Insertion Pipeline
Bowtie2_wholegenome:
  reads:	ZS5_1-HE.fastq.uq.polyn	ZS5_1-HE.filter	percent
uq reads:	56977153	6462154	11.3417%
   reads: 	65817017	7260250	11.0310%
----------------
virus_structural_rna_repbase_filter:
  reads:	ZS5_1-HE.filter	ZS5_1-HE.nostrna	percent
uq reads:	6462154	5493571	85.0115%
   reads: 	7260250	5859769	80.7103%
----------------
TE_filter:
  reads:	ZS5_1-HE.nostrna	ZS5_1-HE.noTE	percent
uq reads:	5493571	5483966	99.8252%
   reads: 	5859769	5832968	99.5426%
----------------
match_dm6_mask_gen:1:
  reads:	ZS5_1-HE.noGEN.front	ZS5_1-HE.noGEN.front.gen	percent
uq reads:	5483966	2220678	40.4940%
   reads: 	5832968	2349930	40.2870%
----------------
match_TE:2:
  reads:	ZS5_1-HE.noGEN.front	ZS5_1-HE.noGEN.front.TE	percent
uq reads:	5483966	151186	2.7569%
   reads: 	5832968	160265	2.7476%
----------------
match_dm6_mask_gen:1:
  reads:	ZS5_1-HE.noGEN.end	ZS5_1-HE.noGEN.end.gen	percent
uq reads:	5483966	1365757	24.9045%
   reads: 	5832968	1508030	25.8536%
----------------
match_TE:2:
  reads:	ZS5_1-HE.noGEN.end	ZS5_1-HE.noGEN.end.TE	percent
uq reads:	5483966	98980	1.8049%
   reads: 	5832968	107434	1.8418%
----------------
Candidate insertion sites in file: ZS5_1-HE_insert.txt
  reads:	18005
  uqreads:	16097
  Number of Candidate sites:	16097

Level 1 collapse of insertion sites in file: ZS5_1-HE_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	520

Level 1 annotation file: ZS5_1-HE_level1siteannotation.xls
Insertion sites in fixed bin:
ZS5_1-HE_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	ZS5_1-HE.noGEN.front	ZS5_1-HE.noGEN.front.gendel	percent
uq reads:	5483966	2220678	40.4940%
   reads: 	5832968	2349930	40.2870%
----------------
match_dm6_mask_gen_del:1:
  reads:	ZS5_1-HE.noGEN.end	ZS5_1-HE.noGEN.end.gendel	percent
uq reads:	5483966	1365757	24.9045%
   reads: 	5832968	1508030	25.8536%
----------------
Candidate breakpoint sites in file: ZS5_1-HE_depletion.xls
  reads:	75941
  uqreads:	68121
  Number of reads supporting candidate sites:	68121

Level 1 collapse of depletion sites in file: ZS5_1-HE_depletion_level1.xls
  Number of Level 1 collapsed sites:	3511