Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-370.fastq.uq.polyn	RAL-370.filter	percent
uq reads:	40132420	4485648	11.1771%
   reads: 	43312765	5263489	12.1523%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-370.filter	RAL-370.nostrna	percent
uq reads:	4485648	2345759	52.2948%
   reads: 	5263489	2744361	52.1396%
----------------
TE_filter:
  reads:	RAL-370.nostrna	RAL-370.noTE	percent
uq reads:	2345759	2333540	99.4791%
   reads: 	2744361	2729370	99.4538%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-370.noGEN.front	RAL-370.noGEN.front.gen	percent
uq reads:	2333540	747267	32.0229%
   reads: 	2729370	889046	32.5733%
----------------
match_TE:2:
  reads:	RAL-370.noGEN.front	RAL-370.noGEN.front.TE	percent
uq reads:	2333540	128065	5.4880%
   reads: 	2729370	133424	4.8885%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-370.noGEN.end	RAL-370.noGEN.end.gen	percent
uq reads:	2333540	550159	23.5762%
   reads: 	2729370	682816	25.0173%
----------------
match_TE:2:
  reads:	RAL-370.noGEN.end	RAL-370.noGEN.end.TE	percent
uq reads:	2333540	106328	4.5565%
   reads: 	2729370	112120	4.1079%
----------------
Candidate insertion sites in file: RAL-370_insert.txt
  reads:	15657
  uqreads:	15368
  Number of Candidate sites:	15368

Level 1 collapse of insertion sites in file: RAL-370_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	595

Level 1 annotation file: RAL-370_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-370_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-370.noGEN.front	RAL-370.noGEN.front.gendel	percent
uq reads:	2333540	763501	32.7186%
   reads: 	2729370	916400	33.5755%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-370.noGEN.end	RAL-370.noGEN.end.gendel	percent
uq reads:	2333540	561462	24.0605%
   reads: 	2729370	705380	25.8441%
----------------
Candidate breakpoint sites in file: RAL-370_depletion.xls
  reads:	37388
  uqreads:	36579
  Number of reads supporting candidate sites:	36579

Level 1 collapse of depletion sites in file: RAL-370_depletion_level1.xls
  Number of Level 1 collapsed sites:	2979