Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-884.fastq.uq.polyn	RAL-884.filter	percent
uq reads:	40093263	5216198	13.0102%
   reads: 	41908136	5719663	13.6481%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-884.filter	RAL-884.nostrna	percent
uq reads:	5216198	2604768	49.9361%
   reads: 	5719663	2839740	49.6487%
----------------
TE_filter:
  reads:	RAL-884.nostrna	RAL-884.noTE	percent
uq reads:	2604768	2590159	99.4391%
   reads: 	2839740	2824234	99.4540%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-884.noGEN.front	RAL-884.noGEN.front.gen	percent
uq reads:	2590159	889438	34.3391%
   reads: 	2824234	1027790	36.3918%
----------------
match_TE:2:
  reads:	RAL-884.noGEN.front	RAL-884.noGEN.front.TE	percent
uq reads:	2590159	99178	3.8290%
   reads: 	2824234	103644	3.6698%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-884.noGEN.end	RAL-884.noGEN.end.gen	percent
uq reads:	2590159	742683	28.6733%
   reads: 	2824234	875011	30.9822%
----------------
match_TE:2:
  reads:	RAL-884.noGEN.end	RAL-884.noGEN.end.TE	percent
uq reads:	2590159	104565	4.0370%
   reads: 	2824234	109762	3.8864%
----------------
Candidate insertion sites in file: RAL-884_insert.txt
  reads:	7571
  uqreads:	7509
  Number of Candidate sites:	7509

Level 1 collapse of insertion sites in file: RAL-884_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	456

Level 1 annotation file: RAL-884_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-884_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-884.noGEN.front	RAL-884.noGEN.front.gendel	percent
uq reads:	2590159	889438	34.3391%
   reads: 	2824234	1027790	36.3918%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-884.noGEN.end	RAL-884.noGEN.end.gendel	percent
uq reads:	2590159	742683	28.6733%
   reads: 	2824234	875011	30.9822%
----------------
Candidate breakpoint sites in file: RAL-884_depletion.xls
  reads:	15550
  uqreads:	15199
  Number of reads supporting candidate sites:	15199

Level 1 collapse of depletion sites in file: RAL-884_depletion_level1.xls
  Number of Level 1 collapsed sites:	1250