Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-801_125b.fastq.uq.polyn	RAL-801_125b.filter	percent
uq reads:	49179213	11082088	22.5341%
   reads: 	52564729	12352804	23.5002%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-801_125b.filter	RAL-801_125b.nostrna	percent
uq reads:	11082088	8466301	76.3963%
   reads: 	12352804	9059821	73.3422%
----------------
TE_filter:
  reads:	RAL-801_125b.nostrna	RAL-801_125b.noTE	percent
uq reads:	8466301	8452509	99.8371%
   reads: 	9059821	9044209	99.8277%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-801_125b.noGEN.front	RAL-801_125b.noGEN.front.gen	percent
uq reads:	8452509	3908580	46.2417%
   reads: 	9044209	4075424	45.0611%
----------------
match_TE:2:
  reads:	RAL-801_125b.noGEN.front	RAL-801_125b.noGEN.front.TE	percent
uq reads:	8452509	540490	6.3944%
   reads: 	9044209	550664	6.0886%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-801_125b.noGEN.end	RAL-801_125b.noGEN.end.gen	percent
uq reads:	8452509	473130	5.5975%
   reads: 	9044209	622953	6.8879%
----------------
match_TE:2:
  reads:	RAL-801_125b.noGEN.end	RAL-801_125b.noGEN.end.TE	percent
uq reads:	8452509	97293	1.1511%
   reads: 	9044209	106224	1.1745%
----------------
Candidate insertion sites in file: RAL-801_125b_insert.txt
  reads:	19685
  uqreads:	19347
  Number of Candidate sites:	19347

Level 1 collapse of insertion sites in file: RAL-801_125b_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	638

Level 1 annotation file: RAL-801_125b_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-801_125b_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-801_125b.noGEN.front	RAL-801_125b.noGEN.front.gendel	percent
uq reads:	8452509	3908580	46.2417%
   reads: 	9044209	4075424	45.0611%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-801_125b.noGEN.end	RAL-801_125b.noGEN.end.gendel	percent
uq reads:	8452509	473130	5.5975%
   reads: 	9044209	622953	6.8879%
----------------
Candidate breakpoint sites in file: RAL-801_125b_depletion.xls
  reads:	50942
  uqreads:	49766
  Number of reads supporting candidate sites:	49766

Level 1 collapse of depletion sites in file: RAL-801_125b_depletion_level1.xls
  Number of Level 1 collapsed sites:	3462