Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-109_125b.fastq.uq.polyn	RAL-109_125b.filter	percent
uq reads:	53688686	5019570	9.3494%
   reads: 	59223392	6436342	10.8679%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-109_125b.filter	RAL-109_125b.nostrna	percent
uq reads:	5019570	4916238	97.9414%
   reads: 	6436342	6137225	95.3527%
----------------
TE_filter:
  reads:	RAL-109_125b.nostrna	RAL-109_125b.noTE	percent
uq reads:	4916238	4898379	99.6367%
   reads: 	6137225	6112533	99.5977%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-109_125b.noGEN.front	RAL-109_125b.noGEN.front.gen	percent
uq reads:	4898379	1340403	27.3642%
   reads: 	6112533	1665355	27.2449%
----------------
match_TE:2:
  reads:	RAL-109_125b.noGEN.front	RAL-109_125b.noGEN.front.TE	percent
uq reads:	4898379	207778	4.2418%
   reads: 	6112533	227942	3.7291%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-109_125b.noGEN.end	RAL-109_125b.noGEN.end.gen	percent
uq reads:	4898379	771337	15.7468%
   reads: 	6112533	1093545	17.8902%
----------------
match_TE:2:
  reads:	RAL-109_125b.noGEN.end	RAL-109_125b.noGEN.end.TE	percent
uq reads:	4898379	138310	2.8236%
   reads: 	6112533	158326	2.5902%
----------------
Candidate insertion sites in file: RAL-109_125b_insert.txt
  reads:	29490
  uqreads:	28473
  Number of Candidate sites:	28473

Level 1 collapse of insertion sites in file: RAL-109_125b_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	719

Level 1 annotation file: RAL-109_125b_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-109_125b_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-109_125b.noGEN.front	RAL-109_125b.noGEN.front.gendel	percent
uq reads:	4898379	1340403	27.3642%
   reads: 	6112533	1665355	27.2449%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-109_125b.noGEN.end	RAL-109_125b.noGEN.end.gendel	percent
uq reads:	4898379	771337	15.7468%
   reads: 	6112533	1093545	17.8902%
----------------
Candidate breakpoint sites in file: RAL-109_125b_depletion.xls
  reads:	78020
  uqreads:	75000
  Number of reads supporting candidate sites:	75000

Level 1 collapse of depletion sites in file: RAL-109_125b_depletion_level1.xls
  Number of Level 1 collapsed sites:	4420