Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-805.fastq.uq.polyn	RAL-805.filter	percent
uq reads:	39108148	5133506	13.1264%
   reads: 	42834700	6649354	15.5233%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-805.filter	RAL-805.nostrna	percent
uq reads:	5133506	2239960	43.6341%
   reads: 	6649354	2630935	39.5668%
----------------
TE_filter:
  reads:	RAL-805.nostrna	RAL-805.noTE	percent
uq reads:	2239960	2227841	99.4590%
   reads: 	2630935	2615771	99.4236%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-805.noGEN.front	RAL-805.noGEN.front.gen	percent
uq reads:	2227841	656571	29.4712%
   reads: 	2615771	847274	32.3910%
----------------
match_TE:2:
  reads:	RAL-805.noGEN.front	RAL-805.noGEN.front.TE	percent
uq reads:	2227841	88923	3.9914%
   reads: 	2615771	95644	3.6564%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-805.noGEN.end	RAL-805.noGEN.end.gen	percent
uq reads:	2227841	591723	26.5604%
   reads: 	2615771	772462	29.5309%
----------------
match_TE:2:
  reads:	RAL-805.noGEN.end	RAL-805.noGEN.end.TE	percent
uq reads:	2227841	87847	3.9431%
   reads: 	2615771	94875	3.6270%
----------------
Candidate insertion sites in file: RAL-805_insert.txt
  reads:	8984
  uqreads:	8791
  Number of Candidate sites:	8791

Level 1 collapse of insertion sites in file: RAL-805_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	491

Level 1 annotation file: RAL-805_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-805_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-805.noGEN.front	RAL-805.noGEN.front.gendel	percent
uq reads:	2227841	656571	29.4712%
   reads: 	2615771	847274	32.3910%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-805.noGEN.end	RAL-805.noGEN.end.gendel	percent
uq reads:	2227841	591723	26.5604%
   reads: 	2615771	772462	29.5309%
----------------
Candidate breakpoint sites in file: RAL-805_depletion.xls
  reads:	20867
  uqreads:	20154
  Number of reads supporting candidate sites:	20154

Level 1 collapse of depletion sites in file: RAL-805_depletion_level1.xls
  Number of Level 1 collapsed sites:	2068