Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-584_95b.fastq.uq.polyn	RAL-584_95b.filter	percent
uq reads:	80363586	20037145	24.9331%
   reads: 	85980515	22123852	25.7312%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-584_95b.filter	RAL-584_95b.nostrna	percent
uq reads:	20037145	10680502	53.3035%
   reads: 	22123852	11378305	51.4300%
----------------
TE_filter:
  reads:	RAL-584_95b.nostrna	RAL-584_95b.noTE	percent
uq reads:	10680502	10647015	99.6865%
   reads: 	11378305	11342735	99.6874%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-584_95b.noGEN.front	RAL-584_95b.noGEN.front.gen	percent
uq reads:	10647015	2436979	22.8888%
   reads: 	11342735	2626951	23.1598%
----------------
match_TE:2:
  reads:	RAL-584_95b.noGEN.front	RAL-584_95b.noGEN.front.TE	percent
uq reads:	10647015	324697	3.0497%
   reads: 	11342735	486518	4.2892%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-584_95b.noGEN.end	RAL-584_95b.noGEN.end.gen	percent
uq reads:	10647015	1735228	16.2978%
   reads: 	11342735	1915168	16.8845%
----------------
match_TE:2:
  reads:	RAL-584_95b.noGEN.end	RAL-584_95b.noGEN.end.TE	percent
uq reads:	10647015	287632	2.7015%
   reads: 	11342735	450199	3.9691%
----------------
Candidate insertion sites in file: RAL-584_95b_insert.txt
  reads:	18715
  uqreads:	18549
  Number of Candidate sites:	18549

Level 1 collapse of insertion sites in file: RAL-584_95b_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	586

Level 1 annotation file: RAL-584_95b_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-584_95b_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-584_95b.noGEN.front	RAL-584_95b.noGEN.front.gendel	percent
uq reads:	10647015	2436979	22.8888%
   reads: 	11342735	2626951	23.1598%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-584_95b.noGEN.end	RAL-584_95b.noGEN.end.gendel	percent
uq reads:	10647015	1735228	16.2978%
   reads: 	11342735	1915168	16.8845%
----------------
Candidate breakpoint sites in file: RAL-584_95b_depletion.xls
  reads:	43434
  uqreads:	42872
  Number of reads supporting candidate sites:	42872

Level 1 collapse of depletion sites in file: RAL-584_95b_depletion_level1.xls
  Number of Level 1 collapsed sites:	3593