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-1_S29_L001_R1_001.good.fq | 181,119 | 26,523,515 | 100.0% | 146.4 bases | 148 bases | 97.2% |
errors | mix-1_S29_L001_R2_001.good.fq | 181,119 | 26,509,043 | 100.0% | 146.4 bases | 148 bases | 96.4% |
errors | mix-1_S29_L002_R1_001.good.fq | 165,913 | 24,291,258 | 100.0% | 146.4 bases | 148 bases | 97.2% |
errors | mix-1_S29_L002_R2_001.good.fq | 165,913 | 24,278,010 | 100.0% | 146.3 bases | 148 bases | 96.1% |
errors | mix-1_S29_L003_R1_001.good.fq | 166,349 | 24,349,444 | 100.0% | 146.4 bases | 148 bases | 97.2% |
errors | mix-1_S29_L003_R2_001.good.fq | 166,349 | 24,335,409 | 100.0% | 146.3 bases | 148 bases | 96.3% |
errors | mix-1_S29_L004_R1_001.good.fq | 156,706 | 22,933,881 | 100.0% | 146.3 bases | 148 bases | 97.1% |
errors | mix-1_S29_L004_R2_001.good.fq | 156,706 | 22,922,177 | 100.0% | 146.3 bases | 148 bases | 95.9% |
total | 1,340,174 | 196,142,737 | 100.0% | 146.4 bases | 148 bases | 96.7% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | NC_002947 | 6,181,873 | 30.6 | 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 | 19956 |
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 | 926 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.046 |
reference sequence | pr(no read start) |
---|---|
NC_002947 | 0.90916 |
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 | 00:02:54 18 Feb 2020 | 00:03:15 18 Feb 2020 | 21 seconds |
Read alignment to reference genome | 00:03:15 18 Feb 2020 | 00:06:14 18 Feb 2020 | 2 minutes 59 seconds |
Preprocessing alignments for candidate junction identification | 00:06:14 18 Feb 2020 | 00:06:33 18 Feb 2020 | 19 seconds |
Preliminary analysis of coverage distribution | 00:06:33 18 Feb 2020 | 00:07:18 18 Feb 2020 | 45 seconds |
Identifying junction candidates | 00:07:18 18 Feb 2020 | 00:07:28 18 Feb 2020 | 10 seconds |
Re-alignment to junction candidates | 00:07:28 18 Feb 2020 | 00:08:30 18 Feb 2020 | 1 minute 2 seconds |
Resolving best read alignments | 00:08:30 18 Feb 2020 | 00:09:00 18 Feb 2020 | 30 seconds |
Creating BAM files | 00:09:00 18 Feb 2020 | 00:09:41 18 Feb 2020 | 41 seconds |
Tabulating error counts | 00:09:41 18 Feb 2020 | 00:09:55 18 Feb 2020 | 14 seconds |
Re-calibrating base error rates | 00:09:55 18 Feb 2020 | 00:09:58 18 Feb 2020 | 3 seconds |
Examining read alignment evidence | 00:09:58 18 Feb 2020 | 00:13:04 18 Feb 2020 | 3 minutes 6 seconds |
Polymorphism statistics | 00:13:04 18 Feb 2020 | 00:13:05 18 Feb 2020 | 1 second |
Output | 00:13:05 18 Feb 2020 | 00:13:29 18 Feb 2020 | 24 seconds |
Total | 10 minutes 35 seconds |