Insertion Pipeline
Bowtie2_wholegenome:
  reads:	NG3N_1-HE.fastq.uq.polyn	NG3N_1-HE.filter	percent
uq reads:	55064116	2309106	4.1935%
   reads: 	63972793	2617881	4.0922%
----------------
virus_structural_rna_repbase_filter:
  reads:	NG3N_1-HE.filter	NG3N_1-HE.nostrna	percent
uq reads:	2309106	2276895	98.6050%
   reads: 	2617881	2565965	98.0169%
----------------
TE_filter:
  reads:	NG3N_1-HE.nostrna	NG3N_1-HE.noTE	percent
uq reads:	2276895	2263099	99.3941%
   reads: 	2565965	2535195	98.8008%
----------------
match_dm6_mask_gen:1:
  reads:	NG3N_1-HE.noGEN.front	NG3N_1-HE.noGEN.front.gen	percent
uq reads:	2263099	1099408	48.5798%
   reads: 	2535195	1204713	47.5195%
----------------
match_TE:2:
  reads:	NG3N_1-HE.noGEN.front	NG3N_1-HE.noGEN.front.TE	percent
uq reads:	2263099	98455	4.3505%
   reads: 	2535195	108796	4.2914%
----------------
match_dm6_mask_gen:1:
  reads:	NG3N_1-HE.noGEN.end	NG3N_1-HE.noGEN.end.gen	percent
uq reads:	2263099	1103845	48.7758%
   reads: 	2535195	1220163	48.1290%
----------------
match_TE:2:
  reads:	NG3N_1-HE.noGEN.end	NG3N_1-HE.noGEN.end.TE	percent
uq reads:	2263099	94909	4.1938%
   reads: 	2535195	105329	4.1547%
----------------
Candidate insertion sites in file: NG3N_1-HE_insert.txt
  reads:	16567
  uqreads:	14897
  Number of Candidate sites:	14897

Level 1 collapse of insertion sites in file: NG3N_1-HE_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	488

Level 1 annotation file: NG3N_1-HE_level1siteannotation.xls
Insertion sites in fixed bin:
NG3N_1-HE_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	NG3N_1-HE.noGEN.front	NG3N_1-HE.noGEN.front.gendel	percent
uq reads:	2263099	1099408	48.5798%
   reads: 	2535195	1204713	47.5195%
----------------
match_dm6_mask_gen_del:1:
  reads:	NG3N_1-HE.noGEN.end	NG3N_1-HE.noGEN.end.gendel	percent
uq reads:	2263099	1103845	48.7758%
   reads: 	2535195	1220163	48.1290%
----------------
Candidate breakpoint sites in file: NG3N_1-HE_depletion.xls
  reads:	62582
  uqreads:	55718
  Number of reads supporting candidate sites:	55718

Level 1 collapse of depletion sites in file: NG3N_1-HE_depletion_level1.xls
  Number of Level 1 collapsed sites:	3719