Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-358.fastq.uq.polyn	RAL-358.filter	percent
uq reads:	22799528	2619791	11.4905%
   reads: 	27314064	3099764	11.3486%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-358.filter	RAL-358.nostrna	percent
uq reads:	2619791	2571923	98.1728%
   reads: 	3099764	3015878	97.2938%
----------------
TE_filter:
  reads:	RAL-358.nostrna	RAL-358.noTE	percent
uq reads:	2571923	2565856	99.7641%
   reads: 	3015878	3007681	99.7282%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-358.noGEN.front	RAL-358.noGEN.front.gen	percent
uq reads:	2565856	1011101	39.4060%
   reads: 	3007681	1194235	39.7062%
----------------
match_TE:2:
  reads:	RAL-358.noGEN.front	RAL-358.noGEN.front.TE	percent
uq reads:	2565856	142274	5.5449%
   reads: 	3007681	153592	5.1067%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-358.noGEN.end	RAL-358.noGEN.end.gen	percent
uq reads:	2565856	373666	14.5630%
   reads: 	3007681	550251	18.2949%
----------------
match_TE:2:
  reads:	RAL-358.noGEN.end	RAL-358.noGEN.end.TE	percent
uq reads:	2565856	74013	2.8845%
   reads: 	3007681	85848	2.8543%
----------------
Candidate insertion sites in file: RAL-358_insert.txt
  reads:	7367
  uqreads:	6418
  Number of Candidate sites:	6418

Level 1 collapse of insertion sites in file: RAL-358_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	422

Level 1 annotation file: RAL-358_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-358_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-358.noGEN.front	RAL-358.noGEN.front.gendel	percent
uq reads:	2565856	1011101	39.4060%
   reads: 	3007681	1194235	39.7062%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-358.noGEN.end	RAL-358.noGEN.end.gendel	percent
uq reads:	2565856	373666	14.5630%
   reads: 	3007681	550251	18.2949%
----------------
Candidate breakpoint sites in file: RAL-358_depletion.xls
  reads:	15985
  uqreads:	13208
  Number of reads supporting candidate sites:	13208

Level 1 collapse of depletion sites in file: RAL-358_depletion_level1.xls
  Number of Level 1 collapsed sites:	1324