0832%
   reads: 	2210312	1737295	78.5995%
----------------
TE_filter:
  reads:	RAL-73.nostrna	RAL-73.noTE	percent
uq reads:	1339818	1327052	99.0472%
   reads: 	1737295	1720821	99.0517%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-73.noGEN.front	RAL-73.noGEN.front.gen	percent
uq reads:	1327052	325287	24.5120%
   reads: 	1720821	580312	33.7230%
----------------
match_TE:2:
  reads:	RAL-73.noGEN.front	RAL-73.noGEN.front.TE	percent
uq reads:	1327052	56211	4.2358%
   reads: 	1720821	58769	3.4152%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-73.noGEN.end	RAL-73.noGEN.end.gen	percent
uq reads:	1327052	307091	23.1408%
   reads: 	1720821	565442	32.8589%
----------------
match_TE:2:
  reads:	RAL-73.noGEN.end	RAL-73.noGEN.end.TE	percent
uq reads:	1327052	55654	4.1938%
   reads: 	1720821	58210	3.3827%
----------------
Candidate insertion sites in file: RAL-73_insert.txt
  reads:	5879
  uqreads:	5734
  Number of Candidate sites:	5734

Level 1 collapse of insertion sites in file: RAL-73_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	411

Level 1 annotation file: RAL-73_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-73_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-73.noGEN.front	RAL-73.noGEN.front.gendel	percent
uq reads:	1327052	325287	24.5120%
   reads: 	1720821	580312	33.7230%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-73.noGEN.end	RAL-73.noGEN.end.gendel	percent
uq reads:	1327052	307091	23.1408%
   reads: 	1720821	565442	32.8589%
----------------
Candidate breakpoint sites in file: RAL-73_depletion.xls
  reads:	14091
  uqreads:	13523
  Number of reads supporting candidate sites:	13523

Level 1 collapse of depletion sites in file: RAL-73_depletion_level1.xls
  Number of Level 1 collapsed sites:	1321