Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-861.fastq.uq.polyn	RAL-861.filter	percent
uq reads:	38706124	7499369	19.3751%
   reads: 	40655771	8338320	20.5096%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-861.filter	RAL-861.nostrna	percent
uq reads:	7499369	2840907	37.8819%
   reads: 	8338320	3022181	36.2445%
----------------
TE_filter:
  reads:	RAL-861.nostrna	RAL-861.noTE	percent
uq reads:	2840907	2829120	99.5851%
   reads: 	3022181	3009898	99.5936%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-861.noGEN.front	RAL-861.noGEN.front.gen	percent
uq reads:	2829120	894988	31.6349%
   reads: 	3009898	1004328	33.3675%
----------------
match_TE:2:
  reads:	RAL-861.noGEN.front	RAL-861.noGEN.front.TE	percent
uq reads:	2829120	105022	3.7122%
   reads: 	3009898	106216	3.5289%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-861.noGEN.end	RAL-861.noGEN.end.gen	percent
uq reads:	2829120	613265	21.6769%
   reads: 	3009898	718049	23.8563%
----------------
match_TE:2:
  reads:	RAL-861.noGEN.end	RAL-861.noGEN.end.TE	percent
uq reads:	2829120	86620	3.0617%
   reads: 	3009898	88184	2.9298%
----------------
Candidate insertion sites in file: RAL-861_insert.txt
  reads:	6366
  uqreads:	6325
  Number of Candidate sites:	6325

Level 1 collapse of insertion sites in file: RAL-861_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	388

Level 1 annotation file: RAL-861_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-861_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-861.noGEN.front	RAL-861.noGEN.front.gendel	percent
uq reads:	2829120	894988	31.6349%
   reads: 	3009898	1004328	33.3675%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-861.noGEN.end	RAL-861.noGEN.end.gendel	percent
uq reads:	2829120	613265	21.6769%
   reads: 	3009898	718049	23.8563%
----------------
Candidate breakpoint sites in file: RAL-861_depletion.xls
  reads:	13573
  uqreads:	13332
  Number of reads supporting candidate sites:	13332

Level 1 collapse of depletion sites in file: RAL-861_depletion_level1.xls
  Number of Level 1 collapsed sites:	1156