Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-440.fastq.uq.polyn	RAL-440.filter	percent
uq reads:	41176530	5659648	13.7448%
   reads: 	42056454	5811391	13.8181%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-440.filter	RAL-440.nostrna	percent
uq reads:	5659648	3098055	54.7394%
   reads: 	5811391	3191634	54.9203%
----------------
TE_filter:
  reads:	RAL-440.nostrna	RAL-440.noTE	percent
uq reads:	3098055	3075829	99.2826%
   reads: 	3191634	3168964	99.2897%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-440.noGEN.front	RAL-440.noGEN.front.gen	percent
uq reads:	3075829	902811	29.3518%
   reads: 	3168964	951882	30.0376%
----------------
match_TE:2:
  reads:	RAL-440.noGEN.front	RAL-440.noGEN.front.TE	percent
uq reads:	3075829	118078	3.8389%
   reads: 	3168964	118991	3.7549%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-440.noGEN.end	RAL-440.noGEN.end.gen	percent
uq reads:	3075829	680306	22.1178%
   reads: 	3168964	725963	22.9085%
----------------
match_TE:2:
  reads:	RAL-440.noGEN.end	RAL-440.noGEN.end.TE	percent
uq reads:	3075829	99052	3.2203%
   reads: 	3168964	100212	3.1623%
----------------
Candidate insertion sites in file: RAL-440_insert.txt
  reads:	12699
  uqreads:	12677
  Number of Candidate sites:	12677

Level 1 collapse of insertion sites in file: RAL-440_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	624

Level 1 annotation file: RAL-440_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-440_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-440.noGEN.front	RAL-440.noGEN.front.gendel	percent
uq reads:	3075829	916737	29.8046%
   reads: 	3168964	966584	30.5016%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-440.noGEN.end	RAL-440.noGEN.end.gendel	percent
uq reads:	3075829	690811	22.4593%
   reads: 	3168964	737259	23.2650%
----------------
Candidate breakpoint sites in file: RAL-440_depletion.xls
  reads:	28717
  uqreads:	28624
  Number of reads supporting candidate sites:	28624

Level 1 collapse of depletion sites in file: RAL-440_depletion_level1.xls
  Number of Level 1 collapsed sites:	2433