Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-307_125b.fastq.uq.polyn	RAL-307_125b.filter	percent
uq reads:	59070206	4825776	8.1696%
   reads: 	65802290	6220421	9.4532%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-307_125b.filter	RAL-307_125b.nostrna	percent
uq reads:	4825776	4618306	95.7008%
   reads: 	6220421	5731399	92.1384%
----------------
TE_filter:
  reads:	RAL-307_125b.nostrna	RAL-307_125b.noTE	percent
uq reads:	4618306	4595861	99.5140%
   reads: 	5731399	5703081	99.5059%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-307_125b.noGEN.front	RAL-307_125b.noGEN.front.gen	percent
uq reads:	4595861	1514374	32.9508%
   reads: 	5703081	1651323	28.9549%
----------------
match_TE:2:
  reads:	RAL-307_125b.noGEN.front	RAL-307_125b.noGEN.front.TE	percent
uq reads:	4595861	243518	5.2986%
   reads: 	5703081	258382	4.5306%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-307_125b.noGEN.end	RAL-307_125b.noGEN.end.gen	percent
uq reads:	4595861	752712	16.3780%
   reads: 	5703081	888109	15.5724%
----------------
match_TE:2:
  reads:	RAL-307_125b.noGEN.end	RAL-307_125b.noGEN.end.TE	percent
uq reads:	4595861	150269	3.2697%
   reads: 	5703081	164360	2.8820%
----------------
Candidate insertion sites in file: RAL-307_125b_insert.txt
  reads:	32789
  uqreads:	31402
  Number of Candidate sites:	31402

Level 1 collapse of insertion sites in file: RAL-307_125b_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	655

Level 1 annotation file: RAL-307_125b_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-307_125b_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-307_125b.noGEN.front	RAL-307_125b.noGEN.front.gendel	percent
uq reads:	4595861	1514374	32.9508%
   reads: 	5703081	1651323	28.9549%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-307_125b.noGEN.end	RAL-307_125b.noGEN.end.gendel	percent
uq reads:	4595861	752712	16.3780%
   reads: 	5703081	888109	15.5724%
----------------
Candidate breakpoint sites in file: RAL-307_125b_depletion.xls
  reads:	91177
  uqreads:	86576
  Number of reads supporting candidate sites:	86576

Level 1 collapse of depletion sites in file: RAL-307_125b_depletion_level1.xls
  Number of Level 1 collapsed sites:	4220