Insertion Pipeline
Bowtie2_wholegenome:
  reads:	SP221_1-HE.fastq.uq.polyn	SP221_1-HE.filter	percent
uq reads:	35934663	1703024	4.7392%
   reads: 	37130935	1765705	4.7553%
----------------
virus_structural_rna_repbase_filter:
  reads:	SP221_1-HE.filter	SP221_1-HE.nostrna	percent
uq reads:	1703024	1313194	77.1095%
   reads: 	1765705	1347597	76.3206%
----------------
TE_filter:
  reads:	SP221_1-HE.nostrna	SP221_1-HE.noTE	percent
uq reads:	1313194	1305836	99.4397%
   reads: 	1347597	1338505	99.3253%
----------------
match_dm6_mask_gen:1:
  reads:	SP221_1-HE.noGEN.front	SP221_1-HE.noGEN.front.gen	percent
uq reads:	1305836	688973	52.7611%
   reads: 	1338505	700373	52.3250%
----------------
match_TE:2:
  reads:	SP221_1-HE.noGEN.front	SP221_1-HE.noGEN.front.TE	percent
uq reads:	1305836	100793	7.7187%
   reads: 	1338505	102818	7.6816%
----------------
match_dm6_mask_gen:1:
  reads:	SP221_1-HE.noGEN.end	SP221_1-HE.noGEN.end.gen	percent
uq reads:	1305836	626170	47.9517%
   reads: 	1338505	637856	47.6544%
----------------
match_TE:2:
  reads:	SP221_1-HE.noGEN.end	SP221_1-HE.noGEN.end.TE	percent
uq reads:	1305836	95092	7.2821%
   reads: 	1338505	97090	7.2536%
----------------
Candidate insertion sites in file: SP221_1-HE_insert.txt
  reads:	23693
  uqreads:	23154
  Number of Candidate sites:	23154

Level 1 collapse of insertion sites in file: SP221_1-HE_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	556

Level 1 annotation file: SP221_1-HE_level1siteannotation.xls
Insertion sites in fixed bin:
SP221_1-HE_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	SP221_1-HE.noGEN.front	SP221_1-HE.noGEN.front.gendel	percent
uq reads:	1305836	688973	52.7611%
   reads: 	1338505	700373	52.3250%
----------------
match_dm6_mask_gen_del:1:
  reads:	SP221_1-HE.noGEN.end	SP221_1-HE.noGEN.end.gendel	percent
uq reads:	1305836	626170	47.9517%
   reads: 	1338505	637856	47.6544%
----------------
Candidate breakpoint sites in file: SP221_1-HE_depletion.xls
  reads:	89734
  uqreads:	87509
  Number of reads supporting candidate sites:	87509

Level 1 collapse of depletion sites in file: SP221_1-HE_depletion_level1.xls
  Number of Level 1 collapsed sites:	4642