Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-256.fastq.uq.polyn	RAL-256.filter	percent
uq reads:	32523477	2381050	7.3210%
   reads: 	34511530	2852117	8.2642%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-256.filter	RAL-256.nostrna	percent
uq reads:	2381050	1979119	83.1196%
   reads: 	2852117	2429164	85.1706%
----------------
TE_filter:
  reads:	RAL-256.nostrna	RAL-256.noTE	percent
uq reads:	1979119	1969489	99.5134%
   reads: 	2429164	2417590	99.5235%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-256.noGEN.front	RAL-256.noGEN.front.gen	percent
uq reads:	1969489	461138	23.4141%
   reads: 	2417590	743458	30.7520%
----------------
match_TE:2:
  reads:	RAL-256.noGEN.front	RAL-256.noGEN.front.TE	percent
uq reads:	1969489	71562	3.6335%
   reads: 	2417590	74491	3.0812%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-256.noGEN.end	RAL-256.noGEN.end.gen	percent
uq reads:	1969489	394531	20.0322%
   reads: 	2417590	672703	27.8254%
----------------
match_TE:2:
  reads:	RAL-256.noGEN.end	RAL-256.noGEN.end.TE	percent
uq reads:	1969489	65609	3.3313%
   reads: 	2417590	68668	2.8403%
----------------
Candidate insertion sites in file: RAL-256_insert.txt
  reads:	5709
  uqreads:	5600
  Number of Candidate sites:	5600

Level 1 collapse of insertion sites in file: RAL-256_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	401

Level 1 annotation file: RAL-256_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-256_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-256.noGEN.front	RAL-256.noGEN.front.gendel	percent
uq reads:	1969489	461138	23.4141%
   reads: 	2417590	743458	30.7520%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-256.noGEN.end	RAL-256.noGEN.end.gendel	percent
uq reads:	1969489	394531	20.0322%
   reads: 	2417590	672703	27.8254%
----------------
Candidate breakpoint sites in file: RAL-256_depletion.xls
  reads:	14003
  uqreads:	13593
  Number of reads supporting candidate sites:	13593

Level 1 collapse of depletion sites in file: RAL-256_depletion_level1.xls
  Number of Level 1 collapsed sites:	1325