Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-161.fastq.uq.polyn	RAL-161.filter	percent
uq reads:	31583030	1711043	5.4176%
   reads: 	33207046	2051266	6.1772%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-161.filter	RAL-161.nostrna	percent
uq reads:	1711043	1654336	96.6858%
   reads: 	2051266	1989392	96.9836%
----------------
TE_filter:
  reads:	RAL-161.nostrna	RAL-161.noTE	percent
uq reads:	1654336	1641331	99.2139%
   reads: 	1989392	1975009	99.2770%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-161.noGEN.front	RAL-161.noGEN.front.gen	percent
uq reads:	1641331	525284	32.0035%
   reads: 	1975009	753602	38.1569%
----------------
match_TE:2:
  reads:	RAL-161.noGEN.front	RAL-161.noGEN.front.TE	percent
uq reads:	1641331	72784	4.4344%
   reads: 	1975009	75401	3.8178%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-161.noGEN.end	RAL-161.noGEN.end.gen	percent
uq reads:	1641331	426538	25.9873%
   reads: 	1975009	649661	32.8941%
----------------
match_TE:2:
  reads:	RAL-161.noGEN.end	RAL-161.noGEN.end.TE	percent
uq reads:	1641331	67790	4.1302%
   reads: 	1975009	70555	3.5724%
----------------
Candidate insertion sites in file: RAL-161_insert.txt
  reads:	5427
  uqreads:	5338
  Number of Candidate sites:	5338

Level 1 collapse of insertion sites in file: RAL-161_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	383

Level 1 annotation file: RAL-161_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-161_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-161.noGEN.front	RAL-161.noGEN.front.gendel	percent
uq reads:	1641331	525284	32.0035%
   reads: 	1975009	753602	38.1569%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-161.noGEN.end	RAL-161.noGEN.end.gendel	percent
uq reads:	1641331	426538	25.9873%
   reads: 	1975009	649661	32.8941%
----------------
Candidate breakpoint sites in file: RAL-161_depletion.xls
  reads:	13467
  uqreads:	12945
  Number of reads supporting candidate sites:	12945

Level 1 collapse of depletion sites in file: RAL-161_depletion_level1.xls
  Number of Level 1 collapsed sites:	1199