Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-642.fastq.uq.polyn	RAL-642.filter	percent
uq reads:	32230874	1854663	5.7543%
   reads: 	33872917	2099848	6.1992%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-642.filter	RAL-642.nostrna	percent
uq reads:	1854663	1754743	94.6125%
   reads: 	2099848	1983292	94.4493%
----------------
TE_filter:
  reads:	RAL-642.nostrna	RAL-642.noTE	percent
uq reads:	1754743	1741144	99.2250%
   reads: 	1983292	1968567	99.2575%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-642.noGEN.front	RAL-642.noGEN.front.gen	percent
uq reads:	1741144	647529	37.1899%
   reads: 	1968567	801816	40.7309%
----------------
match_TE:2:
  reads:	RAL-642.noGEN.front	RAL-642.noGEN.front.TE	percent
uq reads:	1741144	74127	4.2574%
   reads: 	1968567	76231	3.8724%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-642.noGEN.end	RAL-642.noGEN.end.gen	percent
uq reads:	1741144	523826	30.0852%
   reads: 	1968567	675454	34.3120%
----------------
match_TE:2:
  reads:	RAL-642.noGEN.end	RAL-642.noGEN.end.TE	percent
uq reads:	1741144	72961	4.1904%
   reads: 	1968567	75828	3.8519%
----------------
Candidate insertion sites in file: RAL-642_insert.txt
  reads:	6843
  uqreads:	6713
  Number of Candidate sites:	6713

Level 1 collapse of insertion sites in file: RAL-642_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	434

Level 1 annotation file: RAL-642_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-642_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-642.noGEN.front	RAL-642.noGEN.front.gendel	percent
uq reads:	1741144	647529	37.1899%
   reads: 	1968567	801816	40.7309%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-642.noGEN.end	RAL-642.noGEN.end.gendel	percent
uq reads:	1741144	523826	30.0852%
   reads: 	1968567	675454	34.3120%
----------------
Candidate breakpoint sites in file: RAL-642_depletion.xls
  reads:	15266
  uqreads:	14716
  Number of reads supporting candidate sites:	14716

Level 1 collapse of depletion sites in file: RAL-642_depletion_level1.xls
  Number of Level 1 collapsed sites:	1401