Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-748_125b.fastq.uq.polyn	RAL-748_125b.filter	percent
uq reads:	46752759	7665742	16.3963%
   reads: 	49773242	8450109	16.9772%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-748_125b.filter	RAL-748_125b.nostrna	percent
uq reads:	7665742	5793868	75.5813%
   reads: 	8450109	6180960	73.1465%
----------------
TE_filter:
  reads:	RAL-748_125b.nostrna	RAL-748_125b.noTE	percent
uq reads:	5793868	5781902	99.7935%
   reads: 	6180960	6165129	99.7439%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-748_125b.noGEN.front	RAL-748_125b.noGEN.front.gen	percent
uq reads:	5781902	944880	16.3420%
   reads: 	6165129	1051226	17.0512%
----------------
match_TE:2:
  reads:	RAL-748_125b.noGEN.front	RAL-748_125b.noGEN.front.TE	percent
uq reads:	5781902	160631	2.7782%
   reads: 	6165129	166311	2.6976%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-748_125b.noGEN.end	RAL-748_125b.noGEN.end.gen	percent
uq reads:	5781902	483840	8.3682%
   reads: 	6165129	588489	9.5454%
----------------
match_TE:2:
  reads:	RAL-748_125b.noGEN.end	RAL-748_125b.noGEN.end.TE	percent
uq reads:	5781902	103022	1.7818%
   reads: 	6165129	108595	1.7614%
----------------
Candidate insertion sites in file: RAL-748_125b_insert.txt
  reads:	19713
  uqreads:	19160
  Number of Candidate sites:	19160

Level 1 collapse of insertion sites in file: RAL-748_125b_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	584

Level 1 annotation file: RAL-748_125b_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-748_125b_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-748_125b.noGEN.front	RAL-748_125b.noGEN.front.gendel	percent
uq reads:	5781902	944880	16.3420%
   reads: 	6165129	1051226	17.0512%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-748_125b.noGEN.end	RAL-748_125b.noGEN.end.gendel	percent
uq reads:	5781902	483840	8.3682%
   reads: 	6165129	588489	9.5454%
----------------
Candidate breakpoint sites in file: RAL-748_125b_depletion.xls
  reads:	60021
  uqreads:	58174
  Number of reads supporting candidate sites:	58174

Level 1 collapse of depletion sites in file: RAL-748_125b_depletion_level1.xls
  Number of Level 1 collapsed sites:	3672