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-19_S19_L001_R1_001.good.fq | 376,483 | 54,160,303 | 100.0% | 143.9 bases | 149 bases | 93.7% |
errors | ALE-19_S19_L001_R2_001.good.fq | 376,483 | 54,034,265 | 100.0% | 143.5 bases | 149 bases | 93.9% |
errors | ALE-19_S19_L002_R1_001.good.fq | 371,933 | 53,416,712 | 100.0% | 143.6 bases | 149 bases | 95.2% |
errors | ALE-19_S19_L002_R2_001.good.fq | 371,933 | 53,336,805 | 100.0% | 143.4 bases | 149 bases | 94.2% |
errors | ALE-19_S19_L003_R1_001.good.fq | 385,972 | 55,424,187 | 100.0% | 143.6 bases | 149 bases | 95.1% |
errors | ALE-19_S19_L003_R2_001.good.fq | 385,972 | 55,320,679 | 100.0% | 143.3 bases | 149 bases | 94.8% |
errors | ALE-19_S19_L004_R1_001.good.fq | 356,364 | 51,147,955 | 100.0% | 143.5 bases | 149 bases | 95.0% |
errors | ALE-19_S19_L004_R2_001.good.fq | 356,364 | 51,071,171 | 100.0% | 143.3 bases | 149 bases | 93.8% |
total | 2,981,504 | 427,912,077 | 100.0% | 143.5 bases | 149 bases | 94.5% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | NC_002947 | 6,181,873 | 65.5 | 2.9 | 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 | 74047 |
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 | 802 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.040 |
reference sequence | pr(no read start) |
---|---|
NC_002947 | 0.81442 |
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 | ≤ 0 |
Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction | ≥ 6 |
option | value |
---|---|
Mode | Full Polymorphism |
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 | 2 |
Polymorphism frequency cutoff | 0.05 |
Polymorphism minimum variant coverage each strand | 2 |
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 | ≥3 bases |
Skip base substitutions when they create a homopolymer flanked on each side by | ≥5 bases |
program | version |
---|---|
bowtie2 | 2.3.4.1 |
R | 3.4.4 |
step | start | end | elapsed |
---|---|---|---|
Read and reference sequence file input | 03:49:23 18 Feb 2020 | 03:50:08 18 Feb 2020 | 45 seconds |
Read alignment to reference genome | 03:50:08 18 Feb 2020 | 03:56:46 18 Feb 2020 | 6 minutes 38 seconds |
Preprocessing alignments for candidate junction identification | 03:56:46 18 Feb 2020 | 03:57:29 18 Feb 2020 | 43 seconds |
Preliminary analysis of coverage distribution | 03:57:29 18 Feb 2020 | 03:59:12 18 Feb 2020 | 1 minute 43 seconds |
Identifying junction candidates | 03:59:12 18 Feb 2020 | 04:10:27 18 Feb 2020 | 11 minutes 15 seconds |
Re-alignment to junction candidates | 04:10:27 18 Feb 2020 | 04:12:39 18 Feb 2020 | 2 minutes 12 seconds |
Resolving best read alignments | 04:12:39 18 Feb 2020 | 04:13:44 18 Feb 2020 | 1 minute 5 seconds |
Creating BAM files | 04:13:44 18 Feb 2020 | 04:15:20 18 Feb 2020 | 1 minute 36 seconds |
Tabulating error counts | 04:15:20 18 Feb 2020 | 04:15:51 18 Feb 2020 | 31 seconds |
Re-calibrating base error rates | 04:15:51 18 Feb 2020 | 04:15:54 18 Feb 2020 | 3 seconds |
Examining read alignment evidence | 04:15:54 18 Feb 2020 | 04:34:08 18 Feb 2020 | 18 minutes 14 seconds |
Polymorphism statistics | 04:34:08 18 Feb 2020 | 04:34:10 18 Feb 2020 | 2 seconds |
Output | 04:34:10 18 Feb 2020 | 04:38:47 18 Feb 2020 | 4 minutes 37 seconds |
Total | 49 minutes 24 seconds |