Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-373_95b.fastq.uq.polyn	RAL-373_95b.filter	percent
uq reads:	36925455	2180794	5.9059%
   reads: 	39570497	2662689	6.7290%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-373_95b.filter	RAL-373_95b.nostrna	percent
uq reads:	2180794	2095733	96.0995%
   reads: 	2662689	2530244	95.0259%
----------------
TE_filter:
  reads:	RAL-373_95b.nostrna	RAL-373_95b.noTE	percent
uq reads:	2095733	2083553	99.4188%
   reads: 	2530244	2515935	99.4345%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-373_95b.noGEN.front	RAL-373_95b.noGEN.front.gen	percent
uq reads:	2083553	706487	33.9078%
   reads: 	2515935	888822	35.3277%
----------------
match_TE:2:
  reads:	RAL-373_95b.noGEN.front	RAL-373_95b.noGEN.front.TE	percent
uq reads:	2083553	116770	5.6044%
   reads: 	2515935	124428	4.9456%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-373_95b.noGEN.end	RAL-373_95b.noGEN.end.gen	percent
uq reads:	2083553	587482	28.1962%
   reads: 	2515935	756497	30.0682%
----------------
match_TE:2:
  reads:	RAL-373_95b.noGEN.end	RAL-373_95b.noGEN.end.TE	percent
uq reads:	2083553	125396	6.0184%
   reads: 	2515935	134028	5.3272%
----------------
Candidate insertion sites in file: RAL-373_95b_insert.txt
  reads:	14124
  uqreads:	13822
  Number of Candidate sites:	13822

Level 1 collapse of insertion sites in file: RAL-373_95b_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	653

Level 1 annotation file: RAL-373_95b_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-373_95b_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-373_95b.noGEN.front	RAL-373_95b.noGEN.front.gendel	percent
uq reads:	2083553	706487	33.9078%
   reads: 	2515935	888822	35.3277%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-373_95b.noGEN.end	RAL-373_95b.noGEN.end.gendel	percent
uq reads:	2083553	587482	28.1962%
   reads: 	2515935	756497	30.0682%
----------------
Candidate breakpoint sites in file: RAL-373_95b_depletion.xls
  reads:	35951
  uqreads:	35073
  Number of reads supporting candidate sites:	35073

Level 1 collapse of depletion sites in file: RAL-373_95b_depletion_level1.xls
  Number of Level 1 collapsed sites:	3113