Insertion Pipeline
Bowtie2_wholegenome:
  reads:	SB10_1-HE.fastq.uq.polyn	SB10_1-HE.filter	percent
uq reads:	43054637	2156714	5.0092%
   reads: 	46824297	2274088	4.8566%
----------------
virus_structural_rna_repbase_filter:
  reads:	SB10_1-HE.filter	SB10_1-HE.nostrna	percent
uq reads:	2156714	2072475	96.0941%
   reads: 	2274088	2158238	94.9057%
----------------
TE_filter:
  reads:	SB10_1-HE.nostrna	SB10_1-HE.noTE	percent
uq reads:	2072475	2065793	99.6776%
   reads: 	2158238	2142622	99.2764%
----------------
match_dm6_mask_gen:1:
  reads:	SB10_1-HE.noGEN.front	SB10_1-HE.noGEN.front.gen	percent
uq reads:	2065793	1236916	59.8761%
   reads: 	2142622	1262616	58.9285%
----------------
match_TE:2:
  reads:	SB10_1-HE.noGEN.front	SB10_1-HE.noGEN.front.TE	percent
uq reads:	2065793	115023	5.5680%
   reads: 	2142622	119129	5.5600%
----------------
match_dm6_mask_gen:1:
  reads:	SB10_1-HE.noGEN.end	SB10_1-HE.noGEN.end.gen	percent
uq reads:	2065793	1076785	52.1245%
   reads: 	2142622	1104120	51.5313%
----------------
match_TE:2:
  reads:	SB10_1-HE.noGEN.end	SB10_1-HE.noGEN.end.TE	percent
uq reads:	2065793	102466	4.9601%
   reads: 	2142622	106575	4.9740%
----------------
Candidate insertion sites in file: SB10_1-HE_insert.txt
  reads:	25348
  uqreads:	24252
  Number of Candidate sites:	24252

Level 1 collapse of insertion sites in file: SB10_1-HE_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	575

Level 1 annotation file: SB10_1-HE_level1siteannotation.xls
Insertion sites in fixed bin:
SB10_1-HE_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	SB10_1-HE.noGEN.front	SB10_1-HE.noGEN.front.gendel	percent
uq reads:	2065793	1236916	59.8761%
   reads: 	2142622	1262616	58.9285%
----------------
match_dm6_mask_gen_del:1:
  reads:	SB10_1-HE.noGEN.end	SB10_1-HE.noGEN.end.gendel	percent
uq reads:	2065793	1076785	52.1245%
   reads: 	2142622	1104120	51.5313%
----------------
Candidate breakpoint sites in file: SB10_1-HE_depletion.xls
  reads:	86805
  uqreads:	83430
  Number of reads supporting candidate sites:	83430

Level 1 collapse of depletion sites in file: SB10_1-HE_depletion_level1.xls
  Number of Level 1 collapsed sites:	3474