Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-849.fastq.uq.polyn	RAL-849.filter	percent
uq reads:	52825018	4442595	8.4100%
   reads: 	60952457	6173058	10.1277%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-849.filter	RAL-849.nostrna	percent
uq reads:	4442595	4392047	98.8622%
   reads: 	6173058	5943331	96.2786%
----------------
TE_filter:
  reads:	RAL-849.nostrna	RAL-849.noTE	percent
uq reads:	4392047	4381846	99.7677%
   reads: 	5943331	5925872	99.7062%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-849.noGEN.front	RAL-849.noGEN.front.gen	percent
uq reads:	4381846	1238771	28.2705%
   reads: 	5925872	1561613	26.3525%
----------------
match_TE:2:
  reads:	RAL-849.noGEN.front	RAL-849.noGEN.front.TE	percent
uq reads:	4381846	214763	4.9012%
   reads: 	5925872	245533	4.1434%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-849.noGEN.end	RAL-849.noGEN.end.gen	percent
uq reads:	4381846	894565	20.4153%
   reads: 	5925872	1205635	20.3453%
----------------
match_TE:2:
  reads:	RAL-849.noGEN.end	RAL-849.noGEN.end.TE	percent
uq reads:	4381846	173895	3.9685%
   reads: 	5925872	204727	3.4548%
----------------
Candidate insertion sites in file: RAL-849_insert.txt
  reads:	36499
  uqreads:	34996
  Number of Candidate sites:	34996

Level 1 collapse of insertion sites in file: RAL-849_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	743

Level 1 annotation file: RAL-849_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-849_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-849.noGEN.front	RAL-849.noGEN.front.gendel	percent
uq reads:	4381846	1238771	28.2705%
   reads: 	5925872	1561613	26.3525%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-849.noGEN.end	RAL-849.noGEN.end.gendel	percent
uq reads:	4381846	894565	20.4153%
   reads: 	5925872	1205635	20.3453%
----------------
Candidate breakpoint sites in file: RAL-849_depletion.xls
  reads:	94373
  uqreads:	89660
  Number of reads supporting candidate sites:	89660

Level 1 collapse of depletion sites in file: RAL-849_depletion_level1.xls
  Number of Level 1 collapsed sites:	4412