Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-748_95b.fastq.uq.polyn	RAL-748_95b.filter	percent
uq reads:	34722785	5138860	14.7997%
   reads: 	36095020	5473455	15.1640%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-748_95b.filter	RAL-748_95b.nostrna	percent
uq reads:	5138860	3285661	63.9375%
   reads: 	5473455	3488367	63.7325%
----------------
TE_filter:
  reads:	RAL-748_95b.nostrna	RAL-748_95b.noTE	percent
uq reads:	3285661	3270358	99.5342%
   reads: 	3488367	3472533	99.5461%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-748_95b.noGEN.front	RAL-748_95b.noGEN.front.gen	percent
uq reads:	3270358	1023125	31.2848%
   reads: 	3472533	1096917	31.5884%
----------------
match_TE:2:
  reads:	RAL-748_95b.noGEN.front	RAL-748_95b.noGEN.front.TE	percent
uq reads:	3270358	124135	3.7958%
   reads: 	3472533	128619	3.7039%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-748_95b.noGEN.end	RAL-748_95b.noGEN.end.gen	percent
uq reads:	3270358	687435	21.0202%
   reads: 	3472533	756077	21.7731%
----------------
match_TE:2:
  reads:	RAL-748_95b.noGEN.end	RAL-748_95b.noGEN.end.TE	percent
uq reads:	3270358	125524	3.8382%
   reads: 	3472533	132001	3.8013%
----------------
Candidate insertion sites in file: RAL-748_95b_insert.txt
  reads:	13011
  uqreads:	12924
  Number of Candidate sites:	12924

Level 1 collapse of insertion sites in file: RAL-748_95b_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	435

Level 1 annotation file: RAL-748_95b_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-748_95b_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-748_95b.noGEN.front	RAL-748_95b.noGEN.front.gendel	percent
uq reads:	3270358	1023125	31.2848%
   reads: 	3472533	1096917	31.5884%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-748_95b.noGEN.end	RAL-748_95b.noGEN.end.gendel	percent
uq reads:	3270358	687435	21.0202%
   reads: 	3472533	756077	21.7731%
----------------
Candidate breakpoint sites in file: RAL-748_95b_depletion.xls
  reads:	23897
  uqreads:	23741
  Number of reads supporting candidate sites:	23741

Level 1 collapse of depletion sites in file: RAL-748_95b_depletion_level1.xls
  Number of Level 1 collapsed sites:	1981