| mode | bam |
|---|
| runtime_info | | qc3C_version | qc3C 0.5rc10 |
|---|
| run_timestamp | 2021-02-10 05:02:16.625771 |
|---|
|
|---|
| input_args | | bam_file | DRR177172.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 | 922156 |
|---|
| n_analysed_reads | 909224 |
|---|
| n_accepted_reads | 518669 |
|---|
| n_skipped_reads | 0 |
|---|
| n_unmapped | 12932 |
|---|
| n_low_mapq | 190519 |
|---|
| n_ref_len | 1835 |
|---|
| n_secondary | 0 |
|---|
| n_supplementary | 222454 |
|---|
| n_duplicate | 0 |
|---|
| n_weak_mapping | 34057 |
|---|
| n_ref_term | 109 |
|---|
| n_analysed_pairs | 200000 |
|---|
| n_accepted_pairs | 200000 |
|---|
| n_trans_pairs | 101177 |
|---|
| n_cis_pairs | 98823 |
|---|
| n_fully_aligned | 213252 |
|---|
| n_align_term | 186748 |
|---|
| n_no_site_end | 241925 |
|---|
| n_short_inserts | 13287 |
|---|
| classification | | informative | |
|---|
| uninformative | | religation | 1648 |
|---|
| dangling_ends | 6087 |
|---|
| self_circle | 163 |
|---|
| ffrr | 1225 |
|---|
|
|---|
|
|---|
| obs_insert_mean | 313.8665724926159 |
|---|
| obs_insert_median | 311.0 |
|---|
| mean_readlen | 151.0 |
|---|
| unobs_fraction | 0.08038585209003213 |
|---|
| digest_stats | | cs_start | 24353 |
|---|
| cs_term | 158075 |
|---|
| cs_full | 4711 |
|---|
| read_thru | 148527 |
|---|
| is_split | 113363 |
|---|
| vestigial | |
|---|
|
|---|
| separation_bins | | bins | |
|---|
| counts | |
|---|
| vs_all_cis | - 86.55474940044321
- 68.87870232638151
- 58.466146544832675
|
|---|
| vs_accepted | |
|---|
|
|---|
| 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 | 72947 |
|---|
| DpnII/HinfI GATCAATC | 8820 |
|---|
| DpnII/HinfI GATCACTC | 7822 |
|---|
| DpnII/HinfI GATCAGTC | 6067 |
|---|
| DpnII/HinfI GATCATTC | 561 |
|---|
| HinfI/DpnII GAATGATC | 813 |
|---|
| HinfI/DpnII GACTGATC | 8958 |
|---|
| HinfI/DpnII GAGTGATC | 11540 |
|---|
| HinfI/DpnII GATTGATC | 13215 |
|---|
| HinfI/HinfI GAATAATC | 170 |
|---|
| HinfI/HinfI GACTAATC | 1789 |
|---|
| HinfI/HinfI GAGTAATC | 2224 |
|---|
| HinfI/HinfI GATTAATC | 2396 |
|---|
| HinfI/HinfI GAATACTC | 174 |
|---|
| HinfI/HinfI GACTACTC | 1611 |
|---|
| HinfI/HinfI GAGTACTC | 2018 |
|---|
| HinfI/HinfI GATTACTC | 2249 |
|---|
| HinfI/HinfI GAATAGTC | 120 |
|---|
| HinfI/HinfI GACTAGTC | 1254 |
|---|
| HinfI/HinfI GAGTAGTC | 1564 |
|---|
| HinfI/HinfI GATTAGTC | 1703 |
|---|
| HinfI/HinfI GAATATTC | 1 |
|---|
| HinfI/HinfI GACTATTC | 122 |
|---|
| HinfI/HinfI GAGTATTC | 207 |
|---|
| HinfI/HinfI GATTATTC | 182 |
|---|
|
|---|
| remnant_frequency | | DpnII GATC | 100799 |
|---|
| HinfI GAAT | 2220 |
|---|
| HinfI GACT | 14942 |
|---|
| HinfI GAGT | 18830 |
|---|
| HinfI GATT | 21284 |
|---|
|
|---|