Insertion Pipeline
Bowtie2_wholegenome:
  reads:	SF447_1-HE.fastq.uq.polyn	SF447_1-HE.filter	percent
uq reads:	28946688	1342478	4.6378%
   reads: 	30321912	1375164	4.5352%
----------------
virus_structural_rna_repbase_filter:
  reads:	SF447_1-HE.filter	SF447_1-HE.nostrna	percent
uq reads:	1342478	1264258	94.1735%
   reads: 	1375164	1295289	94.1916%
----------------
TE_filter:
  reads:	SF447_1-HE.nostrna	SF447_1-HE.noTE	percent
uq reads:	1264258	1255321	99.2931%
   reads: 	1295289	1285025	99.2076%
----------------
match_dm6_mask_gen:1:
  reads:	SF447_1-HE.noGEN.front	SF447_1-HE.noGEN.front.gen	percent
uq reads:	1255321	626131	49.8782%
   reads: 	1285025	635331	49.4411%
----------------
match_TE:2:
  reads:	SF447_1-HE.noGEN.front	SF447_1-HE.noGEN.front.TE	percent
uq reads:	1255321	97885	7.7976%
   reads: 	1285025	100499	7.8208%
----------------
match_dm6_mask_gen:1:
  reads:	SF447_1-HE.noGEN.end	SF447_1-HE.noGEN.end.gen	percent
uq reads:	1255321	648971	51.6976%
   reads: 	1285025	659019	51.2845%
----------------
match_TE:2:
  reads:	SF447_1-HE.noGEN.end	SF447_1-HE.noGEN.end.TE	percent
uq reads:	1255321	101308	8.0703%
   reads: 	1285025	104068	8.0985%
----------------
Candidate insertion sites in file: SF447_1-HE_insert.txt
  reads:	15733
  uqreads:	15373
  Number of Candidate sites:	15373

Level 1 collapse of insertion sites in file: SF447_1-HE_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	451

Level 1 annotation file: SF447_1-HE_level1siteannotation.xls
Insertion sites in fixed bin:
SF447_1-HE_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	SF447_1-HE.noGEN.front	SF447_1-HE.noGEN.front.gendel	percent
uq reads:	1255321	626131	49.8782%
   reads: 	1285025	635331	49.4411%
----------------
match_dm6_mask_gen_del:1:
  reads:	SF447_1-HE.noGEN.end	SF447_1-HE.noGEN.end.gendel	percent
uq reads:	1255321	648971	51.6976%
   reads: 	1285025	659019	51.2845%
----------------
Candidate breakpoint sites in file: SF447_1-HE_depletion.xls
  reads:	48243
  uqreads:	47083
  Number of reads supporting candidate sites:	47083

Level 1 collapse of depletion sites in file: SF447_1-HE_depletion_level1.xls
  Number of Level 1 collapsed sites:	3114