| mode | bam |
|---|
| runtime_info | | qc3C_version | qc3C 0.5rc10 |
|---|
| run_timestamp | 2021-02-10 05:00:47.487569 |
|---|
|
|---|
| input_args | | bam_file | DRR177164.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 | 879163 |
|---|
| n_analysed_reads | 865654 |
|---|
| n_accepted_reads | 523634 |
|---|
| n_skipped_reads | 0 |
|---|
| n_unmapped | 13509 |
|---|
| n_low_mapq | 186194 |
|---|
| n_ref_len | 1811 |
|---|
| n_secondary | 0 |
|---|
| n_supplementary | 166575 |
|---|
| n_duplicate | 0 |
|---|
| n_weak_mapping | 33801 |
|---|
| n_ref_term | 88 |
|---|
| n_analysed_pairs | 200000 |
|---|
| n_accepted_pairs | 200000 |
|---|
| n_trans_pairs | 101875 |
|---|
| n_cis_pairs | 98125 |
|---|
| n_fully_aligned | 254384 |
|---|
| n_align_term | 145616 |
|---|
| n_no_site_end | 271877 |
|---|
| n_short_inserts | 12505 |
|---|
| classification | | informative | |
|---|
| uninformative | | religation | 2262 |
|---|
| dangling_ends | 4728 |
|---|
| self_circle | 130 |
|---|
| ffrr | 355 |
|---|
|
|---|
|
|---|
| obs_insert_mean | 319.0417727967397 |
|---|
| obs_insert_median | 315.0 |
|---|
| mean_readlen | 127.0 |
|---|
| unobs_fraction | 0.24444444444444446 |
|---|
| digest_stats | | cs_start | 26305 |
|---|
| cs_term | 128123 |
|---|
| cs_full | 5361 |
|---|
| read_thru | 119455 |
|---|
| is_split | 84075 |
|---|
| vestigial | |
|---|
|
|---|
| separation_bins | | bins | |
|---|
| counts | |
|---|
| vs_all_cis | - 87.25605095541401
- 69.30547770700637
- 58.89936305732484
|
|---|
| vs_accepted | - 42.809999999999995
- 34.003
- 28.897499999999997
|
|---|
|
|---|
| digestion | | cutsites | | GATC | | name | DpnII |
|---|
| site | GATC |
|---|
| site_len | 4 |
|---|
|
|---|
| GANTC | | name | HinfI |
|---|
| site | GANTC |
|---|
| site_len | 5 |
|---|
|
|---|
|
|---|
| junctions | | GATCGATC | | enz5p | DpnII |
|---|
| enz3p | DpnII |
|---|
| junction | GATCGATC |
|---|
| vestigial | GATC |
|---|
| junc_len | 8 |
|---|
| vest_len | 4 |
|---|
| pattern | GATCGATC |
|---|
| cross | True |
|---|
|
|---|
| GATCANTC | | enz5p | DpnII |
|---|
| enz3p | HinfI |
|---|
| junction | GATCANTC |
|---|
| vestigial | GATC |
|---|
| junc_len | 8 |
|---|
| vest_len | 4 |
|---|
| pattern | GATCA[ACGT]TC |
|---|
| cross | False |
|---|
|
|---|
| GANTGATC | | enz5p | HinfI |
|---|
| enz3p | DpnII |
|---|
| junction | GANTGATC |
|---|
| vestigial | GANT |
|---|
| junc_len | 8 |
|---|
| vest_len | 4 |
|---|
| pattern | GA[ACGT]TGATC |
|---|
| cross | False |
|---|
|
|---|
| GANTANTC | | enz5p | HinfI |
|---|
| enz3p | HinfI |
|---|
| junction | GANTANTC |
|---|
| vestigial | GANT |
|---|
| junc_len | 8 |
|---|
| vest_len | 4 |
|---|
| pattern | GA[ACGT]TA[ACGT]TC |
|---|
| cross | True |
|---|
|
|---|
|
|---|
|
|---|
| junction_frequency | | DpnII/DpnII GATCGATC | 58778 |
|---|
| DpnII/HinfI GATCAATC | 7115 |
|---|
| DpnII/HinfI GATCACTC | 6168 |
|---|
| DpnII/HinfI GATCAGTC | 4899 |
|---|
| DpnII/HinfI GATCATTC | 447 |
|---|
| HinfI/DpnII GAATGATC | 686 |
|---|
| HinfI/DpnII GACTGATC | 7304 |
|---|
| HinfI/DpnII GAGTGATC | 9386 |
|---|
| HinfI/DpnII GATTGATC | 10564 |
|---|
| HinfI/HinfI GAATAATC | 116 |
|---|
| HinfI/HinfI GACTAATC | 1316 |
|---|
| HinfI/HinfI GAGTAATC | 1818 |
|---|
| HinfI/HinfI GATTAATC | 1850 |
|---|
| HinfI/HinfI GAATACTC | 140 |
|---|
| HinfI/HinfI GACTACTC | 1272 |
|---|
| HinfI/HinfI GAGTACTC | 1621 |
|---|
| HinfI/HinfI GATTACTC | 1754 |
|---|
| HinfI/HinfI GAATAGTC | 100 |
|---|
| HinfI/HinfI GACTAGTC | 1018 |
|---|
| HinfI/HinfI GAGTAGTC | 1303 |
|---|
| HinfI/HinfI GATTAGTC | 1407 |
|---|
| HinfI/HinfI GAATATTC | 0 |
|---|
| HinfI/HinfI GACTATTC | 98 |
|---|
| HinfI/HinfI GAGTATTC | 156 |
|---|
| HinfI/HinfI GATTATTC | 139 |
|---|
|
|---|
| remnant_frequency | | DpnII GATC | 81038 |
|---|
| HinfI GAAT | 2057 |
|---|
| HinfI GACT | 12179 |
|---|
| HinfI GAGT | 15599 |
|---|
| HinfI GATT | 17250 |
|---|
|
|---|