Insertion Pipeline
Bowtie2_wholegenome:
  reads:	L1.fastq.uq.polyn	L1.filter	percent
uq reads:	73364361	3117043	4.2487%
   reads: 	93175614	6122711	6.5712%
----------------
virus_structural_rna_repbase_filter:
  reads:	L1.filter	L1.nostrna	percent
uq reads:	3117043	3065160	98.3355%
   reads: 	6122711	6020298	98.3273%
----------------
TE_filter:
  reads:	L1.nostrna	L1.noTE	percent
uq reads:	3065160	3058783	99.7920%
   reads: 	6020298	6012638	99.8728%
----------------
match_dm6_mask_gen:1:
  reads:	L1.noGEN.front	L1.noGEN.front.gen	percent
uq reads:	3058783	952150	31.1284%
   reads: 	6012638	1885849	31.3648%
----------------
match_TE:2:
  reads:	L1.noGEN.front	L1.noGEN.front.TE	percent
uq reads:	3058783	181568	5.9360%
   reads: 	6012638	206960	3.4421%
----------------
match_dm6_mask_gen:1:
  reads:	L1.noGEN.end	L1.noGEN.end.gen	percent
uq reads:	3058783	737065	24.0967%
   reads: 	6012638	1624765	27.0225%
----------------
match_TE:2:
  reads:	L1.noGEN.end	L1.noGEN.end.TE	percent
uq reads:	3058783	154810	5.0612%
   reads: 	6012638	182260	3.0313%
----------------
Candidate insertion sites in file: L1_insert.txt
  reads:	49178
  uqreads:	45437
  Number of Candidate sites:	45437

Level 1 collapse of insertion sites in file: L1_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	1368

Level 1 annotation file: L1_level1siteannotation.xls
Insertion sites in fixed bin:
L1_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	L1.noGEN.front	L1.noGEN.front.gendel	percent
uq reads:	3058783	952150	31.1284%
   reads: 	6012638	1885849	31.3648%
----------------
match_dm6_mask_gen_del:1:
  reads:	L1.noGEN.end	L1.noGEN.end.gendel	percent
uq reads:	3058783	737065	24.0967%
   reads: 	6012638	1624765	27.0225%
----------------
Candidate breakpoint sites in file: L1_depletion.xls
  reads:	85819
  uqreads:	77666
  Number of reads supporting candidate sites:	77666

Level 1 collapse of depletion sites in file: L1_depletion_level1.xls
  Number of Level 1 collapsed sites:	3777