Insertion Pipeline
Bowtie2_wholegenome:
  reads:	D20-c2.fastq.uq.polyn	D20-c2.filter	percent
uq reads:	43813133	2014404	4.5977%
   reads: 	52937322	2877098	5.4349%
----------------
virus_structural_rna_repbase_filter:
  reads:	D20-c2.filter	D20-c2.nostrna	percent
uq reads:	2014404	1977528	98.1694%
   reads: 	2877098	2817586	97.9315%
----------------
TE_filter:
  reads:	D20-c2.nostrna	D20-c2.noTE	percent
uq reads:	1977528	1971348	99.6875%
   reads: 	2817586	2810634	99.7533%
----------------
match_dm6_mask_gen:1:
  reads:	D20-c2.noGEN.front	D20-c2.noGEN.front.gen	percent
uq reads:	1971348	609944	30.9405%
   reads: 	2810634	1069161	38.0399%
----------------
match_TE:2:
  reads:	D20-c2.noGEN.front	D20-c2.noGEN.front.TE	percent
uq reads:	1971348	110737	5.6173%
   reads: 	2810634	122392	4.3546%
----------------
match_dm6_mask_gen:1:
  reads:	D20-c2.noGEN.end	D20-c2.noGEN.end.gen	percent
uq reads:	1971348	652693	33.1090%
   reads: 	2810634	1110784	39.5208%
----------------
match_TE:2:
  reads:	D20-c2.noGEN.end	D20-c2.noGEN.end.TE	percent
uq reads:	1971348	118104	5.9910%
   reads: 	2810634	129601	4.6111%
----------------
Candidate insertion sites in file: D20-c2_insert.txt
  reads:	17387
  uqreads:	16317
  Number of Candidate sites:	16317

Level 1 collapse of insertion sites in file: D20-c2_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	1080

Level 1 annotation file: D20-c2_level1siteannotation.xls
Insertion sites in fixed bin:
D20-c2_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	D20-c2.noGEN.front	D20-c2.noGEN.front.gendel	percent
uq reads:	1971348	609944	30.9405%
   reads: 	2810634	1069161	38.0399%
----------------
match_dm6_mask_gen_del:1:
  reads:	D20-c2.noGEN.end	D20-c2.noGEN.end.gendel	percent
uq reads:	1971348	652693	33.1090%
   reads: 	2810634	1110784	39.5208%
----------------
Candidate breakpoint sites in file: D20-c2_depletion.xls
  reads:	25711
  uqreads:	23546
  Number of reads supporting candidate sites:	23546

Level 1 collapse of depletion sites in file: D20-c2_depletion_level1.xls
  Number of Level 1 collapsed sites:	2176