Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-802_125b.fastq.uq.polyn	RAL-802_125b.filter	percent
uq reads:	57626737	7393034	12.8292%
   reads: 	66036094	10422454	15.7830%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-802_125b.filter	RAL-802_125b.nostrna	percent
uq reads:	7393034	4937406	66.7846%
   reads: 	10422454	6357725	61.0003%
----------------
TE_filter:
  reads:	RAL-802_125b.nostrna	RAL-802_125b.noTE	percent
uq reads:	4937406	4921354	99.6749%
   reads: 	6357725	6331868	99.5933%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-802_125b.noGEN.front	RAL-802_125b.noGEN.front.gen	percent
uq reads:	4921354	1091744	22.1838%
   reads: 	6331868	1388682	21.9316%
----------------
match_TE:2:
  reads:	RAL-802_125b.noGEN.front	RAL-802_125b.noGEN.front.TE	percent
uq reads:	4921354	195081	3.9640%
   reads: 	6331868	222479	3.5136%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-802_125b.noGEN.end	RAL-802_125b.noGEN.end.gen	percent
uq reads:	4921354	682337	13.8648%
   reads: 	6331868	973794	15.3793%
----------------
match_TE:2:
  reads:	RAL-802_125b.noGEN.end	RAL-802_125b.noGEN.end.TE	percent
uq reads:	4921354	141750	2.8803%
   reads: 	6331868	168063	2.6542%
----------------
Candidate insertion sites in file: RAL-802_125b_insert.txt
  reads:	30389
  uqreads:	29055
  Number of Candidate sites:	29055

Level 1 collapse of insertion sites in file: RAL-802_125b_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	951

Level 1 annotation file: RAL-802_125b_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-802_125b_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-802_125b.noGEN.front	RAL-802_125b.noGEN.front.gendel	percent
uq reads:	4921354	1091744	22.1838%
   reads: 	6331868	1388682	21.9316%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-802_125b.noGEN.end	RAL-802_125b.noGEN.end.gendel	percent
uq reads:	4921354	682337	13.8648%
   reads: 	6331868	973794	15.3793%
----------------
Candidate breakpoint sites in file: RAL-802_125b_depletion.xls
  reads:	86747
  uqreads:	82307
  Number of reads supporting candidate sites:	82307

Level 1 collapse of depletion sites in file: RAL-802_125b_depletion_level1.xls
  Number of Level 1 collapsed sites:	5379