Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-304_100b.fastq.uq.polyn	RAL-304_100b.filter	percent
uq reads:	147140678	12900938	8.7678%
   reads: 	169482794	18340061	10.8212%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-304_100b.filter	RAL-304_100b.nostrna	percent
uq reads:	12900938	8240046	63.8717%
   reads: 	18340061	11531128	62.8740%
----------------
TE_filter:
  reads:	RAL-304_100b.nostrna	RAL-304_100b.noTE	percent
uq reads:	8240046	8217949	99.7318%
   reads: 	11531128	11499253	99.7236%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-304_100b.noGEN.front	RAL-304_100b.noGEN.front.gen	percent
uq reads:	8217949	2863257	34.8415%
   reads: 	11499253	4194867	36.4795%
----------------
match_TE:2:
  reads:	RAL-304_100b.noGEN.front	RAL-304_100b.noGEN.front.TE	percent
uq reads:	8217949	491037	5.9752%
   reads: 	11499253	543134	4.7232%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-304_100b.noGEN.end	RAL-304_100b.noGEN.end.gen	percent
uq reads:	8217949	1839222	22.3805%
   reads: 	11499253	3171323	27.5785%
----------------
match_TE:2:
  reads:	RAL-304_100b.noGEN.end	RAL-304_100b.noGEN.end.TE	percent
uq reads:	8217949	366339	4.4578%
   reads: 	11499253	416180	3.6192%
----------------
Candidate insertion sites in file: RAL-304_100b_insert.txt
  reads:	55278
  uqreads:	51634
  Number of Candidate sites:	51634

Level 1 collapse of insertion sites in file: RAL-304_100b_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	722

Level 1 annotation file: RAL-304_100b_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-304_100b_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-304_100b.noGEN.front	RAL-304_100b.noGEN.front.gendel	percent
uq reads:	8217949	2863257	34.8415%
   reads: 	11499253	4194867	36.4795%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-304_100b.noGEN.end	RAL-304_100b.noGEN.end.gendel	percent
uq reads:	8217949	1839222	22.3805%
   reads: 	11499253	3171323	27.5785%
----------------
Candidate breakpoint sites in file: RAL-304_100b_depletion.xls
  reads:	134732
  uqreads:	123172
  Number of reads supporting candidate sites:	123172

Level 1 collapse of depletion sites in file: RAL-304_100b_depletion_level1.xls
  Number of Level 1 collapsed sites:	4738