Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-336.fastq.uq.polyn	RAL-336.filter	percent
uq reads:	30115088	6686506	22.2032%
   reads: 	31981614	7102261	22.2073%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-336.filter	RAL-336.nostrna	percent
uq reads:	6686506	6173524	92.3281%
   reads: 	7102261	6555954	92.3080%
----------------
TE_filter:
  reads:	RAL-336.nostrna	RAL-336.noTE	percent
uq reads:	6173524	6157912	99.7471%
   reads: 	6555954	6539103	99.7430%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-336.noGEN.front	RAL-336.noGEN.front.gen	percent
uq reads:	6157912	1494808	24.2746%
   reads: 	6539103	1718275	26.2769%
----------------
match_TE:2:
  reads:	RAL-336.noGEN.front	RAL-336.noGEN.front.TE	percent
uq reads:	6157912	198252	3.2195%
   reads: 	6539103	201167	3.0764%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-336.noGEN.end	RAL-336.noGEN.end.gen	percent
uq reads:	6157912	1403656	22.7943%
   reads: 	6539103	1620794	24.7862%
----------------
match_TE:2:
  reads:	RAL-336.noGEN.end	RAL-336.noGEN.end.TE	percent
uq reads:	6157912	207870	3.3757%
   reads: 	6539103	211489	3.2342%
----------------
Candidate insertion sites in file: RAL-336_insert.txt
  reads:	24461
  uqreads:	24398
  Number of Candidate sites:	24398

Level 1 collapse of insertion sites in file: RAL-336_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	287

Level 1 annotation file: RAL-336_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-336_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-336.noGEN.front	RAL-336.noGEN.front.gendel	percent
uq reads:	6157912	1519255	24.6716%
   reads: 	6539103	1748077	26.7327%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-336.noGEN.end	RAL-336.noGEN.end.gendel	percent
uq reads:	6157912	1428979	23.2056%
   reads: 	6539103	1651300	25.2527%
----------------
Candidate breakpoint sites in file: RAL-336_depletion.xls
  reads:	48631
  uqreads:	48023
  Number of reads supporting candidate sites:	48023

Level 1 collapse of depletion sites in file: RAL-336_depletion_level1.xls
  Number of Level 1 collapsed sites:	754