Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-306_125b.fastq.uq.polyn	RAL-306_125b.filter	percent
uq reads:	59056997	12878464	21.8068%
   reads: 	64441284	15409459	23.9124%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-306_125b.filter	RAL-306_125b.nostrna	percent
uq reads:	12878464	8818906	68.4779%
   reads: 	15409459	9755911	63.3112%
----------------
TE_filter:
  reads:	RAL-306_125b.nostrna	RAL-306_125b.noTE	percent
uq reads:	8818906	8802318	99.8119%
   reads: 	9755911	9735152	99.7872%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-306_125b.noGEN.front	RAL-306_125b.noGEN.front.gen	percent
uq reads:	8802318	3045297	34.5965%
   reads: 	9735152	3171716	32.5800%
----------------
match_TE:2:
  reads:	RAL-306_125b.noGEN.front	RAL-306_125b.noGEN.front.TE	percent
uq reads:	8802318	441197	5.0123%
   reads: 	9735152	454092	4.6645%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-306_125b.noGEN.end	RAL-306_125b.noGEN.end.gen	percent
uq reads:	8802318	611349	6.9453%
   reads: 	9735152	733718	7.5368%
----------------
match_TE:2:
  reads:	RAL-306_125b.noGEN.end	RAL-306_125b.noGEN.end.TE	percent
uq reads:	8802318	124064	1.4094%
   reads: 	9735152	135650	1.3934%
----------------
Candidate insertion sites in file: RAL-306_125b_insert.txt
  reads:	24230
  uqreads:	23640
  Number of Candidate sites:	23640

Level 1 collapse of insertion sites in file: RAL-306_125b_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	621

Level 1 annotation file: RAL-306_125b_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-306_125b_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-306_125b.noGEN.front	RAL-306_125b.noGEN.front.gendel	percent
uq reads:	8802318	3045297	34.5965%
   reads: 	9735152	3171716	32.5800%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-306_125b.noGEN.end	RAL-306_125b.noGEN.end.gendel	percent
uq reads:	8802318	611349	6.9453%
   reads: 	9735152	733718	7.5368%
----------------
Candidate breakpoint sites in file: RAL-306_125b_depletion.xls
  reads:	64660
  uqreads:	62753
  Number of reads supporting candidate sites:	62753

Level 1 collapse of depletion sites in file: RAL-306_125b_depletion_level1.xls
  Number of Level 1 collapsed sites:	3900