Insertion Pipeline
Bowtie2_wholegenome:
  reads:	S2R+.fastq.uq.polyn	S2R+.filter	percent
uq reads:	13585905	539257	3.9692%
   reads: 	15335458	859490	5.6046%
----------------
virus_structural_rna_repbase_filter:
  reads:	S2R+.filter	S2R+.nostrna	percent
uq reads:	539257	526670	97.6659%
   reads: 	859490	838333	97.5384%
----------------
TE_filter:
  reads:	S2R+.nostrna	S2R+.noTE	percent
uq reads:	526670	525523	99.7822%
   reads: 	838333	837160	99.8601%
----------------
match_dm6_mask_gen:1:
  reads:	S2R+.noGEN.front	S2R+.noGEN.front.gen	percent
uq reads:	525523	126175	24.0094%
   reads: 	837160	264743	31.6239%
----------------
match_TE:2:
  reads:	S2R+.noGEN.front	S2R+.noGEN.front.TE	percent
uq reads:	525523	33654	6.4039%
   reads: 	837160	35534	4.2446%
----------------
match_dm6_mask_gen:1:
  reads:	S2R+.noGEN.end	S2R+.noGEN.end.gen	percent
uq reads:	525523	118091	22.4711%
   reads: 	837160	255494	30.5191%
----------------
match_TE:2:
  reads:	S2R+.noGEN.end	S2R+.noGEN.end.TE	percent
uq reads:	525523	32485	6.1815%
   reads: 	837160	34143	4.0784%
----------------
Candidate insertion sites in file: S2R+_insert.txt
  reads:	14819
  uqreads:	14639
  Number of Candidate sites:	14639

Level 1 collapse of insertion sites in file: S2R+_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	1238

Level 1 annotation file: S2R+_level1siteannotation.xls
Insertion sites in fixed bin:
S2R+_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	S2R+.noGEN.front	S2R+.noGEN.front.gendel	percent
uq reads:	525523	126175	24.0094%
   reads: 	837160	264743	31.6239%
----------------
match_dm6_mask_gen_del:1:
  reads:	S2R+.noGEN.end	S2R+.noGEN.end.gendel	percent
uq reads:	525523	118091	22.4711%
   reads: 	837160	255494	30.5191%
----------------
Candidate breakpoint sites in file: S2R+_depletion.xls
  reads:	10787
  uqreads:	10552
  Number of reads supporting candidate sites:	10552

Level 1 collapse of depletion sites in file: S2R+_depletion_level1.xls
  Number of Level 1 collapsed sites:	1031