Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-352.fastq.uq.polyn	RAL-352.filter	percent
uq reads:	41597428	6451132	15.5085%
   reads: 	43594187	7006883	16.0730%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-352.filter	RAL-352.nostrna	percent
uq reads:	6451132	4934717	76.4938%
   reads: 	7006883	5375029	76.7107%
----------------
TE_filter:
  reads:	RAL-352.nostrna	RAL-352.noTE	percent
uq reads:	4934717	4913533	99.5707%
   reads: 	5375029	5351501	99.5623%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-352.noGEN.front	RAL-352.noGEN.front.gen	percent
uq reads:	4913533	1053614	21.4431%
   reads: 	5351501	1295014	24.1991%
----------------
match_TE:2:
  reads:	RAL-352.noGEN.front	RAL-352.noGEN.front.TE	percent
uq reads:	4913533	170003	3.4599%
   reads: 	5351501	171847	3.2112%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-352.noGEN.end	RAL-352.noGEN.end.gen	percent
uq reads:	4913533	678646	13.8118%
   reads: 	5351501	895256	16.7291%
----------------
match_TE:2:
  reads:	RAL-352.noGEN.end	RAL-352.noGEN.end.TE	percent
uq reads:	4913533	115093	2.3424%
   reads: 	5351501	117132	2.1888%
----------------
Candidate insertion sites in file: RAL-352_insert.txt
  reads:	8334
  uqreads:	8267
  Number of Candidate sites:	8267

Level 1 collapse of insertion sites in file: RAL-352_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	427

Level 1 annotation file: RAL-352_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-352_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-352.noGEN.front	RAL-352.noGEN.front.gendel	percent
uq reads:	4913533	1068934	21.7549%
   reads: 	5351501	1312024	24.5169%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-352.noGEN.end	RAL-352.noGEN.end.gendel	percent
uq reads:	4913533	693466	14.1134%
   reads: 	5351501	911673	17.0358%
----------------
Candidate breakpoint sites in file: RAL-352_depletion.xls
  reads:	18850
  uqreads:	18500
  Number of reads supporting candidate sites:	18500

Level 1 collapse of depletion sites in file: RAL-352_depletion_level1.xls
  Number of Level 1 collapsed sites:	1363