Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-799.fastq.uq.polyn	RAL-799.filter	percent
uq reads:	37287403	3749237	10.0550%
   reads: 	40406175	4431614	10.9677%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-799.filter	RAL-799.nostrna	percent
uq reads:	3749237	3681593	98.1958%
   reads: 	4431614	4329665	97.6995%
----------------
TE_filter:
  reads:	RAL-799.nostrna	RAL-799.noTE	percent
uq reads:	3681593	3672735	99.7594%
   reads: 	4329665	4318981	99.7532%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-799.noGEN.front	RAL-799.noGEN.front.gen	percent
uq reads:	3672735	1401306	38.1543%
   reads: 	4318981	1775130	41.1007%
----------------
match_TE:2:
  reads:	RAL-799.noGEN.front	RAL-799.noGEN.front.TE	percent
uq reads:	3672735	197968	5.3902%
   reads: 	4318981	204110	4.7259%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-799.noGEN.end	RAL-799.noGEN.end.gen	percent
uq reads:	3672735	534597	14.5558%
   reads: 	4318981	884677	20.4835%
----------------
match_TE:2:
  reads:	RAL-799.noGEN.end	RAL-799.noGEN.end.TE	percent
uq reads:	3672735	104597	2.8479%
   reads: 	4318981	112476	2.6042%
----------------
Candidate insertion sites in file: RAL-799_insert.txt
  reads:	8976
  uqreads:	8734
  Number of Candidate sites:	8734

Level 1 collapse of insertion sites in file: RAL-799_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	449

Level 1 annotation file: RAL-799_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-799_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-799.noGEN.front	RAL-799.noGEN.front.gendel	percent
uq reads:	3672735	1401306	38.1543%
   reads: 	4318981	1775130	41.1007%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-799.noGEN.end	RAL-799.noGEN.end.gendel	percent
uq reads:	3672735	534597	14.5558%
   reads: 	4318981	884677	20.4835%
----------------
Candidate breakpoint sites in file: RAL-799_depletion.xls
  reads:	18539
  uqreads:	17280
  Number of reads supporting candidate sites:	17280

Level 1 collapse of depletion sites in file: RAL-799_depletion_level1.xls
  Number of Level 1 collapsed sites:	1724