Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-563.fastq.uq.polyn	RAL-563.filter	percent
uq reads:	28765500	1393625	4.8448%
   reads: 	33654606	1811905	5.3838%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-563.filter	RAL-563.nostrna	percent
uq reads:	1393625	1347556	96.6943%
   reads: 	1811905	1753494	96.7763%
----------------
TE_filter:
  reads:	RAL-563.nostrna	RAL-563.noTE	percent
uq reads:	1347556	1339479	99.4006%
   reads: 	1753494	1742374	99.3658%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-563.noGEN.front	RAL-563.noGEN.front.gen	percent
uq reads:	1339479	478194	35.7000%
   reads: 	1742374	734455	42.1525%
----------------
match_TE:2:
  reads:	RAL-563.noGEN.front	RAL-563.noGEN.front.TE	percent
uq reads:	1339479	65123	4.8618%
   reads: 	1742374	72315	4.1504%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-563.noGEN.end	RAL-563.noGEN.end.gen	percent
uq reads:	1339479	497573	37.1468%
   reads: 	1742374	726445	41.6928%
----------------
match_TE:2:
  reads:	RAL-563.noGEN.end	RAL-563.noGEN.end.TE	percent
uq reads:	1339479	71039	5.3035%
   reads: 	1742374	78851	4.5255%
----------------
Candidate insertion sites in file: RAL-563_insert.txt
  reads:	7170
  uqreads:	6470
  Number of Candidate sites:	6470

Level 1 collapse of insertion sites in file: RAL-563_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	426

Level 1 annotation file: RAL-563_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-563_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-563.noGEN.front	RAL-563.noGEN.front.gendel	percent
uq reads:	1339479	478194	35.7000%
   reads: 	1742374	734455	42.1525%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-563.noGEN.end	RAL-563.noGEN.end.gendel	percent
uq reads:	1339479	497573	37.1468%
   reads: 	1742374	726445	41.6928%
----------------
Candidate breakpoint sites in file: RAL-563_depletion.xls
  reads:	16362
  uqreads:	14275
  Number of reads supporting candidate sites:	14275

Level 1 collapse of depletion sites in file: RAL-563_depletion_level1.xls
  Number of Level 1 collapsed sites:	1262