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-85_S85_L001_R1_001_3rd_copy.good.fq | 375,293 | 52,485,425 | 100.0% | 139.9 bases | 149 bases | 93.2% |
errors | ALE-85_S85_L001_R2_001_3rd_copy.good.fq | 375,293 | 52,215,571 | 100.0% | 139.1 bases | 149 bases | 94.1% |
errors | ALE-85_S85_L002_R1_001_3rd_copy.good.fq | 375,498 | 52,428,615 | 100.0% | 139.6 bases | 149 bases | 94.7% |
errors | ALE-85_S85_L002_R2_001_3rd_copy.good.fq | 375,498 | 52,228,642 | 100.0% | 139.1 bases | 149 bases | 94.8% |
errors | ALE-85_S85_L003_R1_001_3rd_copy.good.fq | 382,546 | 53,375,728 | 100.0% | 139.5 bases | 149 bases | 94.6% |
errors | ALE-85_S85_L003_R2_001_3rd_copy.good.fq | 382,546 | 53,130,390 | 100.0% | 138.9 bases | 149 bases | 95.4% |
errors | ALE-85_S85_L004_R1_001_3rd_copy.good.fq | 361,581 | 50,446,408 | 100.0% | 139.5 bases | 149 bases | 94.4% |
errors | ALE-85_S85_L004_R2_001_3rd_copy.good.fq | 361,581 | 50,255,031 | 100.0% | 139.0 bases | 149 bases | 94.5% |
total | 2,989,836 | 416,565,810 | 100.0% | 139.3 bases | 149 bases | 94.5% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | NC_002947 | 6,181,873 | 63.8 | 2.1 | 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 | 65264 |
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 | 888 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.044 |
reference sequence | pr(no read start) |
---|---|
NC_002947 | 0.81039 |
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 | 23:26:47 17 Feb 2020 | 23:27:31 17 Feb 2020 | 44 seconds |
Read alignment to reference genome | 23:27:31 17 Feb 2020 | 23:33:59 17 Feb 2020 | 6 minutes 28 seconds |
Preprocessing alignments for candidate junction identification | 23:33:59 17 Feb 2020 | 23:34:41 17 Feb 2020 | 42 seconds |
Preliminary analysis of coverage distribution | 23:34:41 17 Feb 2020 | 23:36:19 17 Feb 2020 | 1 minute 38 seconds |
Identifying junction candidates | 23:36:19 17 Feb 2020 | 23:50:50 17 Feb 2020 | 14 minutes 31 seconds |
Re-alignment to junction candidates | 23:50:50 17 Feb 2020 | 23:53:01 17 Feb 2020 | 2 minutes 11 seconds |
Resolving best read alignments | 23:53:01 17 Feb 2020 | 23:54:05 17 Feb 2020 | 1 minute 4 seconds |
Creating BAM files | 23:54:05 17 Feb 2020 | 23:55:37 17 Feb 2020 | 1 minute 32 seconds |
Tabulating error counts | 23:55:37 17 Feb 2020 | 23:56:07 17 Feb 2020 | 30 seconds |
Re-calibrating base error rates | 23:56:07 17 Feb 2020 | 23:56:10 17 Feb 2020 | 3 seconds |
Examining read alignment evidence | 23:56:10 17 Feb 2020 | 00:02:00 18 Feb 2020 | 5 minutes 50 seconds |
Polymorphism statistics | 00:02:00 18 Feb 2020 | 00:02:01 18 Feb 2020 | 1 second |
Output | 00:02:01 18 Feb 2020 | 00:02:53 18 Feb 2020 | 52 seconds |
Total | 36 minutes 6 seconds |