mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| read file | reads | bases | passed filters | average | longest | mapped | |
|---|---|---|---|---|---|---|---|
| errors | 25-END_S6_L001_R1_001_150407.good.fq | 161,072 | 38,034,798 | 100.0% | 236.1 bases | 275 bases | 97.4% |
| errors | 25-END_S6_L001_R1_001_150520.good.fq | 572,160 | 140,844,517 | 100.0% | 246.2 bases | 275 bases | 99.0% |
| errors | 25-END_S6_L001_R2_001_150407.good.fq | 161,072 | 38,610,886 | 100.0% | 239.7 bases | 275 bases | 54.3% |
| errors | 25-END_S6_L001_R2_001_150520.good.fq | 572,159 | 141,206,349 | 100.0% | 246.8 bases | 275 bases | 86.5% |
| errors | GLY_25_036_S292_L001_R1_001.good.fq | 1,129,779 | 125,657,435 | 100.0% | 111.2 bases | 148 bases | 96.6% |
| errors | GLY_25_036_S292_L001_R2_001.good.fq | 1,129,779 | 125,657,435 | 100.0% | 111.2 bases | 148 bases | 96.5% |
| errors | GLY_25_036_S292_L002_R1_001.good.fq | 1,145,866 | 127,162,713 | 100.0% | 111.0 bases | 148 bases | 96.2% |
| errors | GLY_25_036_S292_L002_R2_001.good.fq | 1,145,866 | 127,162,713 | 100.0% | 111.0 bases | 148 bases | 96.1% |
| total | 6,017,753 | 864,336,846 | 100.0% | 143.6 bases | 275 bases | 94.6% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 170.6 | 10.6 | 100.0% | Escherichia coli str. K-12 substr. MG1655, complete genome. |
| total | 4,641,652 | 100.0% |
fit dispersion is the ratio of the variance to the mean for the negative binomial fit. It is =1 for Poisson and >1 for over-dispersed data.
| option | limit | actual |
|---|---|---|
| Number of alignment pairs examined for constructing junction candidates | ≤ 100000 | 39031 |
| Coverage evenness (position-hash) score of junction candidates | ≥ 2 | ≥ 3 |
| Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold | 100 ≤ n ≤ 5000 | 806 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.097 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.62237 |
pr(no read start) is the probability that there will not be an aligned read whose first base matches a given position on a given strand.
| option | value |
|---|---|
| Coverage evenness (position-hash) score of predicted junctions must be | ≥ 3 |
| Skew score of predicted junction (−log10 probability of unusual coverage evenness) must be | ≤ 0 |
| Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction | ≥ 6 |
| option | value |
|---|---|
| Mode | Full Polymorphism |
| Ploidy | 1 (haploid) |
| Consensus mutation E-value cutoff | 10 |
| Consensus frequency cutoff | 0.75 |
| Consensus minimum variant coverage each strand | OFF |
| Consensus minimum total coverage each strand | OFF |
| Consensus minimum variant coverage | OFF |
| Consensus minimum total coverage | OFF |
| Polymorphism E-value cutoff | 2 |
| Polymorphism frequency cutoff | 0.05 |
| Polymorphism minimum variant coverage each strand | 2 |
| Polymorphism minimum total coverage each strand | OFF |
| Polymorphism minimum variant coverage | OFF |
| Polymorphism minimum total coverage | OFF |
| Polymorphism bias cutoff | OFF |
| Predict indel polymorphisms | YES |
| Skip indel polymorphisms in homopolymers runs of | ≥3 bases |
| Skip base substitutions when they create a homopolymer flanked on each side by | ≥5 bases |
| program | version |
|---|---|
| bowtie2 | 2.3.4.1 |
| R | 3.4.4 |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 00:27:24 03 Jan 2019 | 00:28:48 03 Jan 2019 | 1 minute 24 seconds |
| Read alignment to reference genome | 00:28:49 03 Jan 2019 | 00:44:33 03 Jan 2019 | 15 minutes 44 seconds |
| Preprocessing alignments for candidate junction identification | 00:44:33 03 Jan 2019 | 00:45:49 03 Jan 2019 | 1 minute 16 seconds |
| Preliminary analysis of coverage distribution | 00:45:49 03 Jan 2019 | 00:49:37 03 Jan 2019 | 3 minutes 48 seconds |
| Identifying junction candidates | 00:49:37 03 Jan 2019 | 01:15:00 03 Jan 2019 | 25 minutes 23 seconds |
| Re-alignment to junction candidates | 01:15:00 03 Jan 2019 | 01:20:15 03 Jan 2019 | 5 minutes 15 seconds |
| Resolving best read alignments | 01:20:15 03 Jan 2019 | 01:22:28 03 Jan 2019 | 2 minutes 13 seconds |
| Creating BAM files | 01:22:28 03 Jan 2019 | 01:25:50 03 Jan 2019 | 3 minutes 22 seconds |
| Tabulating error counts | 01:25:50 03 Jan 2019 | 01:27:06 03 Jan 2019 | 1 minute 16 seconds |
| Re-calibrating base error rates | 01:27:06 03 Jan 2019 | 01:27:08 03 Jan 2019 | 2 seconds |
| Examining read alignment evidence | 01:27:08 03 Jan 2019 | 02:44:47 03 Jan 2019 | 1 hour 17 minutes 39 seconds |
| Polymorphism statistics | 02:44:47 03 Jan 2019 | 02:44:50 03 Jan 2019 | 3 seconds |
| Output | 02:44:50 03 Jan 2019 | 02:46:25 03 Jan 2019 | 1 minute 35 seconds |
| Total | 2 hours 19 minutes 0 seconds | ||
