Insertion Pipeline
Bowtie2_wholegenome:
  reads:	D4-c1.fastq.uq.polyn	D4-c1.filter	percent
uq reads:	56969908	3020709	5.3023%
   reads: 	71420175	4288269	6.0043%
----------------
virus_structural_rna_repbase_filter:
  reads:	D4-c1.filter	D4-c1.nostrna	percent
uq reads:	3020709	2940514	97.3452%
   reads: 	4288269	4142910	96.6103%
----------------
TE_filter:
  reads:	D4-c1.nostrna	D4-c1.noTE	percent
uq reads:	2940514	2934901	99.8091%
   reads: 	4142910	4136638	99.8486%
----------------
match_dm6_mask_gen:1:
  reads:	D4-c1.noGEN.front	D4-c1.noGEN.front.gen	percent
uq reads:	2934901	871685	29.7007%
   reads: 	4136638	1352709	32.7007%
----------------
match_TE:2:
  reads:	D4-c1.noGEN.front	D4-c1.noGEN.front.TE	percent
uq reads:	2934901	163567	5.5732%
   reads: 	4136638	186928	4.5188%
----------------
match_dm6_mask_gen:1:
  reads:	D4-c1.noGEN.end	D4-c1.noGEN.end.gen	percent
uq reads:	2934901	825570	28.1294%
   reads: 	4136638	1303522	31.5116%
----------------
match_TE:2:
  reads:	D4-c1.noGEN.end	D4-c1.noGEN.end.TE	percent
uq reads:	2934901	162793	5.5468%
   reads: 	4136638	186188	4.5009%
----------------
Candidate insertion sites in file: D4-c1_insert.txt
  reads:	23182
  uqreads:	21217
  Number of Candidate sites:	21217

Level 1 collapse of insertion sites in file: D4-c1_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	1008

Level 1 annotation file: D4-c1_level1siteannotation.xls
Insertion sites in fixed bin:
D4-c1_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	D4-c1.noGEN.front	D4-c1.noGEN.front.gendel	percent
uq reads:	2934901	871685	29.7007%
   reads: 	4136638	1352709	32.7007%
----------------
match_dm6_mask_gen_del:1:
  reads:	D4-c1.noGEN.end	D4-c1.noGEN.end.gendel	percent
uq reads:	2934901	825570	28.1294%
   reads: 	4136638	1303522	31.5116%
----------------
Candidate breakpoint sites in file: D4-c1_depletion.xls
  reads:	35701
  uqreads:	32422
  Number of reads supporting candidate sites:	32422

Level 1 collapse of depletion sites in file: D4-c1_depletion_level1.xls
  Number of Level 1 collapsed sites:	2633