Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-437_125.fastq.uq.polyn	RAL-437_125.filter	percent
uq reads:	46706736	6091041	13.0410%
   reads: 	49815383	7066263	14.1849%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-437_125.filter	RAL-437_125.nostrna	percent
uq reads:	6091041	5976172	98.1141%
   reads: 	7066263	6829579	96.6505%
----------------
TE_filter:
  reads:	RAL-437_125.nostrna	RAL-437_125.noTE	percent
uq reads:	5976172	5967935	99.8622%
   reads: 	6829579	6820636	99.8691%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-437_125.noGEN.front	RAL-437_125.noGEN.front.gen	percent
uq reads:	5967935	2311577	38.7333%
   reads: 	6820636	2531775	37.1193%
----------------
match_TE:2:
  reads:	RAL-437_125.noGEN.front	RAL-437_125.noGEN.front.TE	percent
uq reads:	5967935	340799	5.7105%
   reads: 	6820636	351490	5.1533%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-437_125.noGEN.end	RAL-437_125.noGEN.end.gen	percent
uq reads:	5967935	760432	12.7420%
   reads: 	6820636	967498	14.1849%
----------------
match_TE:2:
  reads:	RAL-437_125.noGEN.end	RAL-437_125.noGEN.end.TE	percent
uq reads:	5967935	137944	2.3114%
   reads: 	6820636	147809	2.1671%
----------------
Candidate insertion sites in file: RAL-437_125_insert.txt
  reads:	29638
  uqreads:	29237
  Number of Candidate sites:	29237

Level 1 collapse of insertion sites in file: RAL-437_125_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	655

Level 1 annotation file: RAL-437_125_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-437_125_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-437_125.noGEN.front	RAL-437_125.noGEN.front.gendel	percent
uq reads:	5967935	2311577	38.7333%
   reads: 	6820636	2531775	37.1193%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-437_125.noGEN.end	RAL-437_125.noGEN.end.gendel	percent
uq reads:	5967935	760432	12.7420%
   reads: 	6820636	967498	14.1849%
----------------
Candidate breakpoint sites in file: RAL-437_125_depletion.xls
  reads:	69908
  uqreads:	68717
  Number of reads supporting candidate sites:	68717

Level 1 collapse of depletion sites in file: RAL-437_125_depletion_level1.xls
  Number of Level 1 collapsed sites:	3707