Insertion Pipeline
Bowtie2_wholegenome:
  reads:	ZS37_1-HE.fastq.uq.polyn	ZS37_1-HE.filter	percent
uq reads:	61629506	3055177	4.9573%
   reads: 	71384301	3566362	4.9960%
----------------
virus_structural_rna_repbase_filter:
  reads:	ZS37_1-HE.filter	ZS37_1-HE.nostrna	percent
uq reads:	3055177	2752296	90.0863%
   reads: 	3566362	3132028	87.8214%
----------------
TE_filter:
  reads:	ZS37_1-HE.nostrna	ZS37_1-HE.noTE	percent
uq reads:	2752296	2736448	99.4242%
   reads: 	3132028	3091025	98.6908%
----------------
match_dm6_mask_gen:1:
  reads:	ZS37_1-HE.noGEN.front	ZS37_1-HE.noGEN.front.gen	percent
uq reads:	2736448	1354898	49.5130%
   reads: 	3091025	1486814	48.1010%
----------------
match_TE:2:
  reads:	ZS37_1-HE.noGEN.front	ZS37_1-HE.noGEN.front.TE	percent
uq reads:	2736448	109126	3.9879%
   reads: 	3091025	120976	3.9138%
----------------
match_dm6_mask_gen:1:
  reads:	ZS37_1-HE.noGEN.end	ZS37_1-HE.noGEN.end.gen	percent
uq reads:	2736448	1338107	48.8994%
   reads: 	3091025	1482202	47.9518%
----------------
match_TE:2:
  reads:	ZS37_1-HE.noGEN.end	ZS37_1-HE.noGEN.end.TE	percent
uq reads:	2736448	102393	3.7418%
   reads: 	3091025	113373	3.6678%
----------------
Candidate insertion sites in file: ZS37_1-HE_insert.txt
  reads:	22702
  uqreads:	20158
  Number of Candidate sites:	20158

Level 1 collapse of insertion sites in file: ZS37_1-HE_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	634

Level 1 annotation file: ZS37_1-HE_level1siteannotation.xls
Insertion sites in fixed bin:
ZS37_1-HE_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	ZS37_1-HE.noGEN.front	ZS37_1-HE.noGEN.front.gendel	percent
uq reads:	2736448	1354898	49.5130%
   reads: 	3091025	1486814	48.1010%
----------------
match_dm6_mask_gen_del:1:
  reads:	ZS37_1-HE.noGEN.end	ZS37_1-HE.noGEN.end.gendel	percent
uq reads:	2736448	1338107	48.8994%
   reads: 	3091025	1482202	47.9518%
----------------
Candidate breakpoint sites in file: ZS37_1-HE_depletion.xls
  reads:	77954
  uqreads:	69950
  Number of reads supporting candidate sites:	69950

Level 1 collapse of depletion sites in file: ZS37_1-HE_depletion_level1.xls
  Number of Level 1 collapsed sites:	3808