Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-181.fastq.uq.polyn	RAL-181.filter	percent
uq reads:	60460159	5678446	9.3920%
   reads: 	63363549	6102680	9.6312%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-181.filter	RAL-181.nostrna	percent
uq reads:	5678446	4154809	73.1681%
   reads: 	6102680	4467367	73.2034%
----------------
TE_filter:
  reads:	RAL-181.nostrna	RAL-181.noTE	percent
uq reads:	4154809	4133904	99.4968%
   reads: 	4467367	4442953	99.4535%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-181.noGEN.front	RAL-181.noGEN.front.gen	percent
uq reads:	4133904	1212993	29.3426%
   reads: 	4442953	1356182	30.5243%
----------------
match_TE:2:
  reads:	RAL-181.noGEN.front	RAL-181.noGEN.front.TE	percent
uq reads:	4133904	149268	3.6108%
   reads: 	4442953	152825	3.4397%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-181.noGEN.end	RAL-181.noGEN.end.gen	percent
uq reads:	4133904	1036250	25.0671%
   reads: 	4442953	1174481	26.4347%
----------------
match_TE:2:
  reads:	RAL-181.noGEN.end	RAL-181.noGEN.end.TE	percent
uq reads:	4133904	145367	3.5165%
   reads: 	4442953	149534	3.3656%
----------------
Candidate insertion sites in file: RAL-181_insert.txt
  reads:	11813
  uqreads:	11682
  Number of Candidate sites:	11682

Level 1 collapse of insertion sites in file: RAL-181_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	528

Level 1 annotation file: RAL-181_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-181_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-181.noGEN.front	RAL-181.noGEN.front.gendel	percent
uq reads:	4133904	1212993	29.3426%
   reads: 	4442953	1356182	30.5243%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-181.noGEN.end	RAL-181.noGEN.end.gendel	percent
uq reads:	4133904	1036250	25.0671%
   reads: 	4442953	1174481	26.4347%
----------------
Candidate breakpoint sites in file: RAL-181_depletion.xls
  reads:	26988
  uqreads:	26402
  Number of reads supporting candidate sites:	26402

Level 1 collapse of depletion sites in file: RAL-181_depletion_level1.xls
  Number of Level 1 collapsed sites:	2171