Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-852.fastq.uq.polyn	RAL-852.filter	percent
uq reads:	21648102	3675660	16.9791%
   reads: 	22713274	4027333	17.7312%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-852.filter	RAL-852.nostrna	percent
uq reads:	3675660	3058666	83.2141%
   reads: 	4027333	3361709	83.4723%
----------------
TE_filter:
  reads:	RAL-852.nostrna	RAL-852.noTE	percent
uq reads:	3058666	3052124	99.7861%
   reads: 	3361709	3354709	99.7918%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-852.noGEN.front	RAL-852.noGEN.front.gen	percent
uq reads:	3052124	1253428	41.0674%
   reads: 	3354709	1452511	43.2977%
----------------
match_TE:2:
  reads:	RAL-852.noGEN.front	RAL-852.noGEN.front.TE	percent
uq reads:	3052124	173469	5.6836%
   reads: 	3354709	175316	5.2260%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-852.noGEN.end	RAL-852.noGEN.end.gen	percent
uq reads:	3052124	312467	10.2377%
   reads: 	3354709	485045	14.4586%
----------------
match_TE:2:
  reads:	RAL-852.noGEN.end	RAL-852.noGEN.end.TE	percent
uq reads:	3052124	70012	2.2939%
   reads: 	3354709	72833	2.1711%
----------------
Candidate insertion sites in file: RAL-852_insert.txt
  reads:	5617
  uqreads:	5553
  Number of Candidate sites:	5553

Level 1 collapse of insertion sites in file: RAL-852_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	330

Level 1 annotation file: RAL-852_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-852_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-852.noGEN.front	RAL-852.noGEN.front.gendel	percent
uq reads:	3052124	1253428	41.0674%
   reads: 	3354709	1452511	43.2977%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-852.noGEN.end	RAL-852.noGEN.end.gendel	percent
uq reads:	3052124	312467	10.2377%
   reads: 	3354709	485045	14.4586%
----------------
Candidate breakpoint sites in file: RAL-852_depletion.xls
  reads:	12091
  uqreads:	11248
  Number of reads supporting candidate sites:	11248

Level 1 collapse of depletion sites in file: RAL-852_depletion_level1.xls
  Number of Level 1 collapsed sites:	984