Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-646.fastq.uq.polyn	RAL-646.filter	percent
uq reads:	30641497	3453690	11.2713%
   reads: 	32055994	3824664	11.9312%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-646.filter	RAL-646.nostrna	percent
uq reads:	3453690	2540104	73.5475%
   reads: 	3824664	2780868	72.7088%
----------------
TE_filter:
  reads:	RAL-646.nostrna	RAL-646.noTE	percent
uq reads:	2540104	2527899	99.5195%
   reads: 	2780868	2767284	99.5115%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-646.noGEN.front	RAL-646.noGEN.front.gen	percent
uq reads:	2527899	631760	24.9915%
   reads: 	2767284	784102	28.3347%
----------------
match_TE:2:
  reads:	RAL-646.noGEN.front	RAL-646.noGEN.front.TE	percent
uq reads:	2527899	79683	3.1521%
   reads: 	2767284	81120	2.9314%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-646.noGEN.end	RAL-646.noGEN.end.gen	percent
uq reads:	2527899	510515	20.1952%
   reads: 	2767284	658804	23.8069%
----------------
match_TE:2:
  reads:	RAL-646.noGEN.end	RAL-646.noGEN.end.TE	percent
uq reads:	2527899	79655	3.1510%
   reads: 	2767284	81584	2.9482%
----------------
Candidate insertion sites in file: RAL-646_insert.txt
  reads:	6194
  uqreads:	6128
  Number of Candidate sites:	6128

Level 1 collapse of insertion sites in file: RAL-646_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	393

Level 1 annotation file: RAL-646_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-646_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-646.noGEN.front	RAL-646.noGEN.front.gendel	percent
uq reads:	2527899	631760	24.9915%
   reads: 	2767284	784102	28.3347%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-646.noGEN.end	RAL-646.noGEN.end.gendel	percent
uq reads:	2527899	510515	20.1952%
   reads: 	2767284	658804	23.8069%
----------------
Candidate breakpoint sites in file: RAL-646_depletion.xls
  reads:	13359
  uqreads:	12890
  Number of reads supporting candidate sites:	12890

Level 1 collapse of depletion sites in file: RAL-646_depletion_level1.xls
  Number of Level 1 collapsed sites:	1137