Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-233.fastq.uq.polyn	RAL-233.filter	percent
uq reads:	28044523	1684641	6.0070%
   reads: 	29584945	2014735	6.8100%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-233.filter	RAL-233.nostrna	percent
uq reads:	1684641	1643605	97.5641%
   reads: 	2014735	1967573	97.6591%
----------------
TE_filter:
  reads:	RAL-233.nostrna	RAL-233.noTE	percent
uq reads:	1643605	1629466	99.1398%
   reads: 	1967573	1947906	99.0004%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-233.noGEN.front	RAL-233.noGEN.front.gen	percent
uq reads:	1629466	454676	27.9034%
   reads: 	1947906	667928	34.2895%
----------------
match_TE:2:
  reads:	RAL-233.noGEN.front	RAL-233.noGEN.front.TE	percent
uq reads:	1629466	58665	3.6003%
   reads: 	1947906	61178	3.1407%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-233.noGEN.end	RAL-233.noGEN.end.gen	percent
uq reads:	1629466	358312	21.9895%
   reads: 	1947906	571421	29.3351%
----------------
match_TE:2:
  reads:	RAL-233.noGEN.end	RAL-233.noGEN.end.TE	percent
uq reads:	1629466	50015	3.0694%
   reads: 	1947906	52523	2.6964%
----------------
Candidate insertion sites in file: RAL-233_insert.txt
  reads:	5442
  uqreads:	5353
  Number of Candidate sites:	5353

Level 1 collapse of insertion sites in file: RAL-233_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	423

Level 1 annotation file: RAL-233_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-233_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-233.noGEN.front	RAL-233.noGEN.front.gendel	percent
uq reads:	1629466	454676	27.9034%
   reads: 	1947906	667928	34.2895%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-233.noGEN.end	RAL-233.noGEN.end.gendel	percent
uq reads:	1629466	358312	21.9895%
   reads: 	1947906	571421	29.3351%
----------------
Candidate breakpoint sites in file: RAL-233_depletion.xls
  reads:	12514
  uqreads:	12220
  Number of reads supporting candidate sites:	12220

Level 1 collapse of depletion sites in file: RAL-233_depletion_level1.xls
  Number of Level 1 collapsed sites:	1133