Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-303_100b.fastq.uq.polyn	RAL-303_100b.filter	percent
uq reads:	154058752	16277621	10.5659%
   reads: 	170166433	19851109	11.6657%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-303_100b.filter	RAL-303_100b.nostrna	percent
uq reads:	16277621	11855041	72.8303%
   reads: 	19851109	14340294	72.2393%
----------------
TE_filter:
  reads:	RAL-303_100b.nostrna	RAL-303_100b.noTE	percent
uq reads:	11855041	11800840	99.5428%
   reads: 	14340294	14267150	99.4899%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-303_100b.noGEN.front	RAL-303_100b.noGEN.front.gen	percent
uq reads:	11800840	4974463	42.1535%
   reads: 	14267150	5836299	40.9073%
----------------
match_TE:2:
  reads:	RAL-303_100b.noGEN.front	RAL-303_100b.noGEN.front.TE	percent
uq reads:	11800840	781277	6.6205%
   reads: 	14267150	816353	5.7219%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-303_100b.noGEN.end	RAL-303_100b.noGEN.end.gen	percent
uq reads:	11800840	1971113	16.7032%
   reads: 	14267150	2778139	19.4723%
----------------
match_TE:2:
  reads:	RAL-303_100b.noGEN.end	RAL-303_100b.noGEN.end.TE	percent
uq reads:	11800840	374347	3.1722%
   reads: 	14267150	407753	2.8580%
----------------
Candidate insertion sites in file: RAL-303_100b_insert.txt
  reads:	55778
  uqreads:	54076
  Number of Candidate sites:	54076

Level 1 collapse of insertion sites in file: RAL-303_100b_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	1133

Level 1 annotation file: RAL-303_100b_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-303_100b_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-303_100b.noGEN.front	RAL-303_100b.noGEN.front.gendel	percent
uq reads:	11800840	4974463	42.1535%
   reads: 	14267150	5836299	40.9073%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-303_100b.noGEN.end	RAL-303_100b.noGEN.end.gendel	percent
uq reads:	11800840	1971113	16.7032%
   reads: 	14267150	2778139	19.4723%
----------------
Candidate breakpoint sites in file: RAL-303_100b_depletion.xls
  reads:	139794
  uqreads:	134410
  Number of reads supporting candidate sites:	134410

Level 1 collapse of depletion sites in file: RAL-303_100b_depletion_level1.xls
  Number of Level 1 collapsed sites:	5758