Insertion Pipeline
Bowtie2_wholegenome:
  reads:	ISO1-AS-Ova.fastq.uq.polyn	ISO1-AS-Ova.filter	percent
uq reads:	91994940	3908009	4.2481%
   reads: 	139693978	8929544	6.3922%
----------------
virus_structural_rna_repbase_filter:
  reads:	ISO1-AS-Ova.filter	ISO1-AS-Ova.nostrna	percent
uq reads:	3908009	1689553	43.2331%
   reads: 	8929544	3167469	35.4718%
----------------
TE_filter:
  reads:	ISO1-AS-Ova.nostrna	ISO1-AS-Ova.noTE	percent
uq reads:	1689553	1682398	99.5765%
   reads: 	3167469	3155970	99.6370%
----------------
match_dm6_mask_gen:1:
  reads:	ISO1-AS-Ova.noGEN.front	ISO1-AS-Ova.noGEN.front.gen	percent
uq reads:	1682398	590272	35.0852%
   reads: 	3155970	841185	26.6538%
----------------
match_TE:2:
  reads:	ISO1-AS-Ova.noGEN.front	ISO1-AS-Ova.noGEN.front.TE	percent
uq reads:	1682398	95752	5.6914%
   reads: 	3155970	142415	4.5126%
----------------
match_dm6_mask_gen:1:
  reads:	ISO1-AS-Ova.noGEN.end	ISO1-AS-Ova.noGEN.end.gen	percent
uq reads:	1682398	506177	30.0866%
   reads: 	3155970	752474	23.8429%
----------------
match_TE:2:
  reads:	ISO1-AS-Ova.noGEN.end	ISO1-AS-Ova.noGEN.end.TE	percent
uq reads:	1682398	101882	6.0558%
   reads: 	3155970	161444	5.1155%
----------------
Candidate insertion sites in file: ISO1-AS-Ova_insert.txt
  reads:	21731
  uqreads:	16391
  Number of Candidate sites:	16391

Level 1 collapse of insertion sites in file: ISO1-AS-Ova_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	170

Level 1 annotation file: ISO1-AS-Ova_level1siteannotation.xls
Insertion sites in fixed bin:
ISO1-AS-Ova_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	ISO1-AS-Ova.noGEN.front	ISO1-AS-Ova.noGEN.front.gendel	percent
uq reads:	1682398	590272	35.0852%
   reads: 	3155970	841185	26.6538%
----------------
match_dm6_mask_gen_del:1:
  reads:	ISO1-AS-Ova.noGEN.end	ISO1-AS-Ova.noGEN.end.gendel	percent
uq reads:	1682398	506177	30.0866%
   reads: 	3155970	752474	23.8429%
----------------
Candidate breakpoint sites in file: ISO1-AS-Ova_depletion.xls
  reads:	23270
  uqreads:	19740
  Number of reads supporting candidate sites:	19740

Level 1 collapse of depletion sites in file: ISO1-AS-Ova_depletion_level1.xls
  Number of Level 1 collapsed sites:	136