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 | ALE-65_S65_L001_R1_001.good.fq | 403,929 | 57,899,993 | 100.0% | 143.3 bases | 149 bases | 94.1% |
errors | ALE-65_S65_L001_R2_001.good.fq | 403,929 | 57,752,024 | 100.0% | 143.0 bases | 149 bases | 94.3% |
errors | ALE-65_S65_L002_R1_001.good.fq | 397,486 | 56,889,773 | 100.0% | 143.1 bases | 149 bases | 95.6% |
errors | ALE-65_S65_L002_R2_001.good.fq | 397,486 | 56,789,312 | 100.0% | 142.9 bases | 149 bases | 94.8% |
errors | ALE-65_S65_L003_R1_001.good.fq | 413,305 | 59,165,711 | 100.0% | 143.2 bases | 149 bases | 95.5% |
errors | ALE-65_S65_L003_R2_001.good.fq | 413,305 | 59,034,969 | 100.0% | 142.8 bases | 149 bases | 95.4% |
errors | ALE-65_S65_L004_R1_001.good.fq | 381,417 | 54,565,923 | 100.0% | 143.1 bases | 149 bases | 95.5% |
errors | ALE-65_S65_L004_R2_001.good.fq | 381,417 | 54,472,805 | 100.0% | 142.8 bases | 149 bases | 94.5% |
total | 3,192,274 | 456,570,510 | 100.0% | 143.0 bases | 149 bases | 95.0% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | NC_002947 | 6,181,873 | 70.4 | 2.2 | 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 | 57672 |
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 | 696 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.034 |
reference sequence | pr(no read start) |
---|---|
NC_002947 | 0.80047 |
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 | 23:10:59 18 Feb 2020 | 23:11:47 18 Feb 2020 | 48 seconds |
Read alignment to reference genome | 23:11:47 18 Feb 2020 | 23:18:41 18 Feb 2020 | 6 minutes 54 seconds |
Preprocessing alignments for candidate junction identification | 23:18:41 18 Feb 2020 | 23:19:25 18 Feb 2020 | 44 seconds |
Preliminary analysis of coverage distribution | 23:19:25 18 Feb 2020 | 23:21:14 18 Feb 2020 | 1 minute 49 seconds |
Identifying junction candidates | 23:21:14 18 Feb 2020 | 23:26:13 18 Feb 2020 | 4 minutes 59 seconds |
Re-alignment to junction candidates | 23:26:13 18 Feb 2020 | 23:28:30 18 Feb 2020 | 2 minutes 17 seconds |
Resolving best read alignments | 23:28:30 18 Feb 2020 | 23:29:40 18 Feb 2020 | 1 minute 10 seconds |
Creating BAM files | 23:29:40 18 Feb 2020 | 23:31:20 18 Feb 2020 | 1 minute 40 seconds |
Tabulating error counts | 23:31:20 18 Feb 2020 | 23:31:54 18 Feb 2020 | 34 seconds |
Re-calibrating base error rates | 23:31:54 18 Feb 2020 | 23:31:56 18 Feb 2020 | 2 seconds |
Examining read alignment evidence | 23:31:56 18 Feb 2020 | 23:38:25 18 Feb 2020 | 6 minutes 29 seconds |
Polymorphism statistics | 23:38:25 18 Feb 2020 | 23:38:26 18 Feb 2020 | 1 second |
Output | 23:38:26 18 Feb 2020 | 23:39:19 18 Feb 2020 | 53 seconds |
Total | 28 minutes 20 seconds |