Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-340_100b.fastq.uq.polyn	RAL-340_100b.filter	percent
uq reads:	131163798	32986383	25.1490%
   reads: 	160043044	42993708	26.8638%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-340_100b.filter	RAL-340_100b.nostrna	percent
uq reads:	32986383	28504084	86.4117%
   reads: 	42993708	35933872	83.5794%
----------------
TE_filter:
  reads:	RAL-340_100b.nostrna	RAL-340_100b.noTE	percent
uq reads:	28504084	28470542	99.8823%
   reads: 	35933872	35886232	99.8674%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-340_100b.noGEN.front	RAL-340_100b.noGEN.front.gen	percent
uq reads:	28470542	10355046	36.3711%
   reads: 	35886232	12682484	35.3408%
----------------
match_TE:2:
  reads:	RAL-340_100b.noGEN.front	RAL-340_100b.noGEN.front.TE	percent
uq reads:	28470542	1307396	4.5921%
   reads: 	35886232	1431591	3.9892%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-340_100b.noGEN.end	RAL-340_100b.noGEN.end.gen	percent
uq reads:	28470542	10718611	37.6481%
   reads: 	35886232	13095360	36.4913%
----------------
match_TE:2:
  reads:	RAL-340_100b.noGEN.end	RAL-340_100b.noGEN.end.TE	percent
uq reads:	28470542	1473591	5.1758%
   reads: 	35886232	1605077	4.4727%
----------------
Candidate insertion sites in file: RAL-340_100b_insert.txt
  reads:	213357
  uqreads:	208335
  Number of Candidate sites:	208335

Level 1 collapse of insertion sites in file: RAL-340_100b_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	1946

Level 1 annotation file: RAL-340_100b_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-340_100b_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-340_100b.noGEN.front	RAL-340_100b.noGEN.front.gendel	percent
uq reads:	28470542	10355046	36.3711%
   reads: 	35886232	12682484	35.3408%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-340_100b.noGEN.end	RAL-340_100b.noGEN.end.gendel	percent
uq reads:	28470542	10718611	37.6481%
   reads: 	35886232	13095360	36.4913%
----------------
Candidate breakpoint sites in file: RAL-340_100b_depletion.xls
  reads:	431821
  uqreads:	420338
  Number of reads supporting candidate sites:	420338

Level 1 collapse of depletion sites in file: RAL-340_100b_depletion_level1.xls
  Number of Level 1 collapsed sites:	4386