Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-443.fastq.uq.polyn	RAL-443.filter	percent
uq reads:	45847615	3849905	8.3972%
   reads: 	54521088	5892880	10.8084%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-443.filter	RAL-443.nostrna	percent
uq reads:	3849905	3620371	94.0379%
   reads: 	5892880	5326958	90.3965%
----------------
TE_filter:
  reads:	RAL-443.nostrna	RAL-443.noTE	percent
uq reads:	3620371	3604468	99.5607%
   reads: 	5326958	5307541	99.6355%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-443.noGEN.front	RAL-443.noGEN.front.gen	percent
uq reads:	3604468	788967	21.8886%
   reads: 	5307541	1101416	20.7519%
----------------
match_TE:2:
  reads:	RAL-443.noGEN.front	RAL-443.noGEN.front.TE	percent
uq reads:	3604468	114459	3.1755%
   reads: 	5307541	149787	2.8222%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-443.noGEN.end	RAL-443.noGEN.end.gen	percent
uq reads:	3604468	758069	21.0314%
   reads: 	5307541	1071203	20.1827%
----------------
match_TE:2:
  reads:	RAL-443.noGEN.end	RAL-443.noGEN.end.TE	percent
uq reads:	3604468	115136	3.1943%
   reads: 	5307541	153301	2.8884%
----------------
Candidate insertion sites in file: RAL-443_insert.txt
  reads:	17357
  uqreads:	16653
  Number of Candidate sites:	16653

Level 1 collapse of insertion sites in file: RAL-443_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	641

Level 1 annotation file: RAL-443_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-443_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-443.noGEN.front	RAL-443.noGEN.front.gendel	percent
uq reads:	3604468	803142	22.2818%
   reads: 	5307541	1128650	21.2650%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-443.noGEN.end	RAL-443.noGEN.end.gendel	percent
uq reads:	3604468	770694	21.3816%
   reads: 	5307541	1091927	20.5731%
----------------
Candidate breakpoint sites in file: RAL-443_depletion.xls
  reads:	43001
  uqreads:	41408
  Number of reads supporting candidate sites:	41408

Level 1 collapse of depletion sites in file: RAL-443_depletion_level1.xls
  Number of Level 1 collapsed sites:	3264