Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-362_125b.fastq.uq.polyn	RAL-362_125b.filter	percent
uq reads:	47903568	9069402	18.9326%
   reads: 	53852551	11791144	21.8952%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-362_125b.filter	RAL-362_125b.nostrna	percent
uq reads:	9069402	6266188	69.0915%
   reads: 	11791144	7138017	60.5371%
----------------
TE_filter:
  reads:	RAL-362_125b.nostrna	RAL-362_125b.noTE	percent
uq reads:	6266188	6252676	99.7844%
   reads: 	7138017	7118974	99.7332%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-362_125b.noGEN.front	RAL-362_125b.noGEN.front.gen	percent
uq reads:	6252676	2375161	37.9863%
   reads: 	7118974	2499985	35.1172%
----------------
match_TE:2:
  reads:	RAL-362_125b.noGEN.front	RAL-362_125b.noGEN.front.TE	percent
uq reads:	6252676	367183	5.8724%
   reads: 	7118974	382938	5.3791%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-362_125b.noGEN.end	RAL-362_125b.noGEN.end.gen	percent
uq reads:	6252676	568049	9.0849%
   reads: 	7118974	689486	9.6852%
----------------
match_TE:2:
  reads:	RAL-362_125b.noGEN.end	RAL-362_125b.noGEN.end.TE	percent
uq reads:	6252676	129367	2.0690%
   reads: 	7118974	144907	2.0355%
----------------
Candidate insertion sites in file: RAL-362_125b_insert.txt
  reads:	25162
  uqreads:	24179
  Number of Candidate sites:	24179

Level 1 collapse of insertion sites in file: RAL-362_125b_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	646

Level 1 annotation file: RAL-362_125b_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-362_125b_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-362_125b.noGEN.front	RAL-362_125b.noGEN.front.gendel	percent
uq reads:	6252676	2375161	37.9863%
   reads: 	7118974	2499985	35.1172%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-362_125b.noGEN.end	RAL-362_125b.noGEN.end.gendel	percent
uq reads:	6252676	568049	9.0849%
   reads: 	7118974	689486	9.6852%
----------------
Candidate breakpoint sites in file: RAL-362_125b_depletion.xls
  reads:	64436
  uqreads:	61848
  Number of reads supporting candidate sites:	61848

Level 1 collapse of depletion sites in file: RAL-362_125b_depletion_level1.xls
  Number of Level 1 collapsed sites:	3947