Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-900_95b.fastq.uq.polyn	RAL-900_95b.filter	percent
uq reads:	28314532	3022324	10.6741%
   reads: 	29398670	3240416	11.0223%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-900_95b.filter	RAL-900_95b.nostrna	percent
uq reads:	3022324	2701921	89.3988%
   reads: 	3240416	2852111	88.0168%
----------------
TE_filter:
  reads:	RAL-900_95b.nostrna	RAL-900_95b.noTE	percent
uq reads:	2701921	2690273	99.5689%
   reads: 	2852111	2840219	99.5830%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-900_95b.noGEN.front	RAL-900_95b.noGEN.front.gen	percent
uq reads:	2690273	707577	26.3013%
   reads: 	2840219	753628	26.5342%
----------------
match_TE:2:
  reads:	RAL-900_95b.noGEN.front	RAL-900_95b.noGEN.front.TE	percent
uq reads:	2690273	74418	2.7662%
   reads: 	2840219	77869	2.7417%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-900_95b.noGEN.end	RAL-900_95b.noGEN.end.gen	percent
uq reads:	2690273	548993	20.4066%
   reads: 	2840219	592047	20.8451%
----------------
match_TE:2:
  reads:	RAL-900_95b.noGEN.end	RAL-900_95b.noGEN.end.TE	percent
uq reads:	2690273	68075	2.5304%
   reads: 	2840219	72287	2.5451%
----------------
Candidate insertion sites in file: RAL-900_95b_insert.txt
  reads:	6858
  uqreads:	6810
  Number of Candidate sites:	6810

Level 1 collapse of insertion sites in file: RAL-900_95b_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	373

Level 1 annotation file: RAL-900_95b_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-900_95b_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-900_95b.noGEN.front	RAL-900_95b.noGEN.front.gendel	percent
uq reads:	2690273	707577	26.3013%
   reads: 	2840219	753628	26.5342%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-900_95b.noGEN.end	RAL-900_95b.noGEN.end.gendel	percent
uq reads:	2690273	548993	20.4066%
   reads: 	2840219	592047	20.8451%
----------------
Candidate breakpoint sites in file: RAL-900_95b_depletion.xls
  reads:	13982
  uqreads:	13925
  Number of reads supporting candidate sites:	13925

Level 1 collapse of depletion sites in file: RAL-900_95b_depletion_level1.xls
  Number of Level 1 collapsed sites:	1028