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-46_S46_L001_R1_001.good.fq | 401,699 | 57,766,114 | 100.0% | 143.8 bases | 149 bases | 93.7% |
errors | ALE-46_S46_L001_R2_001.good.fq | 401,699 | 57,575,933 | 100.0% | 143.3 bases | 149 bases | 93.9% |
errors | ALE-46_S46_L002_R1_001.good.fq | 389,963 | 55,990,520 | 100.0% | 143.6 bases | 149 bases | 95.1% |
errors | ALE-46_S46_L002_R2_001.good.fq | 389,963 | 55,855,894 | 100.0% | 143.2 bases | 149 bases | 94.3% |
errors | ALE-46_S46_L003_R1_001.good.fq | 401,950 | 57,671,078 | 100.0% | 143.5 bases | 149 bases | 94.9% |
errors | ALE-46_S46_L003_R2_001.good.fq | 401,950 | 57,505,805 | 100.0% | 143.1 bases | 149 bases | 94.9% |
errors | ALE-46_S46_L004_R1_001.good.fq | 374,215 | 53,691,505 | 100.0% | 143.5 bases | 149 bases | 94.8% |
errors | ALE-46_S46_L004_R2_001.good.fq | 374,215 | 53,559,945 | 100.0% | 143.1 bases | 149 bases | 93.9% |
total | 3,135,654 | 449,616,794 | 100.0% | 143.4 bases | 149 bases | 94.4% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | NC_002947 | 6,181,873 | 69.1 | 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 | 76000 |
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 | 603 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.030 |
reference sequence | pr(no read start) |
---|---|
NC_002947 | 0.80393 |
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 | 21:26:05 17 Feb 2020 | 21:26:52 17 Feb 2020 | 47 seconds |
Read alignment to reference genome | 21:26:52 17 Feb 2020 | 21:33:48 17 Feb 2020 | 6 minutes 56 seconds |
Preprocessing alignments for candidate junction identification | 21:33:48 17 Feb 2020 | 21:34:32 17 Feb 2020 | 44 seconds |
Preliminary analysis of coverage distribution | 21:34:32 17 Feb 2020 | 21:36:19 17 Feb 2020 | 1 minute 47 seconds |
Identifying junction candidates | 21:36:19 17 Feb 2020 | 21:43:50 17 Feb 2020 | 7 minutes 31 seconds |
Re-alignment to junction candidates | 21:43:50 17 Feb 2020 | 21:46:02 17 Feb 2020 | 2 minutes 12 seconds |
Resolving best read alignments | 21:46:02 17 Feb 2020 | 21:47:10 17 Feb 2020 | 1 minute 8 seconds |
Creating BAM files | 21:47:10 17 Feb 2020 | 21:48:50 17 Feb 2020 | 1 minute 40 seconds |
Tabulating error counts | 21:48:50 17 Feb 2020 | 21:49:23 17 Feb 2020 | 33 seconds |
Re-calibrating base error rates | 21:49:23 17 Feb 2020 | 21:49:26 17 Feb 2020 | 3 seconds |
Examining read alignment evidence | 21:49:26 17 Feb 2020 | 21:55:52 17 Feb 2020 | 6 minutes 26 seconds |
Polymorphism statistics | 21:55:52 17 Feb 2020 | 21:55:53 17 Feb 2020 | 1 second |
Output | 21:55:53 17 Feb 2020 | 21:56:33 17 Feb 2020 | 40 seconds |
Total | 30 minutes 28 seconds |