Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-406.fastq.uq.polyn	RAL-406.filter	percent
uq reads:	44183582	3349380	7.5806%
   reads: 	49073136	4144704	8.4460%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-406.filter	RAL-406.nostrna	percent
uq reads:	3349380	3199823	95.5348%
   reads: 	4144704	3843673	92.7370%
----------------
TE_filter:
  reads:	RAL-406.nostrna	RAL-406.noTE	percent
uq reads:	3199823	3183665	99.4950%
   reads: 	3843673	3823580	99.4772%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-406.noGEN.front	RAL-406.noGEN.front.gen	percent
uq reads:	3183665	736034	23.1191%
   reads: 	3823580	860885	22.5152%
----------------
match_TE:2:
  reads:	RAL-406.noGEN.front	RAL-406.noGEN.front.TE	percent
uq reads:	3183665	99107	3.1130%
   reads: 	3823580	110903	2.9005%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-406.noGEN.end	RAL-406.noGEN.end.gen	percent
uq reads:	3183665	693382	21.7794%
   reads: 	3823580	814682	21.3068%
----------------
match_TE:2:
  reads:	RAL-406.noGEN.end	RAL-406.noGEN.end.TE	percent
uq reads:	3183665	98647	3.0985%
   reads: 	3823580	110576	2.8919%
----------------
Candidate insertion sites in file: RAL-406_insert.txt
  reads:	18228
  uqreads:	17582
  Number of Candidate sites:	17582

Level 1 collapse of insertion sites in file: RAL-406_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	579

Level 1 annotation file: RAL-406_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-406_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-406.noGEN.front	RAL-406.noGEN.front.gendel	percent
uq reads:	3183665	747575	23.4816%
   reads: 	3823580	874712	22.8768%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-406.noGEN.end	RAL-406.noGEN.end.gendel	percent
uq reads:	3183665	703527	22.0980%
   reads: 	3823580	826515	21.6163%
----------------
Candidate breakpoint sites in file: RAL-406_depletion.xls
  reads:	44640
  uqreads:	42862
  Number of reads supporting candidate sites:	42862

Level 1 collapse of depletion sites in file: RAL-406_depletion_level1.xls
  Number of Level 1 collapsed sites:	3090