| mode | bam |
|---|
| runtime_info | | qc3C_version | qc3C 0.5rc10 |
|---|
| run_timestamp | 2021-02-10 05:00:36.288114 |
|---|
|
|---|
| input_args | | bam_file | DRR177163.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 | 819424 |
|---|
| n_analysed_reads | 811402 |
|---|
| n_accepted_reads | 503298 |
|---|
| n_skipped_reads | 0 |
|---|
| n_unmapped | 8022 |
|---|
| n_low_mapq | 158515 |
|---|
| n_ref_len | 1386 |
|---|
| n_secondary | 0 |
|---|
| n_supplementary | 163238 |
|---|
| n_duplicate | 0 |
|---|
| n_weak_mapping | 26957 |
|---|
| n_ref_term | 69 |
|---|
| n_analysed_pairs | 200000 |
|---|
| n_accepted_pairs | 200000 |
|---|
| n_trans_pairs | 96593 |
|---|
| n_cis_pairs | 103407 |
|---|
| n_fully_aligned | 249375 |
|---|
| n_align_term | 150625 |
|---|
| n_no_site_end | 267149 |
|---|
| n_short_inserts | 22893 |
|---|
| classification | | informative | |
|---|
| uninformative | | religation | 3465 |
|---|
| dangling_ends | 13599 |
|---|
| self_circle | 116 |
|---|
| ffrr | 335 |
|---|
|
|---|
|
|---|
| obs_insert_mean | 297.17234345057796 |
|---|
| obs_insert_median | 295.0 |
|---|
| mean_readlen | 127.0 |
|---|
| unobs_fraction | 0.1932203389830508 |
|---|
| digest_stats | | cs_start | 59371 |
|---|
| cs_term | 132851 |
|---|
| cs_full | 5430 |
|---|
| read_thru | 123326 |
|---|
| is_split | 87264 |
|---|
| vestigial | |
|---|
|
|---|
| separation_bins | | bins | |
|---|
| counts | |
|---|
| vs_all_cis | - 77.86126664539151
- 61.8836248996683
- 52.819441623874596
|
|---|
| vs_accepted | - 40.257
- 31.996000000000002
- 27.309499999999996
|
|---|
|
|---|
| 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 | 60634 |
|---|
| DpnII/HinfI GATCAATC | 7324 |
|---|
| DpnII/HinfI GATCACTC | 6245 |
|---|
| DpnII/HinfI GATCAGTC | 5039 |
|---|
| DpnII/HinfI GATCATTC | 487 |
|---|
| HinfI/DpnII GAATGATC | 784 |
|---|
| HinfI/DpnII GACTGATC | 7510 |
|---|
| HinfI/DpnII GAGTGATC | 9378 |
|---|
| HinfI/DpnII GATTGATC | 11284 |
|---|
| HinfI/HinfI GAATAATC | 144 |
|---|
| HinfI/HinfI GACTAATC | 1415 |
|---|
| HinfI/HinfI GAGTAATC | 1951 |
|---|
| HinfI/HinfI GATTAATC | 2091 |
|---|
| HinfI/HinfI GAATACTC | 173 |
|---|
| HinfI/HinfI GACTACTC | 1300 |
|---|
| HinfI/HinfI GAGTACTC | 1560 |
|---|
| HinfI/HinfI GATTACTC | 1920 |
|---|
| HinfI/HinfI GAATAGTC | 98 |
|---|
| HinfI/HinfI GACTAGTC | 950 |
|---|
| HinfI/HinfI GAGTAGTC | 1243 |
|---|
| HinfI/HinfI GATTAGTC | 1400 |
|---|
| HinfI/HinfI GAATATTC | 3 |
|---|
| HinfI/HinfI GACTATTC | 104 |
|---|
| HinfI/HinfI GAGTATTC | 164 |
|---|
| HinfI/HinfI GATTATTC | 125 |
|---|
|
|---|
| remnant_frequency | | DpnII GATC | 83791 |
|---|
| HinfI GAAT | 2364 |
|---|
| HinfI GACT | 12514 |
|---|
| HinfI GAGT | 15707 |
|---|
| HinfI GATT | 18475 |
|---|
|
|---|