Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-40.fastq.uq.polyn	RAL-40.filter	percent
uq reads:	59497248	5388203	9.0562%
   reads: 	67519994	6965316	10.3159%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-40.filter	RAL-40.nostrna	percent
uq reads:	5388203	3258134	60.4679%
   reads: 	6965316	4063456	58.3384%
----------------
TE_filter:
  reads:	RAL-40.nostrna	RAL-40.noTE	percent
uq reads:	3258134	3245841	99.6227%
   reads: 	4063456	4046851	99.5914%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-40.noGEN.front	RAL-40.noGEN.front.gen	percent
uq reads:	3245841	1023871	31.5441%
   reads: 	4046851	1239047	30.6176%
----------------
match_TE:2:
  reads:	RAL-40.noGEN.front	RAL-40.noGEN.front.TE	percent
uq reads:	3245841	173166	5.3350%
   reads: 	4046851	187999	4.6456%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-40.noGEN.end	RAL-40.noGEN.end.gen	percent
uq reads:	3245841	643736	19.8326%
   reads: 	4046851	859062	21.2279%
----------------
match_TE:2:
  reads:	RAL-40.noGEN.end	RAL-40.noGEN.end.TE	percent
uq reads:	3245841	123984	3.8198%
   reads: 	4046851	138611	3.4252%
----------------
Candidate insertion sites in file: RAL-40_insert.txt
  reads:	23023
  uqreads:	21797
  Number of Candidate sites:	21797

Level 1 collapse of insertion sites in file: RAL-40_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	668

Level 1 annotation file: RAL-40_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-40_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-40.noGEN.front	RAL-40.noGEN.front.gendel	percent
uq reads:	3245841	1042943	32.1317%
   reads: 	4046851	1264173	31.2384%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-40.noGEN.end	RAL-40.noGEN.end.gendel	percent
uq reads:	3245841	655770	20.2034%
   reads: 	4046851	875255	21.6281%
----------------
Candidate breakpoint sites in file: RAL-40_depletion.xls
  reads:	57269
  uqreads:	53609
  Number of reads supporting candidate sites:	53609

Level 1 collapse of depletion sites in file: RAL-40_depletion_level1.xls
  Number of Level 1 collapsed sites:	3471