Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-153.fastq.uq.polyn	RAL-153.filter	percent
uq reads:	24889219	2776147	11.1540%
   reads: 	26655098	3204209	12.0210%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-153.filter	RAL-153.nostrna	percent
uq reads:	2776147	2309694	83.1978%
   reads: 	3204209	2711099	84.6106%
----------------
TE_filter:
  reads:	RAL-153.nostrna	RAL-153.noTE	percent
uq reads:	2309694	2303573	99.7350%
   reads: 	2711099	2704872	99.7703%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-153.noGEN.front	RAL-153.noGEN.front.gen	percent
uq reads:	2303573	857839	37.2395%
   reads: 	2704872	1113540	41.1679%
----------------
match_TE:2:
  reads:	RAL-153.noGEN.front	RAL-153.noGEN.front.TE	percent
uq reads:	2303573	88560	3.8445%
   reads: 	2704872	92446	3.4178%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-153.noGEN.end	RAL-153.noGEN.end.gen	percent
uq reads:	2303573	656041	28.4793%
   reads: 	2704872	904182	33.4279%
----------------
match_TE:2:
  reads:	RAL-153.noGEN.end	RAL-153.noGEN.end.TE	percent
uq reads:	2303573	83172	3.6106%
   reads: 	2704872	89385	3.3046%
----------------
Candidate insertion sites in file: RAL-153_insert.txt
  reads:	10498
  uqreads:	10308
  Number of Candidate sites:	10308

Level 1 collapse of insertion sites in file: RAL-153_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	259

Level 1 annotation file: RAL-153_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-153_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-153.noGEN.front	RAL-153.noGEN.front.gendel	percent
uq reads:	2303573	857839	37.2395%
   reads: 	2704872	1113540	41.1679%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-153.noGEN.end	RAL-153.noGEN.end.gendel	percent
uq reads:	2303573	656041	28.4793%
   reads: 	2704872	904182	33.4279%
----------------
Candidate breakpoint sites in file: RAL-153_depletion.xls
  reads:	23425
  uqreads:	22875
  Number of reads supporting candidate sites:	22875

Level 1 collapse of depletion sites in file: RAL-153_depletion_level1.xls
  Number of Level 1 collapsed sites:	778