Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-853_110b.fastq.uq.polyn	RAL-853_110b.filter	percent
uq reads:	39643470	7156345	18.0518%
   reads: 	40957147	7677825	18.7460%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-853_110b.filter	RAL-853_110b.nostrna	percent
uq reads:	7156345	3057045	42.7180%
   reads: 	7677825	3287073	42.8126%
----------------
TE_filter:
  reads:	RAL-853_110b.nostrna	RAL-853_110b.noTE	percent
uq reads:	3057045	3047897	99.7008%
   reads: 	3287073	3277577	99.7111%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-853_110b.noGEN.front	RAL-853_110b.noGEN.front.gen	percent
uq reads:	3047897	1052118	34.5195%
   reads: 	3277577	1185130	36.1587%
----------------
match_TE:2:
  reads:	RAL-853_110b.noGEN.front	RAL-853_110b.noGEN.front.TE	percent
uq reads:	3047897	143237	4.6995%
   reads: 	3277577	147082	4.4875%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-853_110b.noGEN.end	RAL-853_110b.noGEN.end.gen	percent
uq reads:	3047897	502370	16.4825%
   reads: 	3277577	625563	19.0861%
----------------
match_TE:2:
  reads:	RAL-853_110b.noGEN.end	RAL-853_110b.noGEN.end.TE	percent
uq reads:	3047897	80923	2.6550%
   reads: 	3277577	85046	2.5948%
----------------
Candidate insertion sites in file: RAL-853_110b_insert.txt
  reads:	12011
  uqreads:	11956
  Number of Candidate sites:	11956

Level 1 collapse of insertion sites in file: RAL-853_110b_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	626

Level 1 annotation file: RAL-853_110b_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-853_110b_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-853_110b.noGEN.front	RAL-853_110b.noGEN.front.gendel	percent
uq reads:	3047897	1052118	34.5195%
   reads: 	3277577	1185130	36.1587%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-853_110b.noGEN.end	RAL-853_110b.noGEN.end.gendel	percent
uq reads:	3047897	502370	16.4825%
   reads: 	3277577	625563	19.0861%
----------------
Candidate breakpoint sites in file: RAL-853_110b_depletion.xls
  reads:	29545
  uqreads:	29321
  Number of reads supporting candidate sites:	29321

Level 1 collapse of depletion sites in file: RAL-853_110b_depletion_level1.xls
  Number of Level 1 collapsed sites:	2567