Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-441.fastq.uq.polyn	RAL-441.filter	percent
uq reads:	38931252	4933112	12.6713%
   reads: 	41257415	5458100	13.2294%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-441.filter	RAL-441.nostrna	percent
uq reads:	4933112	2819570	57.1560%
   reads: 	5458100	3075408	56.3458%
----------------
TE_filter:
  reads:	RAL-441.nostrna	RAL-441.noTE	percent
uq reads:	2819570	2807161	99.5599%
   reads: 	3075408	3061414	99.5450%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-441.noGEN.front	RAL-441.noGEN.front.gen	percent
uq reads:	2807161	722224	25.7279%
   reads: 	3061414	826136	26.9854%
----------------
match_TE:2:
  reads:	RAL-441.noGEN.front	RAL-441.noGEN.front.TE	percent
uq reads:	2807161	112568	4.0100%
   reads: 	3061414	116446	3.8037%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-441.noGEN.end	RAL-441.noGEN.end.gen	percent
uq reads:	2807161	502756	17.9098%
   reads: 	3061414	604192	19.7357%
----------------
match_TE:2:
  reads:	RAL-441.noGEN.end	RAL-441.noGEN.end.TE	percent
uq reads:	2807161	90513	3.2244%
   reads: 	3061414	95098	3.1063%
----------------
Candidate insertion sites in file: RAL-441_insert.txt
  reads:	11468
  uqreads:	11320
  Number of Candidate sites:	11320

Level 1 collapse of insertion sites in file: RAL-441_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	544

Level 1 annotation file: RAL-441_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-441_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-441.noGEN.front	RAL-441.noGEN.front.gendel	percent
uq reads:	2807161	735330	26.1948%
   reads: 	3061414	842715	27.5270%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-441.noGEN.end	RAL-441.noGEN.end.gendel	percent
uq reads:	2807161	511891	18.2352%
   reads: 	3061414	616811	20.1479%
----------------
Candidate breakpoint sites in file: RAL-441_depletion.xls
  reads:	28079
  uqreads:	27703
  Number of reads supporting candidate sites:	27703

Level 1 collapse of depletion sites in file: RAL-441_depletion_level1.xls
  Number of Level 1 collapsed sites:	2584