mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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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 | SNFM_19_74_1_S210_S1993_L006_R1_001.good.fq | 790,941 | 105,857,728 | 100.0% | 133.8 bases | 141 bases | 94.7% |
| errors | SNFM_19_74_1_S210_S1993_L006_R2_001.good.fq | 790,941 | 105,857,728 | 100.0% | 133.8 bases | 141 bases | 93.5% |
| errors | SNFM_19_74_1_S210_S1993_L008_R1_001.good.fq | 348,645 | 46,448,554 | 100.0% | 133.2 bases | 141 bases | 94.5% |
| errors | SNFM_19_74_1_S210_S1993_L008_R2_001.good.fq | 348,645 | 46,448,554 | 100.0% | 133.2 bases | 141 bases | 92.3% |
| total | 2,279,172 | 304,612,564 | 100.0% | 133.7 bases | 141 bases | 93.9% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | USA300TCH1516_ALE | 2,872,915 | 98.0 | 3.3 | 96.9% | Staphylococcus species strain strain. |
| coverage | distribution | CP000731 | 27,041 | NA | NA | 0.0% | Staphylococcus aureus subsp. aureus USA300_TCH1516 plasmid |
| coverage | distribution | NC_012417 | 3,125 | 3257.0 | 215.3 | 3.1% | Staphylococcus aureus subsp. aureus USA300_TCH1516 plasmid |
| total | 2,903,081 | 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.
Insufficient coverage Reference sequence counted as entirely deleted due to low coverage. Try either the -t,--targeted-sequencing or the -c,--contig-reference option if you want mutations called for these reference sequences.
| option | limit | actual |
|---|---|---|
| Number of alignment pairs examined for constructing junction candidates | ≤ 100000 | 80655 |
| 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 | 201 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.020 |
| reference sequence | pr(no read start) |
|---|---|
| USA300TCH1516_ALE | 0.73015 |
| CP000731 | 0.99474 |
| NC_012417 | 0.04665 |
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 | ≤ 3 |
| Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction | ≥ 1 |
| option | value |
|---|---|
| Mode | Consensus/Mixed Base |
| 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 | 10 |
| Polymorphism frequency cutoff | 0.2 |
| Polymorphism minimum variant coverage each strand | OFF |
| 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 | OFF |
| Skip base substitutions when they create a homopolymer flanked on each side by | OFF |
| program | version |
|---|---|
| bowtie2 | 2.3.4.1 |
| R | 3.4.4 |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 01:46:59 08 Oct 2019 | 01:47:35 08 Oct 2019 | 36 seconds |
| Read alignment to reference genome | 01:47:35 08 Oct 2019 | 01:52:34 08 Oct 2019 | 4 minutes 59 seconds |
| Preprocessing alignments for candidate junction identification | 01:52:34 08 Oct 2019 | 01:53:03 08 Oct 2019 | 29 seconds |
| Preliminary analysis of coverage distribution | 01:53:03 08 Oct 2019 | 01:53:57 08 Oct 2019 | 54 seconds |
| Identifying junction candidates | 01:53:57 08 Oct 2019 | 01:55:16 08 Oct 2019 | 1 minute 19 seconds |
| Re-alignment to junction candidates | 01:55:16 08 Oct 2019 | 01:56:41 08 Oct 2019 | 1 minute 25 seconds |
| Resolving best read alignments | 01:56:41 08 Oct 2019 | 01:57:29 08 Oct 2019 | 48 seconds |
| Creating BAM files | 01:57:29 08 Oct 2019 | 01:58:18 08 Oct 2019 | 49 seconds |
| Tabulating error counts | 01:58:18 08 Oct 2019 | 01:58:41 08 Oct 2019 | 23 seconds |
| Re-calibrating base error rates | 01:58:41 08 Oct 2019 | 01:58:43 08 Oct 2019 | 2 seconds |
| Examining read alignment evidence | 01:58:43 08 Oct 2019 | 02:03:02 08 Oct 2019 | 4 minutes 19 seconds |
| Polymorphism statistics | 02:03:02 08 Oct 2019 | 02:03:03 08 Oct 2019 | 1 second |
| Output | 02:03:03 08 Oct 2019 | 02:03:13 08 Oct 2019 | 10 seconds |
| Total | 16 minutes 14 seconds | ||
