Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-879.fastq.uq.polyn	RAL-879.filter	percent
uq reads:	40384999	4845724	11.9988%
   reads: 	42121684	5196201	12.3362%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-879.filter	RAL-879.nostrna	percent
uq reads:	4845724	2559395	52.8176%
   reads: 	5196201	2791051	53.7133%
----------------
TE_filter:
  reads:	RAL-879.nostrna	RAL-879.noTE	percent
uq reads:	2559395	2543543	99.3806%
   reads: 	2791051	2774448	99.4051%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-879.noGEN.front	RAL-879.noGEN.front.gen	percent
uq reads:	2543543	826542	32.4957%
   reads: 	2774448	969617	34.9481%
----------------
match_TE:2:
  reads:	RAL-879.noGEN.front	RAL-879.noGEN.front.TE	percent
uq reads:	2543543	87765	3.4505%
   reads: 	2774448	95147	3.4294%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-879.noGEN.end	RAL-879.noGEN.end.gen	percent
uq reads:	2543543	697467	27.4211%
   reads: 	2774448	834570	30.0806%
----------------
match_TE:2:
  reads:	RAL-879.noGEN.end	RAL-879.noGEN.end.TE	percent
uq reads:	2543543	91646	3.6031%
   reads: 	2774448	99455	3.5847%
----------------
Candidate insertion sites in file: RAL-879_insert.txt
  reads:	6791
  uqreads:	6750
  Number of Candidate sites:	6750

Level 1 collapse of insertion sites in file: RAL-879_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	409

Level 1 annotation file: RAL-879_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-879_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-879.noGEN.front	RAL-879.noGEN.front.gendel	percent
uq reads:	2543543	826542	32.4957%
   reads: 	2774448	969617	34.9481%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-879.noGEN.end	RAL-879.noGEN.end.gendel	percent
uq reads:	2543543	697467	27.4211%
   reads: 	2774448	834570	30.0806%
----------------
Candidate breakpoint sites in file: RAL-879_depletion.xls
  reads:	13036
  uqreads:	12826
  Number of reads supporting candidate sites:	12826

Level 1 collapse of depletion sites in file: RAL-879_depletion_level1.xls
  Number of Level 1 collapsed sites:	992