Insertion Pipeline
Bowtie2_wholegenome:
  reads:	KR4N_1-HE.fastq.uq.polyn	KR4N_1-HE.filter	percent
uq reads:	50440520	3667229	7.2704%
   reads: 	58308962	4593418	7.8777%
----------------
virus_structural_rna_repbase_filter:
  reads:	KR4N_1-HE.filter	KR4N_1-HE.nostrna	percent
uq reads:	3667229	2080284	56.7263%
   reads: 	4593418	2273797	49.5012%
----------------
TE_filter:
  reads:	KR4N_1-HE.nostrna	KR4N_1-HE.noTE	percent
uq reads:	2080284	2073181	99.6586%
   reads: 	2273797	2262844	99.5183%
----------------
match_dm6_mask_gen:1:
  reads:	KR4N_1-HE.noGEN.front	KR4N_1-HE.noGEN.front.gen	percent
uq reads:	2073181	951504	45.8958%
   reads: 	2262844	1015406	44.8730%
----------------
match_TE:2:
  reads:	KR4N_1-HE.noGEN.front	KR4N_1-HE.noGEN.front.TE	percent
uq reads:	2073181	125488	6.0529%
   reads: 	2262844	138006	6.0988%
----------------
match_dm6_mask_gen:1:
  reads:	KR4N_1-HE.noGEN.end	KR4N_1-HE.noGEN.end.gen	percent
uq reads:	2073181	981432	47.3394%
   reads: 	2262844	1052064	46.4930%
----------------
match_TE:2:
  reads:	KR4N_1-HE.noGEN.end	KR4N_1-HE.noGEN.end.TE	percent
uq reads:	2073181	125488	6.0529%
   reads: 	2262844	138369	6.1148%
----------------
Candidate insertion sites in file: KR4N_1-HE_insert.txt
  reads:	17146
  uqreads:	15675
  Number of Candidate sites:	15675

Level 1 collapse of insertion sites in file: KR4N_1-HE_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	529

Level 1 annotation file: KR4N_1-HE_level1siteannotation.xls
Insertion sites in fixed bin:
KR4N_1-HE_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	KR4N_1-HE.noGEN.front	KR4N_1-HE.noGEN.front.gendel	percent
uq reads:	2073181	951504	45.8958%
   reads: 	2262844	1015406	44.8730%
----------------
match_dm6_mask_gen_del:1:
  reads:	KR4N_1-HE.noGEN.end	KR4N_1-HE.noGEN.end.gendel	percent
uq reads:	2073181	981432	47.3394%
   reads: 	2262844	1052064	46.4930%
----------------
Candidate breakpoint sites in file: KR4N_1-HE_depletion.xls
  reads:	52618
  uqreads:	48330
  Number of reads supporting candidate sites:	48330

Level 1 collapse of depletion sites in file: KR4N_1-HE_depletion_level1.xls
  Number of Level 1 collapsed sites:	3376