Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-59.fastq.uq.polyn	RAL-59.filter	percent
uq reads:	33969392	1904589	5.6068%
   reads: 	36267008	2205935	6.0825%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-59.filter	RAL-59.nostrna	percent
uq reads:	1904589	1871913	98.2844%
   reads: 	2205935	2170390	98.3887%
----------------
TE_filter:
  reads:	RAL-59.nostrna	RAL-59.noTE	percent
uq reads:	1871913	1863544	99.5529%
   reads: 	2170390	2160651	99.5513%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-59.noGEN.front	RAL-59.noGEN.front.gen	percent
uq reads:	1863544	449445	24.1178%
   reads: 	2160651	640629	29.6498%
----------------
match_TE:2:
  reads:	RAL-59.noGEN.front	RAL-59.noGEN.front.TE	percent
uq reads:	1863544	71192	3.8202%
   reads: 	2160651	74207	3.4345%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-59.noGEN.end	RAL-59.noGEN.end.gen	percent
uq reads:	1863544	355326	19.0672%
   reads: 	2160651	547535	25.3412%
----------------
match_TE:2:
  reads:	RAL-59.noGEN.end	RAL-59.noGEN.end.TE	percent
uq reads:	1863544	62141	3.3346%
   reads: 	2160651	65112	3.0135%
----------------
Candidate insertion sites in file: RAL-59_insert.txt
  reads:	6680
  uqreads:	6507
  Number of Candidate sites:	6507

Level 1 collapse of insertion sites in file: RAL-59_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	438

Level 1 annotation file: RAL-59_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-59_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-59.noGEN.front	RAL-59.noGEN.front.gendel	percent
uq reads:	1863544	449445	24.1178%
   reads: 	2160651	640629	29.6498%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-59.noGEN.end	RAL-59.noGEN.end.gendel	percent
uq reads:	1863544	355326	19.0672%
   reads: 	2160651	547535	25.3412%
----------------
Candidate breakpoint sites in file: RAL-59_depletion.xls
  reads:	15238
  uqreads:	14713
  Number of reads supporting candidate sites:	14713

Level 1 collapse of depletion sites in file: RAL-59_depletion_level1.xls
  Number of Level 1 collapsed sites:	1403