Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-787.fastq.uq.polyn	RAL-787.filter	percent
uq reads:	36767536	3483205	9.4736%
   reads: 	39058312	4016840	10.2842%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-787.filter	RAL-787.nostrna	percent
uq reads:	3483205	2232351	64.0890%
   reads: 	4016840	2598947	64.7013%
----------------
TE_filter:
  reads:	RAL-787.nostrna	RAL-787.noTE	percent
uq reads:	2232351	2219722	99.4343%
   reads: 	2598947	2583465	99.4043%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-787.noGEN.front	RAL-787.noGEN.front.gen	percent
uq reads:	2219722	681774	30.7144%
   reads: 	2583465	887075	34.3366%
----------------
match_TE:2:
  reads:	RAL-787.noGEN.front	RAL-787.noGEN.front.TE	percent
uq reads:	2219722	95743	4.3133%
   reads: 	2583465	100038	3.8722%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-787.noGEN.end	RAL-787.noGEN.end.gen	percent
uq reads:	2219722	553244	24.9240%
   reads: 	2583465	752269	29.1186%
----------------
match_TE:2:
  reads:	RAL-787.noGEN.end	RAL-787.noGEN.end.TE	percent
uq reads:	2219722	87937	3.9616%
   reads: 	2583465	92875	3.5950%
----------------
Candidate insertion sites in file: RAL-787_insert.txt
  reads:	8253
  uqreads:	8119
  Number of Candidate sites:	8119

Level 1 collapse of insertion sites in file: RAL-787_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	466

Level 1 annotation file: RAL-787_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-787_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-787.noGEN.front	RAL-787.noGEN.front.gendel	percent
uq reads:	2219722	681774	30.7144%
   reads: 	2583465	887075	34.3366%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-787.noGEN.end	RAL-787.noGEN.end.gendel	percent
uq reads:	2219722	553244	24.9240%
   reads: 	2583465	752269	29.1186%
----------------
Candidate breakpoint sites in file: RAL-787_depletion.xls
  reads:	19420
  uqreads:	18768
  Number of reads supporting candidate sites:	18768

Level 1 collapse of depletion sites in file: RAL-787_depletion_level1.xls
  Number of Level 1 collapsed sites:	1770