Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-765.fastq.uq.polyn	RAL-765.filter	percent
uq reads:	37051500	3267586	8.8190%
   reads: 	38982901	3571704	9.1622%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-765.filter	RAL-765.nostrna	percent
uq reads:	3267586	3226285	98.7360%
   reads: 	3571704	3520628	98.5700%
----------------
TE_filter:
  reads:	RAL-765.nostrna	RAL-765.noTE	percent
uq reads:	3226285	3219254	99.7821%
   reads: 	3520628	3512973	99.7826%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-765.noGEN.front	RAL-765.noGEN.front.gen	percent
uq reads:	3219254	1530910	47.5548%
   reads: 	3512973	1690141	48.1114%
----------------
match_TE:2:
  reads:	RAL-765.noGEN.front	RAL-765.noGEN.front.TE	percent
uq reads:	3219254	201020	6.2443%
   reads: 	3512973	204950	5.8341%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-765.noGEN.end	RAL-765.noGEN.end.gen	percent
uq reads:	3219254	650830	20.2168%
   reads: 	3512973	801896	22.8267%
----------------
match_TE:2:
  reads:	RAL-765.noGEN.end	RAL-765.noGEN.end.TE	percent
uq reads:	3219254	115913	3.6006%
   reads: 	3512973	120063	3.4177%
----------------
Candidate insertion sites in file: RAL-765_insert.txt
  reads:	11789
  uqreads:	11645
  Number of Candidate sites:	11645

Level 1 collapse of insertion sites in file: RAL-765_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	496

Level 1 annotation file: RAL-765_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-765_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-765.noGEN.front	RAL-765.noGEN.front.gendel	percent
uq reads:	3219254	1530910	47.5548%
   reads: 	3512973	1690141	48.1114%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-765.noGEN.end	RAL-765.noGEN.end.gendel	percent
uq reads:	3219254	650830	20.2168%
   reads: 	3512973	801896	22.8267%
----------------
Candidate breakpoint sites in file: RAL-765_depletion.xls
  reads:	22036
  uqreads:	21370
  Number of reads supporting candidate sites:	21370

Level 1 collapse of depletion sites in file: RAL-765_depletion_level1.xls
  Number of Level 1 collapsed sites:	1732