Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-356.fastq.uq.polyn	RAL-356.filter	percent
uq reads:	40929324	3566929	8.7148%
   reads: 	42586530	4017459	9.4336%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-356.filter	RAL-356.nostrna	percent
uq reads:	3566929	2333549	65.4218%
   reads: 	4017459	2747688	68.3937%
----------------
TE_filter:
  reads:	RAL-356.nostrna	RAL-356.noTE	percent
uq reads:	2333549	2313502	99.1409%
   reads: 	2747688	2726880	99.2427%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-356.noGEN.front	RAL-356.noGEN.front.gen	percent
uq reads:	2313502	741591	32.0549%
   reads: 	2726880	1044456	38.3022%
----------------
match_TE:2:
  reads:	RAL-356.noGEN.front	RAL-356.noGEN.front.TE	percent
uq reads:	2313502	85420	3.6922%
   reads: 	2726880	87459	3.2073%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-356.noGEN.end	RAL-356.noGEN.end.gen	percent
uq reads:	2313502	630022	27.2324%
   reads: 	2726880	904323	33.1633%
----------------
match_TE:2:
  reads:	RAL-356.noGEN.end	RAL-356.noGEN.end.TE	percent
uq reads:	2313502	82501	3.5661%
   reads: 	2726880	84839	3.1112%
----------------
Candidate insertion sites in file: RAL-356_insert.txt
  reads:	6646
  uqreads:	6621
  Number of Candidate sites:	6621

Level 1 collapse of insertion sites in file: RAL-356_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	394

Level 1 annotation file: RAL-356_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-356_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-356.noGEN.front	RAL-356.noGEN.front.gendel	percent
uq reads:	2313502	741591	32.0549%
   reads: 	2726880	1044456	38.3022%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-356.noGEN.end	RAL-356.noGEN.end.gendel	percent
uq reads:	2313502	630022	27.2324%
   reads: 	2726880	904323	33.1633%
----------------
Candidate breakpoint sites in file: RAL-356_depletion.xls
  reads:	15097
  uqreads:	14754
  Number of reads supporting candidate sites:	14754

Level 1 collapse of depletion sites in file: RAL-356_depletion_level1.xls
  Number of Level 1 collapsed sites:	1206