Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-307_100b.fastq.uq.polyn	RAL-307_100b.filter	percent
uq reads:	144509832	8700536	6.0207%
   reads: 	167297190	10875502	6.5007%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-307_100b.filter	RAL-307_100b.nostrna	percent
uq reads:	8700536	8554140	98.3174%
   reads: 	10875502	10552237	97.0276%
----------------
TE_filter:
  reads:	RAL-307_100b.nostrna	RAL-307_100b.noTE	percent
uq reads:	8554140	8499942	99.3664%
   reads: 	10552237	10476792	99.2850%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-307_100b.noGEN.front	RAL-307_100b.noGEN.front.gen	percent
uq reads:	8499942	3830707	45.0674%
   reads: 	10476792	4404723	42.0427%
----------------
match_TE:2:
  reads:	RAL-307_100b.noGEN.front	RAL-307_100b.noGEN.front.TE	percent
uq reads:	8499942	609385	7.1693%
   reads: 	10476792	653874	6.2412%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-307_100b.noGEN.end	RAL-307_100b.noGEN.end.gen	percent
uq reads:	8499942	1434210	16.8732%
   reads: 	10476792	2011093	19.1957%
----------------
match_TE:2:
  reads:	RAL-307_100b.noGEN.end	RAL-307_100b.noGEN.end.TE	percent
uq reads:	8499942	299638	3.5252%
   reads: 	10476792	343130	3.2751%
----------------
Candidate insertion sites in file: RAL-307_100b_insert.txt
  reads:	52053
  uqreads:	47128
  Number of Candidate sites:	47128

Level 1 collapse of insertion sites in file: RAL-307_100b_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	705

Level 1 annotation file: RAL-307_100b_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-307_100b_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-307_100b.noGEN.front	RAL-307_100b.noGEN.front.gendel	percent
uq reads:	8499942	3830707	45.0674%
   reads: 	10476792	4404723	42.0427%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-307_100b.noGEN.end	RAL-307_100b.noGEN.end.gendel	percent
uq reads:	8499942	1434210	16.8732%
   reads: 	10476792	2011093	19.1957%
----------------
Candidate breakpoint sites in file: RAL-307_100b_depletion.xls
  reads:	145957
  uqreads:	130568
  Number of reads supporting candidate sites:	130568

Level 1 collapse of depletion sites in file: RAL-307_100b_depletion_level1.xls
  Number of Level 1 collapsed sites:	4709