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-80_S80_L001_R1_001.good.fq | 361,100 | 51,810,302 | 100.0% | 143.5 bases | 149 bases | 93.5% |
errors | ALE-80_S80_L001_R2_001.good.fq | 361,100 | 51,634,169 | 100.0% | 143.0 bases | 149 bases | 93.9% |
errors | ALE-80_S80_L002_R1_001.good.fq | 348,729 | 49,948,381 | 100.0% | 143.2 bases | 149 bases | 94.9% |
errors | ALE-80_S80_L002_R2_001.good.fq | 348,729 | 49,805,953 | 100.0% | 142.8 bases | 149 bases | 94.5% |
errors | ALE-80_S80_L003_R1_001.good.fq | 366,105 | 52,422,909 | 100.0% | 143.2 bases | 149 bases | 94.9% |
errors | ALE-80_S80_L003_R2_001.good.fq | 366,105 | 52,250,952 | 100.0% | 142.7 bases | 149 bases | 95.1% |
errors | ALE-80_S80_L004_R1_001.good.fq | 334,477 | 47,892,043 | 100.0% | 143.2 bases | 149 bases | 94.7% |
errors | ALE-80_S80_L004_R2_001.good.fq | 334,477 | 47,754,635 | 100.0% | 142.8 bases | 149 bases | 94.0% |
total | 2,820,822 | 403,519,344 | 100.0% | 143.1 bases | 149 bases | 94.4% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | NC_002947 | 6,181,873 | 61.9 | 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 | 59667 |
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 | 955 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.047 |
reference sequence | pr(no read start) |
---|---|
NC_002947 | 0.82196 |
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 | 19:50:48 18 Feb 2020 | 19:51:30 18 Feb 2020 | 42 seconds |
Read alignment to reference genome | 19:51:30 18 Feb 2020 | 19:57:45 18 Feb 2020 | 6 minutes 15 seconds |
Preprocessing alignments for candidate junction identification | 19:57:45 18 Feb 2020 | 19:58:24 18 Feb 2020 | 39 seconds |
Preliminary analysis of coverage distribution | 19:58:24 18 Feb 2020 | 20:00:00 18 Feb 2020 | 1 minute 36 seconds |
Identifying junction candidates | 20:00:00 18 Feb 2020 | 20:08:34 18 Feb 2020 | 8 minutes 34 seconds |
Re-alignment to junction candidates | 20:08:34 18 Feb 2020 | 20:10:42 18 Feb 2020 | 2 minutes 8 seconds |
Resolving best read alignments | 20:10:42 18 Feb 2020 | 20:11:43 18 Feb 2020 | 1 minute 1 second |
Creating BAM files | 20:11:43 18 Feb 2020 | 20:13:14 18 Feb 2020 | 1 minute 31 seconds |
Tabulating error counts | 20:13:14 18 Feb 2020 | 20:13:43 18 Feb 2020 | 29 seconds |
Re-calibrating base error rates | 20:13:43 18 Feb 2020 | 20:13:46 18 Feb 2020 | 3 seconds |
Examining read alignment evidence | 20:13:46 18 Feb 2020 | 20:19:28 18 Feb 2020 | 5 minutes 42 seconds |
Polymorphism statistics | 20:19:28 18 Feb 2020 | 20:19:29 18 Feb 2020 | 1 second |
Output | 20:19:29 18 Feb 2020 | 20:20:26 18 Feb 2020 | 57 seconds |
Total | 29 minutes 38 seconds |