Insertion Pipeline
Bowtie2_wholegenome:
  reads:	CO4N_1-HE.fastq.uq.polyn	CO4N_1-HE.filter	percent
uq reads:	56477721	2289071	4.0531%
   reads: 	64861584	2565106	3.9547%
----------------
virus_structural_rna_repbase_filter:
  reads:	CO4N_1-HE.filter	CO4N_1-HE.nostrna	percent
uq reads:	2289071	2273901	99.3373%
   reads: 	2565106	2540816	99.0531%
----------------
TE_filter:
  reads:	CO4N_1-HE.nostrna	CO4N_1-HE.noTE	percent
uq reads:	2273901	2266056	99.6550%
   reads: 	2540816	2519177	99.1483%
----------------
match_dm6_mask_gen:1:
  reads:	CO4N_1-HE.noGEN.front	CO4N_1-HE.noGEN.front.gen	percent
uq reads:	2266056	1098308	48.4678%
   reads: 	2519177	1204972	47.8320%
----------------
match_TE:2:
  reads:	CO4N_1-HE.noGEN.front	CO4N_1-HE.noGEN.front.TE	percent
uq reads:	2266056	94128	4.1538%
   reads: 	2519177	104045	4.1301%
----------------
match_dm6_mask_gen:1:
  reads:	CO4N_1-HE.noGEN.end	CO4N_1-HE.noGEN.end.gen	percent
uq reads:	2266056	1117743	49.3255%
   reads: 	2519177	1236199	49.0715%
----------------
match_TE:2:
  reads:	CO4N_1-HE.noGEN.end	CO4N_1-HE.noGEN.end.TE	percent
uq reads:	2266056	91064	4.0186%
   reads: 	2519177	100806	4.0015%
----------------
Candidate insertion sites in file: CO4N_1-HE_insert.txt
  reads:	17358
  uqreads:	15667
  Number of Candidate sites:	15667

Level 1 collapse of insertion sites in file: CO4N_1-HE_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	557

Level 1 annotation file: CO4N_1-HE_level1siteannotation.xls
Insertion sites in fixed bin:
CO4N_1-HE_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	CO4N_1-HE.noGEN.front	CO4N_1-HE.noGEN.front.gendel	percent
uq reads:	2266056	1098308	48.4678%
   reads: 	2519177	1204972	47.8320%
----------------
match_dm6_mask_gen_del:1:
  reads:	CO4N_1-HE.noGEN.end	CO4N_1-HE.noGEN.end.gendel	percent
uq reads:	2266056	1117743	49.3255%
   reads: 	2519177	1236199	49.0715%
----------------
Candidate breakpoint sites in file: CO4N_1-HE_depletion.xls
  reads:	66652
  uqreads:	59420
  Number of reads supporting candidate sites:	59420

Level 1 collapse of depletion sites in file: CO4N_1-HE_depletion_level1.xls
  Number of Level 1 collapsed sites:	3896