Insertion Pipeline
Bowtie2_wholegenome:
  reads:	SB16_1-HE.fastq.uq.polyn	SB16_1-HE.filter	percent
uq reads:	43499246	2250673	5.1741%
   reads: 	47601014	2503849	5.2601%
----------------
virus_structural_rna_repbase_filter:
  reads:	SB16_1-HE.filter	SB16_1-HE.nostrna	percent
uq reads:	2250673	2172836	96.5416%
   reads: 	2503849	2361071	94.2977%
----------------
TE_filter:
  reads:	SB16_1-HE.nostrna	SB16_1-HE.noTE	percent
uq reads:	2172836	2163983	99.5926%
   reads: 	2361071	2345257	99.3302%
----------------
match_dm6_mask_gen:1:
  reads:	SB16_1-HE.noGEN.front	SB16_1-HE.noGEN.front.gen	percent
uq reads:	2163983	1186252	54.8180%
   reads: 	2345257	1219244	51.9876%
----------------
match_TE:2:
  reads:	SB16_1-HE.noGEN.front	SB16_1-HE.noGEN.front.TE	percent
uq reads:	2163983	164981	7.6240%
   reads: 	2345257	190018	8.1022%
----------------
match_dm6_mask_gen:1:
  reads:	SB16_1-HE.noGEN.end	SB16_1-HE.noGEN.end.gen	percent
uq reads:	2163983	1160267	53.6172%
   reads: 	2345257	1194012	50.9118%
----------------
match_TE:2:
  reads:	SB16_1-HE.noGEN.end	SB16_1-HE.noGEN.end.TE	percent
uq reads:	2163983	164638	7.6081%
   reads: 	2345257	193447	8.2484%
----------------
Candidate insertion sites in file: SB16_1-HE_insert.txt
  reads:	29601
  uqreads:	28369
  Number of Candidate sites:	28369

Level 1 collapse of insertion sites in file: SB16_1-HE_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	564

Level 1 annotation file: SB16_1-HE_level1siteannotation.xls
Insertion sites in fixed bin:
SB16_1-HE_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	SB16_1-HE.noGEN.front	SB16_1-HE.noGEN.front.gendel	percent
uq reads:	2163983	1186252	54.8180%
   reads: 	2345257	1219244	51.9876%
----------------
match_dm6_mask_gen_del:1:
  reads:	SB16_1-HE.noGEN.end	SB16_1-HE.noGEN.end.gendel	percent
uq reads:	2163983	1160267	53.6172%
   reads: 	2345257	1194012	50.9118%
----------------
Candidate breakpoint sites in file: SB16_1-HE_depletion.xls
  reads:	108751
  uqreads:	105154
  Number of reads supporting candidate sites:	105154

Level 1 collapse of depletion sites in file: SB16_1-HE_depletion_level1.xls
  Number of Level 1 collapsed sites:	3711