mode	bam
runtime_info	qc3C_version qc3C 0.5rc10 run_timestamp 2021-02-10 04:59:31.484882
input_args	bam_file DRR177158.bam fasta_file GCF_000230535.1_PelSin_1.0_genomic.fna.gz enzymes HindIII seed 12345 sample_rate None min_mapq 60 max_obs 200000
n_parsed_reads	685538
n_analysed_reads	685538
n_accepted_reads	524649
n_skipped_reads	0
n_unmapped	0
n_low_mapq	99983
n_ref_len	784
n_secondary	0
n_supplementary	0
n_duplicate	0
n_weak_mapping	60415
n_ref_term	45
n_analysed_pairs	200000
n_accepted_pairs	200000
n_trans_pairs	120856
n_cis_pairs	79144
n_fully_aligned	186990
n_align_term	213010
n_no_site_end	218388
n_short_inserts	11190
classification	informative fr 18017 rf 15553 ffrr 33837 uninformative religation 1684 dangling_ends 8764 self_circle 1512 ffrr 1461
obs_insert_mean	232.77723406734242
obs_insert_median	231.0
mean_readlen	127.0
unobs_fraction	0.0
digest_stats	cs_start 37 cs_term 181612 cs_full 1763 read_thru 156203 is_split 115991 vestigial AAGCT
separation_bins	bins 1000 5000 10000 counts 67954 58390 50681 vs_all_cis 85.86121500050541 73.7769129687658 64.03643990700495 vs_accepted 33.977000000000004 29.195 25.3405
digestion	cutsites AAGCTT name HindIII site AAGCTT site_len 6 junctions AAGCTAGCTT enz5p HindIII enz3p HindIII junction AAGCTAGCTT vestigial AAGCT junc_len 10 vest_len 5 pattern AAGCTAGCTT cross True
junction_frequency	HindIII/HindIII AAGCTAGCTT 156203
remnant_frequency	HindIII AAGCT 181612