Insertion Pipeline
Bowtie2_wholegenome:
  reads:	1182-4H.fastq.uq.polyn	1182-4H.filter	percent
uq reads:	36582624	1432336	3.9153%
   reads: 	41893366	2591110	6.1850%
----------------
virus_structural_rna_repbase_filter:
  reads:	1182-4H.filter	1182-4H.nostrna	percent
uq reads:	1432336	1397218	97.5482%
   reads: 	2591110	2540501	98.0468%
----------------
TE_filter:
  reads:	1182-4H.nostrna	1182-4H.noTE	percent
uq reads:	1397218	1395897	99.9055%
   reads: 	2540501	2539153	99.9469%
----------------
match_dm6_mask_gen:1:
  reads:	1182-4H.noGEN.front	1182-4H.noGEN.front.gen	percent
uq reads:	1395897	361913	25.9269%
   reads: 	2539153	784962	30.9143%
----------------
match_TE:2:
  reads:	1182-4H.noGEN.front	1182-4H.noGEN.front.TE	percent
uq reads:	1395897	88855	6.3654%
   reads: 	2539153	96503	3.8006%
----------------
match_dm6_mask_gen:1:
  reads:	1182-4H.noGEN.end	1182-4H.noGEN.end.gen	percent
uq reads:	1395897	306230	21.9379%
   reads: 	2539153	723998	28.5134%
----------------
match_TE:2:
  reads:	1182-4H.noGEN.end	1182-4H.noGEN.end.TE	percent
uq reads:	1395897	82178	5.8871%
   reads: 	2539153	90950	3.5819%
----------------
Candidate insertion sites in file: 1182-4H_insert.txt
  reads:	23277
  uqreads:	22269
  Number of Candidate sites:	22269

Level 1 collapse of insertion sites in file: 1182-4H_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	1198

Level 1 annotation file: 1182-4H_level1siteannotation.xls
Insertion sites in fixed bin:
1182-4H_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	1182-4H.noGEN.front	1182-4H.noGEN.front.gendel	percent
uq reads:	1395897	361913	25.9269%
   reads: 	2539153	784962	30.9143%
----------------
match_dm6_mask_gen_del:1:
  reads:	1182-4H.noGEN.end	1182-4H.noGEN.end.gendel	percent
uq reads:	1395897	306230	21.9379%
   reads: 	2539153	723998	28.5134%
----------------
Candidate breakpoint sites in file: 1182-4H_depletion.xls
  reads:	32709
  uqreads:	29142
  Number of reads supporting candidate sites:	29142

Level 1 collapse of depletion sites in file: 1182-4H_depletion_level1.xls
  Number of Level 1 collapsed sites:	2591