Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-776.fastq.uq.polyn	RAL-776.filter	percent
uq reads:	36893227	3188706	8.6431%
   reads: 	39304900	3681067	9.3654%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-776.filter	RAL-776.nostrna	percent
uq reads:	3188706	2075249	65.0812%
   reads: 	3681067	2336517	63.4739%
----------------
TE_filter:
  reads:	RAL-776.nostrna	RAL-776.noTE	percent
uq reads:	2075249	2062414	99.3815%
   reads: 	2336517	2320643	99.3206%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-776.noGEN.front	RAL-776.noGEN.front.gen	percent
uq reads:	2062414	768375	37.2561%
   reads: 	2320643	922159	39.7372%
----------------
match_TE:2:
  reads:	RAL-776.noGEN.front	RAL-776.noGEN.front.TE	percent
uq reads:	2062414	96294	4.6690%
   reads: 	2320643	100346	4.3241%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-776.noGEN.end	RAL-776.noGEN.end.gen	percent
uq reads:	2062414	647853	31.4124%
   reads: 	2320643	794759	34.2474%
----------------
match_TE:2:
  reads:	RAL-776.noGEN.end	RAL-776.noGEN.end.TE	percent
uq reads:	2062414	94604	4.5871%
   reads: 	2320643	99536	4.2892%
----------------
Candidate insertion sites in file: RAL-776_insert.txt
  reads:	11277
  uqreads:	11057
  Number of Candidate sites:	11057

Level 1 collapse of insertion sites in file: RAL-776_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	492

Level 1 annotation file: RAL-776_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-776_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-776.noGEN.front	RAL-776.noGEN.front.gendel	percent
uq reads:	2062414	768375	37.2561%
   reads: 	2320643	922159	39.7372%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-776.noGEN.end	RAL-776.noGEN.end.gendel	percent
uq reads:	2062414	647853	31.4124%
   reads: 	2320643	794759	34.2474%
----------------
Candidate breakpoint sites in file: RAL-776_depletion.xls
  reads:	25182
  uqreads:	24346
  Number of reads supporting candidate sites:	24346

Level 1 collapse of depletion sites in file: RAL-776_depletion_level1.xls
  Number of Level 1 collapsed sites:	1916