Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-818.fastq.uq.polyn	RAL-818.filter	percent
uq reads:	33990326	3220919	9.4760%
   reads: 	37203794	4245010	11.4102%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-818.filter	RAL-818.nostrna	percent
uq reads:	3220919	1720702	53.4227%
   reads: 	4245010	2066335	48.6768%
----------------
TE_filter:
  reads:	RAL-818.nostrna	RAL-818.noTE	percent
uq reads:	1720702	1705921	99.1410%
   reads: 	2066335	2047114	99.0698%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-818.noGEN.front	RAL-818.noGEN.front.gen	percent
uq reads:	1705921	561589	32.9200%
   reads: 	2047114	773495	37.7847%
----------------
match_TE:2:
  reads:	RAL-818.noGEN.front	RAL-818.noGEN.front.TE	percent
uq reads:	1705921	70890	4.1555%
   reads: 	2047114	73944	3.6121%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-818.noGEN.end	RAL-818.noGEN.end.gen	percent
uq reads:	1705921	460585	26.9992%
   reads: 	2047114	655117	32.0020%
----------------
match_TE:2:
  reads:	RAL-818.noGEN.end	RAL-818.noGEN.end.TE	percent
uq reads:	1705921	62866	3.6852%
   reads: 	2047114	66348	3.2411%
----------------
Candidate insertion sites in file: RAL-818_insert.txt
  reads:	8174
  uqreads:	7943
  Number of Candidate sites:	7943

Level 1 collapse of insertion sites in file: RAL-818_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	447

Level 1 annotation file: RAL-818_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-818_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-818.noGEN.front	RAL-818.noGEN.front.gendel	percent
uq reads:	1705921	570062	33.4167%
   reads: 	2047114	786765	38.4329%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-818.noGEN.end	RAL-818.noGEN.end.gendel	percent
uq reads:	1705921	466814	27.3643%
   reads: 	2047114	666174	32.5421%
----------------
Candidate breakpoint sites in file: RAL-818_depletion.xls
  reads:	20560
  uqreads:	19735
  Number of reads supporting candidate sites:	19735

Level 1 collapse of depletion sites in file: RAL-818_depletion_level1.xls
  Number of Level 1 collapsed sites:	1692