Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-853_125b.fastq.uq.polyn	RAL-853_125b.filter	percent
uq reads:	58744714	7357217	12.5240%
   reads: 	67828842	10318286	15.2122%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-853_125b.filter	RAL-853_125b.nostrna	percent
uq reads:	7357217	5200880	70.6909%
   reads: 	10318286	6664812	64.5922%
----------------
TE_filter:
  reads:	RAL-853_125b.nostrna	RAL-853_125b.noTE	percent
uq reads:	5200880	5192201	99.8331%
   reads: 	6664812	6652329	99.8127%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-853_125b.noGEN.front	RAL-853_125b.noGEN.front.gen	percent
uq reads:	5192201	973295	18.7453%
   reads: 	6652329	1361568	20.4675%
----------------
match_TE:2:
  reads:	RAL-853_125b.noGEN.front	RAL-853_125b.noGEN.front.TE	percent
uq reads:	5192201	179010	3.4477%
   reads: 	6652329	198949	2.9907%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-853_125b.noGEN.end	RAL-853_125b.noGEN.end.gen	percent
uq reads:	5192201	737066	14.1956%
   reads: 	6652329	1113005	16.7311%
----------------
match_TE:2:
  reads:	RAL-853_125b.noGEN.end	RAL-853_125b.noGEN.end.TE	percent
uq reads:	5192201	151288	2.9138%
   reads: 	6652329	171130	2.5725%
----------------
Candidate insertion sites in file: RAL-853_125b_insert.txt
  reads:	33002
  uqreads:	31502
  Number of Candidate sites:	31502

Level 1 collapse of insertion sites in file: RAL-853_125b_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	829

Level 1 annotation file: RAL-853_125b_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-853_125b_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-853_125b.noGEN.front	RAL-853_125b.noGEN.front.gendel	percent
uq reads:	5192201	973295	18.7453%
   reads: 	6652329	1361568	20.4675%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-853_125b.noGEN.end	RAL-853_125b.noGEN.end.gendel	percent
uq reads:	5192201	737066	14.1956%
   reads: 	6652329	1113005	16.7311%
----------------
Candidate breakpoint sites in file: RAL-853_125b_depletion.xls
  reads:	87817
  uqreads:	83035
  Number of reads supporting candidate sites:	83035

Level 1 collapse of depletion sites in file: RAL-853_125b_depletion_level1.xls
  Number of Level 1 collapsed sites:	4467