Insertion Pipeline
Bowtie2_wholegenome:
  reads:	EF78_1-HE.fastq.uq.polyn	EF78_1-HE.filter	percent
uq reads:	31131085	1563604	5.0226%
   reads: 	33249038	1618116	4.8667%
----------------
virus_structural_rna_repbase_filter:
  reads:	EF78_1-HE.filter	EF78_1-HE.nostrna	percent
uq reads:	1563604	1545891	98.8672%
   reads: 	1618116	1590956	98.3215%
----------------
TE_filter:
  reads:	EF78_1-HE.nostrna	EF78_1-HE.noTE	percent
uq reads:	1545891	1541982	99.7471%
   reads: 	1590956	1585804	99.6762%
----------------
match_dm6_mask_gen:1:
  reads:	EF78_1-HE.noGEN.front	EF78_1-HE.noGEN.front.gen	percent
uq reads:	1541982	891234	57.7980%
   reads: 	1585804	907403	57.2204%
----------------
match_TE:2:
  reads:	EF78_1-HE.noGEN.front	EF78_1-HE.noGEN.front.TE	percent
uq reads:	1541982	96947	6.2872%
   reads: 	1585804	99897	6.2995%
----------------
match_dm6_mask_gen:1:
  reads:	EF78_1-HE.noGEN.end	EF78_1-HE.noGEN.end.gen	percent
uq reads:	1541982	864003	56.0320%
   reads: 	1585804	881205	55.5683%
----------------
match_TE:2:
  reads:	EF78_1-HE.noGEN.end	EF78_1-HE.noGEN.end.TE	percent
uq reads:	1541982	95995	6.2254%
   reads: 	1585804	99032	6.2449%
----------------
Candidate insertion sites in file: EF78_1-HE_insert.txt
  reads:	22084
  uqreads:	21352
  Number of Candidate sites:	21352

Level 1 collapse of insertion sites in file: EF78_1-HE_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	694

Level 1 annotation file: EF78_1-HE_level1siteannotation.xls
Insertion sites in fixed bin:
EF78_1-HE_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	EF78_1-HE.noGEN.front	EF78_1-HE.noGEN.front.gendel	percent
uq reads:	1541982	891234	57.7980%
   reads: 	1585804	907403	57.2204%
----------------
match_dm6_mask_gen_del:1:
  reads:	EF78_1-HE.noGEN.end	EF78_1-HE.noGEN.end.gendel	percent
uq reads:	1541982	864003	56.0320%
   reads: 	1585804	881205	55.5683%
----------------
Candidate breakpoint sites in file: EF78_1-HE_depletion.xls
  reads:	69693
  uqreads:	67652
  Number of reads supporting candidate sites:	67652

Level 1 collapse of depletion sites in file: EF78_1-HE_depletion_level1.xls
  Number of Level 1 collapsed sites:	3731