| mode | bam |
|---|
| runtime_info | | qc3C_version | qc3C 0.5rc10 |
|---|
| run_timestamp | 2021-02-10 05:01:51.036925 |
|---|
|
|---|
| input_args | | bam_file | DRR177170.bam |
|---|
| fasta_file | GCF_000230535.1_PelSin_1.0_genomic.fna.gz |
|---|
| enzymes | |
|---|
| seed | 12345 |
|---|
| sample_rate | None |
|---|
| min_mapq | 60 |
|---|
| max_obs | 200000 |
|---|
|
|---|
| n_parsed_reads | 848687 |
|---|
| n_analysed_reads | 848687 |
|---|
| n_accepted_reads | 578175 |
|---|
| n_skipped_reads | 0 |
|---|
| n_unmapped | 0 |
|---|
| n_low_mapq | 189190 |
|---|
| n_ref_len | 1810 |
|---|
| n_secondary | 0 |
|---|
| n_supplementary | 0 |
|---|
| n_duplicate | 0 |
|---|
| n_weak_mapping | 79975 |
|---|
| n_ref_term | 112 |
|---|
| n_analysed_pairs | 200000 |
|---|
| n_accepted_pairs | 200000 |
|---|
| n_trans_pairs | 114334 |
|---|
| n_cis_pairs | 85666 |
|---|
| n_fully_aligned | 137841 |
|---|
| n_align_term | 262159 |
|---|
| n_no_site_end | 175408 |
|---|
| n_short_inserts | 17441 |
|---|
| classification | | informative | |
|---|
| uninformative | | religation | 424 |
|---|
| dangling_ends | 11561 |
|---|
| self_circle | 2307 |
|---|
| ffrr | 2104 |
|---|
|
|---|
|
|---|
| obs_insert_mean | 213.10605162928482 |
|---|
| obs_insert_median | 210.0 |
|---|
| mean_readlen | 151.0 |
|---|
| unobs_fraction | 0.0 |
|---|
| digest_stats | | cs_start | 14194 |
|---|
| cs_term | 224592 |
|---|
| cs_full | 1547 |
|---|
| read_thru | 214869 |
|---|
| is_split | 174138 |
|---|
| vestigial | |
|---|
|
|---|
| separation_bins | | bins | |
|---|
| counts | |
|---|
| vs_all_cis | - 79.64069759297738
- 65.57327294375833
- 55.365022295893354
|
|---|
| vs_accepted | - 34.112500000000004
- 28.087
- 23.7145
|
|---|
|
|---|
| digestion | | cutsites | | GATC | | name | DpnII |
|---|
| site | GATC |
|---|
| site_len | 4 |
|---|
|
|---|
|
|---|
| junctions | | GATCGATC | | enz5p | DpnII |
|---|
| enz3p | DpnII |
|---|
| junction | GATCGATC |
|---|
| vestigial | GATC |
|---|
| junc_len | 8 |
|---|
| vest_len | 4 |
|---|
| pattern | GATCGATC |
|---|
| cross | True |
|---|
|
|---|
|
|---|
|
|---|
| junction_frequency | | DpnII/DpnII GATCGATC | 214869 |
|---|
|
|---|
| remnant_frequency | |
|---|