Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-812.fastq.uq.polyn	RAL-812.filter	percent
uq reads:	35629160	1583836	4.4453%
   reads: 	38414210	2091342	5.4442%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-812.filter	RAL-812.nostrna	percent
uq reads:	1583836	1534698	96.8975%
   reads: 	2091342	2025904	96.8710%
----------------
TE_filter:
  reads:	RAL-812.nostrna	RAL-812.noTE	percent
uq reads:	1534698	1524691	99.3479%
   reads: 	2025904	2013132	99.3696%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-812.noGEN.front	RAL-812.noGEN.front.gen	percent
uq reads:	1524691	562803	36.9126%
   reads: 	2013132	864027	42.9195%
----------------
match_TE:2:
  reads:	RAL-812.noGEN.front	RAL-812.noGEN.front.TE	percent
uq reads:	1524691	76546	5.0204%
   reads: 	2013132	80743	4.0108%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-812.noGEN.end	RAL-812.noGEN.end.gen	percent
uq reads:	1524691	477688	31.3302%
   reads: 	2013132	754405	37.4742%
----------------
match_TE:2:
  reads:	RAL-812.noGEN.end	RAL-812.noGEN.end.TE	percent
uq reads:	1524691	70912	4.6509%
   reads: 	2013132	75976	3.7740%
----------------
Candidate insertion sites in file: RAL-812_insert.txt
  reads:	8645
  uqreads:	8381
  Number of Candidate sites:	8381

Level 1 collapse of insertion sites in file: RAL-812_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	511

Level 1 annotation file: RAL-812_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-812_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-812.noGEN.front	RAL-812.noGEN.front.gendel	percent
uq reads:	1524691	562803	36.9126%
   reads: 	2013132	864027	42.9195%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-812.noGEN.end	RAL-812.noGEN.end.gendel	percent
uq reads:	1524691	477688	31.3302%
   reads: 	2013132	754405	37.4742%
----------------
Candidate breakpoint sites in file: RAL-812_depletion.xls
  reads:	20183
  uqreads:	19367
  Number of reads supporting candidate sites:	19367

Level 1 collapse of depletion sites in file: RAL-812_depletion_level1.xls
  Number of Level 1 collapsed sites:	1793