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-82_S82_L001_R1_001.good.fq | 437,920 | 62,352,627 | 100.0% | 142.4 bases | 149 bases | 93.5% |
errors | ALE-82_S82_L001_R2_001.good.fq | 437,920 | 62,120,731 | 100.0% | 141.9 bases | 149 bases | 93.9% |
errors | ALE-82_S82_L002_R1_001.good.fq | 427,502 | 60,782,125 | 100.0% | 142.2 bases | 149 bases | 94.8% |
errors | ALE-82_S82_L002_R2_001.good.fq | 427,502 | 60,607,116 | 100.0% | 141.8 bases | 149 bases | 94.3% |
errors | ALE-82_S82_L003_R1_001.good.fq | 448,891 | 63,764,399 | 100.0% | 142.0 bases | 149 bases | 94.8% |
errors | ALE-82_S82_L003_R2_001.good.fq | 448,891 | 63,548,473 | 100.0% | 141.6 bases | 149 bases | 94.9% |
errors | ALE-82_S82_L004_R1_001.good.fq | 410,390 | 58,294,460 | 100.0% | 142.0 bases | 149 bases | 94.7% |
errors | ALE-82_S82_L004_R2_001.good.fq | 410,390 | 58,127,659 | 100.0% | 141.6 bases | 149 bases | 94.0% |
total | 3,449,406 | 489,597,590 | 100.0% | 141.9 bases | 149 bases | 94.4% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | NC_002947 | 6,181,873 | 75.1 | 2.4 | 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 | 80144 |
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 | 945 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.047 |
reference sequence | pr(no read start) |
---|---|
NC_002947 | 0.78729 |
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 | 08:25:26 18 Feb 2020 | 08:26:17 18 Feb 2020 | 51 seconds |
Read alignment to reference genome | 08:26:18 18 Feb 2020 | 08:33:53 18 Feb 2020 | 7 minutes 35 seconds |
Preprocessing alignments for candidate junction identification | 08:33:53 18 Feb 2020 | 08:34:42 18 Feb 2020 | 49 seconds |
Preliminary analysis of coverage distribution | 08:34:42 18 Feb 2020 | 08:36:38 18 Feb 2020 | 1 minute 56 seconds |
Identifying junction candidates | 08:36:38 18 Feb 2020 | 08:52:31 18 Feb 2020 | 15 minutes 53 seconds |
Re-alignment to junction candidates | 08:52:31 18 Feb 2020 | 08:55:06 18 Feb 2020 | 2 minutes 35 seconds |
Resolving best read alignments | 08:55:06 18 Feb 2020 | 08:56:21 18 Feb 2020 | 1 minute 15 seconds |
Creating BAM files | 08:56:21 18 Feb 2020 | 08:58:10 18 Feb 2020 | 1 minute 49 seconds |
Tabulating error counts | 08:58:10 18 Feb 2020 | 08:58:46 18 Feb 2020 | 36 seconds |
Re-calibrating base error rates | 08:58:46 18 Feb 2020 | 08:58:49 18 Feb 2020 | 3 seconds |
Examining read alignment evidence | 08:58:49 18 Feb 2020 | 09:05:41 18 Feb 2020 | 6 minutes 52 seconds |
Polymorphism statistics | 09:05:41 18 Feb 2020 | 09:05:41 18 Feb 2020 | 0 seconds |
Output | 09:05:41 18 Feb 2020 | 09:06:41 18 Feb 2020 | 1 minute 0 seconds |
Total | 41 minutes 14 seconds |