Insertion Pipeline
Bowtie2_wholegenome:
  reads:	UK120_1-HE.fastq.uq.polyn	UK120_1-HE.filter	percent
uq reads:	29794857	1675427	5.6232%
   reads: 	31007580	1700608	5.4845%
----------------
virus_structural_rna_repbase_filter:
  reads:	UK120_1-HE.filter	UK120_1-HE.nostrna	percent
uq reads:	1675427	1630044	97.2913%
   reads: 	1700608	1654047	97.2621%
----------------
TE_filter:
  reads:	UK120_1-HE.nostrna	UK120_1-HE.noTE	percent
uq reads:	1630044	1626448	99.7794%
   reads: 	1654047	1649555	99.7284%
----------------
match_dm6_mask_gen:1:
  reads:	UK120_1-HE.noGEN.front	UK120_1-HE.noGEN.front.gen	percent
uq reads:	1626448	983958	60.4974%
   reads: 	1649555	995053	60.3225%
----------------
match_TE:2:
  reads:	UK120_1-HE.noGEN.front	UK120_1-HE.noGEN.front.TE	percent
uq reads:	1626448	91867	5.6483%
   reads: 	1649555	93756	5.6837%
----------------
match_dm6_mask_gen:1:
  reads:	UK120_1-HE.noGEN.end	UK120_1-HE.noGEN.end.gen	percent
uq reads:	1626448	854410	52.5323%
   reads: 	1649555	864143	52.3864%
----------------
match_TE:2:
  reads:	UK120_1-HE.noGEN.end	UK120_1-HE.noGEN.end.TE	percent
uq reads:	1626448	83250	5.1185%
   reads: 	1649555	85050	5.1559%
----------------
Candidate insertion sites in file: UK120_1-HE_insert.txt
  reads:	15144
  uqreads:	14853
  Number of Candidate sites:	14853

Level 1 collapse of insertion sites in file: UK120_1-HE_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	596

Level 1 annotation file: UK120_1-HE_level1siteannotation.xls
Insertion sites in fixed bin:
UK120_1-HE_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	UK120_1-HE.noGEN.front	UK120_1-HE.noGEN.front.gendel	percent
uq reads:	1626448	983958	60.4974%
   reads: 	1649555	995053	60.3225%
----------------
match_dm6_mask_gen_del:1:
  reads:	UK120_1-HE.noGEN.end	UK120_1-HE.noGEN.end.gendel	percent
uq reads:	1626448	854410	52.5323%
   reads: 	1649555	864143	52.3864%
----------------
Candidate breakpoint sites in file: UK120_1-HE_depletion.xls
  reads:	63846
  uqreads:	62957
  Number of reads supporting candidate sites:	62957

Level 1 collapse of depletion sites in file: UK120_1-HE_depletion_level1.xls
  Number of Level 1 collapsed sites:	2740