Insertion Pipeline
Bowtie2_wholegenome:
  reads:	ISO1-AS-LSg123.fastq.uq.polyn	ISO1-AS-LSg123.filter	percent
uq reads:	201515564	3341145	1.6580%
   reads: 	432093653	5787068	1.3393%
----------------
virus_structural_rna_repbase_filter:
  reads:	ISO1-AS-LSg123.filter	ISO1-AS-LSg123.nostrna	percent
uq reads:	3341145	2154036	64.4700%
   reads: 	5787068	3282719	56.7251%
----------------
TE_filter:
  reads:	ISO1-AS-LSg123.nostrna	ISO1-AS-LSg123.noTE	percent
uq reads:	2154036	2137747	99.2438%
   reads: 	3282719	3244804	98.8450%
----------------
match_dm6_mask_gen:1:
  reads:	ISO1-AS-LSg123.noGEN.front	ISO1-AS-LSg123.noGEN.front.gen	percent
uq reads:	2137747	751164	35.1381%
   reads: 	3244804	943822	29.0872%
----------------
match_TE:2:
  reads:	ISO1-AS-LSg123.noGEN.front	ISO1-AS-LSg123.noGEN.front.TE	percent
uq reads:	2137747	93151	4.3574%
   reads: 	3244804	139539	4.3004%
----------------
match_dm6_mask_gen:1:
  reads:	ISO1-AS-LSg123.noGEN.end	ISO1-AS-LSg123.noGEN.end.gen	percent
uq reads:	2137747	566810	26.5144%
   reads: 	3244804	739469	22.7893%
----------------
match_TE:2:
  reads:	ISO1-AS-LSg123.noGEN.end	ISO1-AS-LSg123.noGEN.end.TE	percent
uq reads:	2137747	111632	5.2219%
   reads: 	3244804	162574	5.0103%
----------------
Candidate insertion sites in file: ISO1-AS-LSg123_insert.txt
  reads:	47620
  uqreads:	27704
  Number of Candidate sites:	27704

Level 1 collapse of insertion sites in file: ISO1-AS-LSg123_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	318

Level 1 annotation file: ISO1-AS-LSg123_level1siteannotation.xls
Insertion sites in fixed bin:
ISO1-AS-LSg123_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	ISO1-AS-LSg123.noGEN.front	ISO1-AS-LSg123.noGEN.front.gendel	percent
uq reads:	2137747	751164	35.1381%
   reads: 	3244804	943822	29.0872%
----------------
match_dm6_mask_gen_del:1:
  reads:	ISO1-AS-LSg123.noGEN.end	ISO1-AS-LSg123.noGEN.end.gendel	percent
uq reads:	2137747	566810	26.5144%
   reads: 	3244804	739469	22.7893%
----------------
Candidate breakpoint sites in file: ISO1-AS-LSg123_depletion.xls
  reads:	20289
  uqreads:	12960
  Number of reads supporting candidate sites:	12960

Level 1 collapse of depletion sites in file: ISO1-AS-LSg123_depletion_level1.xls
  Number of Level 1 collapsed sites:	150