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 | mix-4_S32_L001_R1_001.good.fq | 206,540 | 30,149,101 | 100.0% | 146.0 bases | 148 bases | 95.6% |
errors | mix-4_S32_L001_R2_001.good.fq | 206,540 | 30,126,797 | 100.0% | 145.9 bases | 148 bases | 95.1% |
errors | mix-4_S32_L002_R1_001.good.fq | 189,733 | 27,687,085 | 100.0% | 145.9 bases | 148 bases | 95.6% |
errors | mix-4_S32_L002_R2_001.good.fq | 189,733 | 27,667,028 | 100.0% | 145.8 bases | 148 bases | 94.7% |
errors | mix-4_S32_L003_R1_001.good.fq | 194,240 | 28,346,482 | 100.0% | 145.9 bases | 148 bases | 95.5% |
errors | mix-4_S32_L003_R2_001.good.fq | 194,240 | 28,326,758 | 100.0% | 145.8 bases | 148 bases | 94.9% |
errors | mix-4_S32_L004_R1_001.good.fq | 181,100 | 26,417,682 | 100.0% | 145.9 bases | 148 bases | 95.6% |
errors | mix-4_S32_L004_R2_001.good.fq | 181,100 | 26,400,543 | 100.0% | 145.8 bases | 148 bases | 94.6% |
total | 1,543,226 | 225,121,476 | 100.0% | 145.9 bases | 148 bases | 95.2% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | NC_002947 | 6,181,873 | 34.4 | 2.0 | 100.0% | Pseudomonas putida KT2440 chromosome, complete genome. |
total | 6,181,873 | 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 | 23756 |
Coverage evenness (position-hash) score of junction candidates | ≥ 2 | ≥ 2 |
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold | 100 ≤ n ≤ 5000 | 1626 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.079 |
reference sequence | pr(no read start) |
---|---|
NC_002947 | 0.89760 |
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 | 06:07:19 18 Feb 2020 | 06:07:43 18 Feb 2020 | 24 seconds |
Read alignment to reference genome | 06:07:43 18 Feb 2020 | 06:11:06 18 Feb 2020 | 3 minutes 23 seconds |
Preprocessing alignments for candidate junction identification | 06:11:06 18 Feb 2020 | 06:11:28 18 Feb 2020 | 22 seconds |
Preliminary analysis of coverage distribution | 06:11:28 18 Feb 2020 | 06:12:19 18 Feb 2020 | 51 seconds |
Identifying junction candidates | 06:12:19 18 Feb 2020 | 06:12:43 18 Feb 2020 | 24 seconds |
Re-alignment to junction candidates | 06:12:43 18 Feb 2020 | 06:14:02 18 Feb 2020 | 1 minute 19 seconds |
Resolving best read alignments | 06:14:02 18 Feb 2020 | 06:14:36 18 Feb 2020 | 34 seconds |
Creating BAM files | 06:14:36 18 Feb 2020 | 06:15:23 18 Feb 2020 | 47 seconds |
Tabulating error counts | 06:15:23 18 Feb 2020 | 06:15:39 18 Feb 2020 | 16 seconds |
Re-calibrating base error rates | 06:15:39 18 Feb 2020 | 06:15:41 18 Feb 2020 | 2 seconds |
Examining read alignment evidence | 06:15:41 18 Feb 2020 | 06:19:05 18 Feb 2020 | 3 minutes 24 seconds |
Polymorphism statistics | 06:19:05 18 Feb 2020 | 06:19:05 18 Feb 2020 | 0 seconds |
Output | 06:19:05 18 Feb 2020 | 06:19:37 18 Feb 2020 | 32 seconds |
Total | 12 minutes 18 seconds |