Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-595.fastq.uq.polyn	RAL-595.filter	percent
uq reads:	31172233	4968467	15.9388%
   reads: 	35241760	6371716	18.0800%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-595.filter	RAL-595.nostrna	percent
uq reads:	4968467	2545771	51.2386%
   reads: 	6371716	2773329	43.5256%
----------------
TE_filter:
  reads:	RAL-595.nostrna	RAL-595.noTE	percent
uq reads:	2545771	2538443	99.7122%
   reads: 	2773329	2763862	99.6586%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-595.noGEN.front	RAL-595.noGEN.front.gen	percent
uq reads:	2538443	560116	22.0653%
   reads: 	2763862	653523	23.6453%
----------------
match_TE:2:
  reads:	RAL-595.noGEN.front	RAL-595.noGEN.front.TE	percent
uq reads:	2538443	73797	2.9072%
   reads: 	2763862	78274	2.8321%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-595.noGEN.end	RAL-595.noGEN.end.gen	percent
uq reads:	2538443	462488	18.2194%
   reads: 	2763862	544420	19.6978%
----------------
match_TE:2:
  reads:	RAL-595.noGEN.end	RAL-595.noGEN.end.TE	percent
uq reads:	2538443	67948	2.6768%
   reads: 	2763862	72385	2.6190%
----------------
Candidate insertion sites in file: RAL-595_insert.txt
  reads:	5934
  uqreads:	5577
  Number of Candidate sites:	5577

Level 1 collapse of insertion sites in file: RAL-595_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	357

Level 1 annotation file: RAL-595_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-595_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-595.noGEN.front	RAL-595.noGEN.front.gendel	percent
uq reads:	2538443	560116	22.0653%
   reads: 	2763862	653523	23.6453%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-595.noGEN.end	RAL-595.noGEN.end.gendel	percent
uq reads:	2538443	462488	18.2194%
   reads: 	2763862	544420	19.6978%
----------------
Candidate breakpoint sites in file: RAL-595_depletion.xls
  reads:	14510
  uqreads:	13309
  Number of reads supporting candidate sites:	13309

Level 1 collapse of depletion sites in file: RAL-595_depletion_level1.xls
  Number of Level 1 collapsed sites:	1284