Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-176.fastq.uq.polyn	RAL-176.filter	percent
uq reads:	71633410	7624470	10.6437%
   reads: 	79014077	9226230	11.6767%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-176.filter	RAL-176.nostrna	percent
uq reads:	7624470	6869237	90.0946%
   reads: 	9226230	8349425	90.4966%
----------------
TE_filter:
  reads:	RAL-176.nostrna	RAL-176.noTE	percent
uq reads:	6869237	6846442	99.6682%
   reads: 	8349425	8320450	99.6530%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-176.noGEN.front	RAL-176.noGEN.front.gen	percent
uq reads:	6846442	2251836	32.8906%
   reads: 	8320450	3212556	38.6104%
----------------
match_TE:2:
  reads:	RAL-176.noGEN.front	RAL-176.noGEN.front.TE	percent
uq reads:	6846442	286309	4.1819%
   reads: 	8320450	298393	3.5863%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-176.noGEN.end	RAL-176.noGEN.end.gen	percent
uq reads:	6846442	2495194	36.4451%
   reads: 	8320450	3415814	41.0532%
----------------
match_TE:2:
  reads:	RAL-176.noGEN.end	RAL-176.noGEN.end.TE	percent
uq reads:	6846442	335946	4.9069%
   reads: 	8320450	350796	4.2161%
----------------
Candidate insertion sites in file: RAL-176_insert.txt
  reads:	39209
  uqreads:	38421
  Number of Candidate sites:	38421

Level 1 collapse of insertion sites in file: RAL-176_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	614

Level 1 annotation file: RAL-176_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-176_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-176.noGEN.front	RAL-176.noGEN.front.gendel	percent
uq reads:	6846442	2251836	32.8906%
   reads: 	8320450	3212556	38.6104%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-176.noGEN.end	RAL-176.noGEN.end.gendel	percent
uq reads:	6846442	2495194	36.4451%
   reads: 	8320450	3415814	41.0532%
----------------
Candidate breakpoint sites in file: RAL-176_depletion.xls
  reads:	87585
  uqreads:	84065
  Number of reads supporting candidate sites:	84065

Level 1 collapse of depletion sites in file: RAL-176_depletion_level1.xls
  Number of Level 1 collapsed sites:	2301