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 | 26-END_S7_L001_R1_001_150407.good.fq | 231,149 | 42,855,722 | 100.0% | 185.4 bases | 275 bases | 96.8% |
| errors | 26-END_S7_L001_R1_001_150520.good.fq | 819,447 | 164,831,609 | 100.0% | 201.1 bases | 275 bases | 98.4% |
| errors | 26-END_S7_L001_R2_001_150407.good.fq | 231,148 | 45,071,179 | 100.0% | 195.0 bases | 275 bases | 63.7% |
| errors | 26-END_S7_L001_R2_001_150520.good.fq | 819,445 | 168,262,154 | 100.0% | 205.3 bases | 275 bases | 81.0% |
| errors | GLY_26_025_S300_L001_R1_001.good.fq | 915,292 | 127,928,145 | 100.0% | 139.8 bases | 148 bases | 98.0% |
| errors | GLY_26_025_S300_L001_R2_001.good.fq | 915,292 | 127,928,145 | 100.0% | 139.8 bases | 148 bases | 97.9% |
| errors | GLY_26_025_S300_L002_R1_001.good.fq | 907,318 | 127,715,152 | 100.0% | 140.8 bases | 149 bases | 97.9% |
| errors | GLY_26_025_S300_L002_R2_001.good.fq | 907,318 | 127,715,152 | 100.0% | 140.8 bases | 149 bases | 97.7% |
| total | 5,746,409 | 932,307,258 | 100.0% | 162.2 bases | 275 bases | 94.1% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 174.9 | 4.3 | 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 | 22109 |
| 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 | 210 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.025 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.62328 |
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 | 20:27:55 02 Jan 2019 | 20:29:26 02 Jan 2019 | 1 minute 31 seconds |
| Read alignment to reference genome | 20:29:27 02 Jan 2019 | 20:46:00 02 Jan 2019 | 16 minutes 33 seconds |
| Preprocessing alignments for candidate junction identification | 20:46:00 02 Jan 2019 | 20:47:16 02 Jan 2019 | 1 minute 16 seconds |
| Preliminary analysis of coverage distribution | 20:47:16 02 Jan 2019 | 20:51:09 02 Jan 2019 | 3 minutes 53 seconds |
| Identifying junction candidates | 20:51:09 02 Jan 2019 | 20:53:30 02 Jan 2019 | 2 minutes 21 seconds |
| Re-alignment to junction candidates | 20:53:30 02 Jan 2019 | 20:58:02 02 Jan 2019 | 4 minutes 32 seconds |
| Resolving best read alignments | 20:58:02 02 Jan 2019 | 21:00:11 02 Jan 2019 | 2 minutes 9 seconds |
| Creating BAM files | 21:00:11 02 Jan 2019 | 21:03:40 02 Jan 2019 | 3 minutes 29 seconds |
| Tabulating error counts | 21:03:40 02 Jan 2019 | 21:04:58 02 Jan 2019 | 1 minute 18 seconds |
| Re-calibrating base error rates | 21:04:58 02 Jan 2019 | 21:05:00 02 Jan 2019 | 2 seconds |
| Examining read alignment evidence | 21:05:00 02 Jan 2019 | 22:29:50 02 Jan 2019 | 1 hour 24 minutes 50 seconds |
| Polymorphism statistics | 22:29:50 02 Jan 2019 | 22:29:53 02 Jan 2019 | 3 seconds |
| Output | 22:29:53 02 Jan 2019 | 22:30:40 02 Jan 2019 | 47 seconds |
| Total | 2 hours 2 minutes 44 seconds | ||
