Insertion Pipeline
Bowtie2_wholegenome:
  reads:	SP188_1-HE.fastq.uq.polyn	SP188_1-HE.filter	percent
uq reads:	34966779	1149745	3.2881%
   reads: 	36293295	1184005	3.2623%
----------------
virus_structural_rna_repbase_filter:
  reads:	SP188_1-HE.filter	SP188_1-HE.nostrna	percent
uq reads:	1149745	1097128	95.4236%
   reads: 	1184005	1129749	95.4176%
----------------
TE_filter:
  reads:	SP188_1-HE.nostrna	SP188_1-HE.noTE	percent
uq reads:	1097128	1091035	99.4446%
   reads: 	1129749	1122634	99.3702%
----------------
match_dm6_mask_gen:1:
  reads:	SP188_1-HE.noGEN.front	SP188_1-HE.noGEN.front.gen	percent
uq reads:	1091035	562013	51.5119%
   reads: 	1122634	572460	50.9926%
----------------
match_TE:2:
  reads:	SP188_1-HE.noGEN.front	SP188_1-HE.noGEN.front.TE	percent
uq reads:	1091035	119646	10.9663%
   reads: 	1122634	123730	11.0214%
----------------
match_dm6_mask_gen:1:
  reads:	SP188_1-HE.noGEN.end	SP188_1-HE.noGEN.end.gen	percent
uq reads:	1091035	481575	44.1393%
   reads: 	1122634	492781	43.8951%
----------------
match_TE:2:
  reads:	SP188_1-HE.noGEN.end	SP188_1-HE.noGEN.end.TE	percent
uq reads:	1091035	107791	9.8797%
   reads: 	1122634	111866	9.9646%
----------------
Candidate insertion sites in file: SP188_1-HE_insert.txt
  reads:	22470
  uqreads:	21790
  Number of Candidate sites:	21790

Level 1 collapse of insertion sites in file: SP188_1-HE_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	556

Level 1 annotation file: SP188_1-HE_level1siteannotation.xls
Insertion sites in fixed bin:
SP188_1-HE_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	SP188_1-HE.noGEN.front	SP188_1-HE.noGEN.front.gendel	percent
uq reads:	1091035	562013	51.5119%
   reads: 	1122634	572460	50.9926%
----------------
match_dm6_mask_gen_del:1:
  reads:	SP188_1-HE.noGEN.end	SP188_1-HE.noGEN.end.gendel	percent
uq reads:	1091035	481575	44.1393%
   reads: 	1122634	492781	43.8951%
----------------
Candidate breakpoint sites in file: SP188_1-HE_depletion.xls
  reads:	76563
  uqreads:	74508
  Number of reads supporting candidate sites:	74508

Level 1 collapse of depletion sites in file: SP188_1-HE_depletion_level1.xls
  Number of Level 1 collapsed sites:	4109