Insertion Pipeline
Bowtie2_wholegenome:
  reads:	FR229_2-HE.fastq.uq.polyn	FR229_2-HE.filter	percent
uq reads:	35353504	1471363	4.1619%
   reads: 	37664035	1532572	4.0691%
----------------
virus_structural_rna_repbase_filter:
  reads:	FR229_2-HE.filter	FR229_2-HE.nostrna	percent
uq reads:	1471363	1455631	98.9308%
   reads: 	1532572	1502023	98.0067%
----------------
TE_filter:
  reads:	FR229_2-HE.nostrna	FR229_2-HE.noTE	percent
uq reads:	1455631	1448071	99.4806%
   reads: 	1502023	1491192	99.2789%
----------------
match_dm6_mask_gen:1:
  reads:	FR229_2-HE.noGEN.front	FR229_2-HE.noGEN.front.gen	percent
uq reads:	1448071	868781	59.9957%
   reads: 	1491192	884629	59.3236%
----------------
match_TE:2:
  reads:	FR229_2-HE.noGEN.front	FR229_2-HE.noGEN.front.TE	percent
uq reads:	1448071	117034	8.0821%
   reads: 	1491192	120517	8.0819%
----------------
match_dm6_mask_gen:1:
  reads:	FR229_2-HE.noGEN.end	FR229_2-HE.noGEN.end.gen	percent
uq reads:	1448071	463214	31.9883%
   reads: 	1491192	478759	32.1058%
----------------
match_TE:2:
  reads:	FR229_2-HE.noGEN.end	FR229_2-HE.noGEN.end.TE	percent
uq reads:	1448071	74727	5.1605%
   reads: 	1491192	78011	5.2315%
----------------
Candidate insertion sites in file: FR229_2-HE_insert.txt
  reads:	24366
  uqreads:	23165
  Number of Candidate sites:	23165

Level 1 collapse of insertion sites in file: FR229_2-HE_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	597

Level 1 annotation file: FR229_2-HE_level1siteannotation.xls
Insertion sites in fixed bin:
FR229_2-HE_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	FR229_2-HE.noGEN.front	FR229_2-HE.noGEN.front.gendel	percent
uq reads:	1448071	868781	59.9957%
   reads: 	1491192	884629	59.3236%
----------------
match_dm6_mask_gen_del:1:
  reads:	FR229_2-HE.noGEN.end	FR229_2-HE.noGEN.end.gendel	percent
uq reads:	1448071	463214	31.9883%
   reads: 	1491192	478759	32.1058%
----------------
Candidate breakpoint sites in file: FR229_2-HE_depletion.xls
  reads:	69440
  uqreads:	65957
  Number of reads supporting candidate sites:	65957

Level 1 collapse of depletion sites in file: FR229_2-HE_depletion_level1.xls
  Number of Level 1 collapsed sites:	3607