Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-882.fastq.uq.polyn	RAL-882.filter	percent
uq reads:	40784397	3858818	9.4615%
   reads: 	44337187	4858187	10.9574%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-882.filter	RAL-882.nostrna	percent
uq reads:	3858818	1896438	49.1456%
   reads: 	4858187	2359798	48.5736%
----------------
TE_filter:
  reads:	RAL-882.nostrna	RAL-882.noTE	percent
uq reads:	1896438	1885021	99.3980%
   reads: 	2359798	2344560	99.3543%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-882.noGEN.front	RAL-882.noGEN.front.gen	percent
uq reads:	1885021	616430	32.7015%
   reads: 	2344560	859438	36.6567%
----------------
match_TE:2:
  reads:	RAL-882.noGEN.front	RAL-882.noGEN.front.TE	percent
uq reads:	1885021	88027	4.6698%
   reads: 	2344560	94201	4.0179%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-882.noGEN.end	RAL-882.noGEN.end.gen	percent
uq reads:	1885021	529686	28.0997%
   reads: 	2344560	758474	32.3504%
----------------
match_TE:2:
  reads:	RAL-882.noGEN.end	RAL-882.noGEN.end.TE	percent
uq reads:	1885021	86680	4.5984%
   reads: 	2344560	93585	3.9916%
----------------
Candidate insertion sites in file: RAL-882_insert.txt
  reads:	9839
  uqreads:	9577
  Number of Candidate sites:	9577

Level 1 collapse of insertion sites in file: RAL-882_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	555

Level 1 annotation file: RAL-882_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-882_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-882.noGEN.front	RAL-882.noGEN.front.gendel	percent
uq reads:	1885021	616430	32.7015%
   reads: 	2344560	859438	36.6567%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-882.noGEN.end	RAL-882.noGEN.end.gendel	percent
uq reads:	1885021	529686	28.0997%
   reads: 	2344560	758474	32.3504%
----------------
Candidate breakpoint sites in file: RAL-882_depletion.xls
  reads:	21018
  uqreads:	20180
  Number of reads supporting candidate sites:	20180

Level 1 collapse of depletion sites in file: RAL-882_depletion_level1.xls
  Number of Level 1 collapsed sites:	2001