Insertion Pipeline
Bowtie2_wholegenome:
  reads:	FR207_2-HE.fastq.uq.polyn	FR207_2-HE.filter	percent
uq reads:	33555202	1332910	3.9723%
   reads: 	35687569	1382928	3.8751%
----------------
virus_structural_rna_repbase_filter:
  reads:	FR207_2-HE.filter	FR207_2-HE.nostrna	percent
uq reads:	1332910	1319407	98.9870%
   reads: 	1382928	1359943	98.3379%
----------------
TE_filter:
  reads:	FR207_2-HE.nostrna	FR207_2-HE.noTE	percent
uq reads:	1319407	1314038	99.5931%
   reads: 	1359943	1351713	99.3948%
----------------
match_dm6_mask_gen:1:
  reads:	FR207_2-HE.noGEN.front	FR207_2-HE.noGEN.front.gen	percent
uq reads:	1314038	781680	59.4869%
   reads: 	1351713	794376	58.7681%
----------------
match_TE:2:
  reads:	FR207_2-HE.noGEN.front	FR207_2-HE.noGEN.front.TE	percent
uq reads:	1314038	104286	7.9363%
   reads: 	1351713	107239	7.9336%
----------------
match_dm6_mask_gen:1:
  reads:	FR207_2-HE.noGEN.end	FR207_2-HE.noGEN.end.gen	percent
uq reads:	1314038	439834	33.4719%
   reads: 	1351713	452376	33.4669%
----------------
match_TE:2:
  reads:	FR207_2-HE.noGEN.end	FR207_2-HE.noGEN.end.TE	percent
uq reads:	1314038	70115	5.3358%
   reads: 	1351713	72855	5.3898%
----------------
Candidate insertion sites in file: FR207_2-HE_insert.txt
  reads:	20390
  uqreads:	19443
  Number of Candidate sites:	19443

Level 1 collapse of insertion sites in file: FR207_2-HE_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	542

Level 1 annotation file: FR207_2-HE_level1siteannotation.xls
Insertion sites in fixed bin:
FR207_2-HE_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	FR207_2-HE.noGEN.front	FR207_2-HE.noGEN.front.gendel	percent
uq reads:	1314038	781680	59.4869%
   reads: 	1351713	794376	58.7681%
----------------
match_dm6_mask_gen_del:1:
  reads:	FR207_2-HE.noGEN.end	FR207_2-HE.noGEN.end.gendel	percent
uq reads:	1314038	439834	33.4719%
   reads: 	1351713	452376	33.4669%
----------------
Candidate breakpoint sites in file: FR207_2-HE_depletion.xls
  reads:	69099
  uqreads:	66145
  Number of reads supporting candidate sites:	66145

Level 1 collapse of depletion sites in file: FR207_2-HE_depletion_level1.xls
  Number of Level 1 collapsed sites:	3397