Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-386.fastq.uq.polyn	RAL-386.filter	percent
uq reads:	19649880	1134247	5.7723%
   reads: 	20326095	1281017	6.3023%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-386.filter	RAL-386.nostrna	percent
uq reads:	1134247	1101734	97.1335%
   reads: 	1281017	1246708	97.3217%
----------------
TE_filter:
  reads:	RAL-386.nostrna	RAL-386.noTE	percent
uq reads:	1101734	1096551	99.5296%
   reads: 	1246708	1241323	99.5681%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-386.noGEN.front	RAL-386.noGEN.front.gen	percent
uq reads:	1096551	400532	36.5265%
   reads: 	1241323	503355	40.5499%
----------------
match_TE:2:
  reads:	RAL-386.noGEN.front	RAL-386.noGEN.front.TE	percent
uq reads:	1096551	46458	4.2367%
   reads: 	1241323	47597	3.8344%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-386.noGEN.end	RAL-386.noGEN.end.gen	percent
uq reads:	1096551	299923	27.3515%
   reads: 	1241323	398614	32.1120%
----------------
match_TE:2:
  reads:	RAL-386.noGEN.end	RAL-386.noGEN.end.TE	percent
uq reads:	1096551	41049	3.7435%
   reads: 	1241323	42658	3.4365%
----------------
Candidate insertion sites in file: RAL-386_insert.txt
  reads:	3416
  uqreads:	3404
  Number of Candidate sites:	3404

Level 1 collapse of insertion sites in file: RAL-386_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	166

Level 1 annotation file: RAL-386_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-386_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-386.noGEN.front	RAL-386.noGEN.front.gendel	percent
uq reads:	1096551	400532	36.5265%
   reads: 	1241323	503355	40.5499%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-386.noGEN.end	RAL-386.noGEN.end.gendel	percent
uq reads:	1096551	299923	27.3515%
   reads: 	1241323	398614	32.1120%
----------------
Candidate breakpoint sites in file: RAL-386_depletion.xls
  reads:	9412
  uqreads:	9272
  Number of reads supporting candidate sites:	9272

Level 1 collapse of depletion sites in file: RAL-386_depletion_level1.xls
  Number of Level 1 collapsed sites:	591