Insertion Pipeline
Bowtie2_wholegenome:
  reads:	EB148_1-HE.fastq.uq.polyn	EB148_1-HE.filter	percent
uq reads:	34470174	1614421	4.6835%
   reads: 	37611743	1723097	4.5813%
----------------
virus_structural_rna_repbase_filter:
  reads:	EB148_1-HE.filter	EB148_1-HE.nostrna	percent
uq reads:	1614421	1364904	84.5445%
   reads: 	1723097	1448274	84.0506%
----------------
TE_filter:
  reads:	EB148_1-HE.nostrna	EB148_1-HE.noTE	percent
uq reads:	1364904	1359741	99.6217%
   reads: 	1448274	1435205	99.0976%
----------------
match_dm6_mask_gen:1:
  reads:	EB148_1-HE.noGEN.front	EB148_1-HE.noGEN.front.gen	percent
uq reads:	1359741	770032	56.6308%
   reads: 	1435205	796282	55.4821%
----------------
match_TE:2:
  reads:	EB148_1-HE.noGEN.front	EB148_1-HE.noGEN.front.TE	percent
uq reads:	1359741	79660	5.8585%
   reads: 	1435205	83784	5.8378%
----------------
match_dm6_mask_gen:1:
  reads:	EB148_1-HE.noGEN.end	EB148_1-HE.noGEN.end.gen	percent
uq reads:	1359741	732127	53.8431%
   reads: 	1435205	759911	52.9479%
----------------
match_TE:2:
  reads:	EB148_1-HE.noGEN.end	EB148_1-HE.noGEN.end.TE	percent
uq reads:	1359741	76136	5.5993%
   reads: 	1435205	80329	5.5970%
----------------
Candidate insertion sites in file: EB148_1-HE_insert.txt
  reads:	21825
  uqreads:	20656
  Number of Candidate sites:	20656

Level 1 collapse of insertion sites in file: EB148_1-HE_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	640

Level 1 annotation file: EB148_1-HE_level1siteannotation.xls
Insertion sites in fixed bin:
EB148_1-HE_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	EB148_1-HE.noGEN.front	EB148_1-HE.noGEN.front.gendel	percent
uq reads:	1359741	770032	56.6308%
   reads: 	1435205	796282	55.4821%
----------------
match_dm6_mask_gen_del:1:
  reads:	EB148_1-HE.noGEN.end	EB148_1-HE.noGEN.end.gendel	percent
uq reads:	1359741	732127	53.8431%
   reads: 	1435205	759911	52.9479%
----------------
Candidate breakpoint sites in file: EB148_1-HE_depletion.xls
  reads:	77607
  uqreads:	74042
  Number of reads supporting candidate sites:	74042

Level 1 collapse of depletion sites in file: EB148_1-HE_depletion_level1.xls
  Number of Level 1 collapsed sites:	3937