mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.29.0 revision 8f9c342918e4
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| read file | reads | bases | passed filters | average | longest | mapped | |
|---|---|---|---|---|---|---|---|
| errors | qtrim-IND_KHP_HOT_A9_F049_I0_R1_S39_L004_R2_001 | 3,556,736 | 354,527,502 | 100.0% | 99.7 bases | 100 bases | 93.8% |
| errors | qtrim-IND_KHP_HOT_A9_F049_I0_R1_S39_L004_R1_001 | 3,556,763 | 355,549,110 | 100.0% | 100.0 bases | 100 bases | 95.1% |
| total | 7,113,499 | 710,076,612 | 100.0% | 99.8 bases | 100 bases | 94.4% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 144.3 | 2.1 | 98.1% | 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 | 100096 |
| Coverage evenness (position-hash) score of junction candidates | ≥ 2 | ≥ 4 |
| Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold | 100 ≤ n ≤ 5000 | 626 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.028 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.54668 |
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 | OFF |
| Consensus minimum coverage each strand | OFF |
| Polymorphism E-value cutoff | 2 |
| Polymorphism frequency cutoff | 0.15 |
| Polymorphism minimum coverage each strand | 2 |
| 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 | ≥2 bases |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 05:03:08 13 Jan 2017 | 05:04:25 13 Jan 2017 | 1 minute 17 seconds |
| Read alignment to reference genome | 05:04:26 13 Jan 2017 | 05:08:34 13 Jan 2017 | 4 minutes 8 seconds |
| Preprocessing alignments for candidate junction identification | 05:08:34 13 Jan 2017 | 05:11:06 13 Jan 2017 | 2 minutes 32 seconds |
| Preliminary analysis of coverage distribution | 05:11:06 13 Jan 2017 | 05:13:59 13 Jan 2017 | 2 minutes 53 seconds |
| Identifying junction candidates | 05:13:59 13 Jan 2017 | 05:15:27 13 Jan 2017 | 1 minute 28 seconds |
| Re-alignment to junction candidates | 05:15:27 13 Jan 2017 | 05:16:14 13 Jan 2017 | 47 seconds |
| Resolving alignments with junction candidates | 05:16:14 13 Jan 2017 | 05:20:27 13 Jan 2017 | 4 minutes 13 seconds |
| Creating BAM files | 05:20:27 13 Jan 2017 | 05:22:10 13 Jan 2017 | 1 minute 43 seconds |
| Tabulating error counts | 05:22:10 13 Jan 2017 | 05:25:12 13 Jan 2017 | 3 minutes 2 seconds |
| Re-calibrating base error rates | 05:25:12 13 Jan 2017 | 05:25:13 13 Jan 2017 | 1 second |
| Examining read alignment evidence | 05:25:13 13 Jan 2017 | 06:57:16 13 Jan 2017 | 1 hour 32 minutes 3 seconds |
| Polymorphism statistics | 06:57:16 13 Jan 2017 | 06:57:21 13 Jan 2017 | 5 seconds |
| Output | 06:57:21 13 Jan 2017 | 06:58:27 13 Jan 2017 | 1 minute 6 seconds |
| Total | 1 hour 55 minutes 18 seconds | ||
