Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-338.fastq.uq.polyn	RAL-338.filter	percent
uq reads:	27137367	3095274	11.4059%
   reads: 	28677771	3540308	12.3451%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-338.filter	RAL-338.nostrna	percent
uq reads:	3095274	2004133	64.7482%
   reads: 	3540308	2295981	64.8526%
----------------
TE_filter:
  reads:	RAL-338.nostrna	RAL-338.noTE	percent
uq reads:	2004133	1997513	99.6697%
   reads: 	2295981	2288470	99.6729%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-338.noGEN.front	RAL-338.noGEN.front.gen	percent
uq reads:	1997513	365175	18.2815%
   reads: 	2288470	555407	24.2698%
----------------
match_TE:2:
  reads:	RAL-338.noGEN.front	RAL-338.noGEN.front.TE	percent
uq reads:	1997513	51516	2.5790%
   reads: 	2288470	54608	2.3862%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-338.noGEN.end	RAL-338.noGEN.end.gen	percent
uq reads:	1997513	326513	16.3460%
   reads: 	2288470	508633	22.2259%
----------------
match_TE:2:
  reads:	RAL-338.noGEN.end	RAL-338.noGEN.end.TE	percent
uq reads:	1997513	53330	2.6698%
   reads: 	2288470	57246	2.5015%
----------------
Candidate insertion sites in file: RAL-338_insert.txt
  reads:	5194
  uqreads:	5139
  Number of Candidate sites:	5139

Level 1 collapse of insertion sites in file: RAL-338_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	376

Level 1 annotation file: RAL-338_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-338_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-338.noGEN.front	RAL-338.noGEN.front.gendel	percent
uq reads:	1997513	370889	18.5675%
   reads: 	2288470	566915	24.7727%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-338.noGEN.end	RAL-338.noGEN.end.gendel	percent
uq reads:	1997513	332161	16.6287%
   reads: 	2288470	520249	22.7335%
----------------
Candidate breakpoint sites in file: RAL-338_depletion.xls
  reads:	12963
  uqreads:	12540
  Number of reads supporting candidate sites:	12540

Level 1 collapse of depletion sites in file: RAL-338_depletion_level1.xls
  Number of Level 1 collapsed sites:	1099