breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
read file | reads | bases | passed filters | average | longest | mapped | |
---|---|---|---|---|---|---|---|
errors | Plate-1-BOP-1000-ACEF-END-4_S8_L001_R1_001.good.fq | 392,231 | 56,255,787 | 100.0% | 143.4 bases | 149 bases | 98.1% |
errors | Plate-1-BOP-1000-ACEF-END-4_S8_L001_R2_001.good.fq | 392,231 | 56,084,128 | 100.0% | 143.0 bases | 149 bases | 98.0% |
errors | Plate-1-BOP-1000-ACEF-END-4_S8_L002_R1_001.good.fq | 363,986 | 52,240,691 | 100.0% | 143.5 bases | 149 bases | 98.2% |
errors | Plate-1-BOP-1000-ACEF-END-4_S8_L002_R2_001.good.fq | 363,986 | 52,097,322 | 100.0% | 143.1 bases | 149 bases | 97.6% |
errors | Plate-1-BOP-1000-ACEF-END-4_S8_L003_R1_001.good.fq | 380,461 | 54,561,108 | 100.0% | 143.4 bases | 149 bases | 98.0% |
errors | Plate-1-BOP-1000-ACEF-END-4_S8_L003_R2_001.good.fq | 380,461 | 54,390,034 | 100.0% | 143.0 bases | 149 bases | 97.8% |
errors | Plate-1-BOP-1000-ACEF-END-4_S8_L004_R1_001.good.fq | 388,301 | 55,653,554 | 100.0% | 143.3 bases | 149 bases | 98.2% |
errors | Plate-1-BOP-1000-ACEF-END-4_S8_L004_R2_001.good.fq | 388,301 | 55,501,351 | 100.0% | 142.9 bases | 149 bases | 97.9% |
total | 3,049,958 | 436,783,975 | 100.0% | 143.2 bases | 149 bases | 98.0% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | NC_000913 | 4,641,652 | 91.0 | 2.9 | 100.0% | Escherichia coli str. K-12 substr. MG1655, complete genome. |
total | 4,641,652 | 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 | 15458 |
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 | 1497 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.098 |
reference sequence | pr(no read start) |
---|---|
NC_000913 | 0.75529 |
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 |
Minimum probablilty assigned that no mapped read will start at a given position and strand for junction prediction | 0.1 |
Junction allow suboptimal matches | FALSE |
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 | 2.2.6 |
R | 3.4.4 |
step | start | end | elapsed |
---|---|---|---|
Read and reference sequence file input | 10:34:47 06 Apr 2022 | 10:35:42 06 Apr 2022 | 55 seconds |
Read alignment to reference genome | 10:35:43 06 Apr 2022 | 10:41:49 06 Apr 2022 | 6 minutes 6 seconds |
Preprocessing alignments for candidate junction identification | 10:41:49 06 Apr 2022 | 10:42:28 06 Apr 2022 | 39 seconds |
Preliminary analysis of coverage distribution | 10:42:28 06 Apr 2022 | 10:44:20 06 Apr 2022 | 1 minute 52 seconds |
Identifying junction candidates | 10:44:20 06 Apr 2022 | 10:44:30 06 Apr 2022 | 10 seconds |
Re-alignment to junction candidates | 10:44:30 06 Apr 2022 | 10:46:34 06 Apr 2022 | 2 minutes 4 seconds |
Resolving best read alignments | 10:46:34 06 Apr 2022 | 10:47:31 06 Apr 2022 | 57 seconds |
Creating BAM files | 10:47:31 06 Apr 2022 | 10:49:12 06 Apr 2022 | 1 minute 41 seconds |
Tabulating error counts | 10:49:12 06 Apr 2022 | 10:49:51 06 Apr 2022 | 39 seconds |
Re-calibrating base error rates | 10:49:51 06 Apr 2022 | 10:49:54 06 Apr 2022 | 3 seconds |
Examining read alignment evidence | 10:49:54 06 Apr 2022 | 10:58:05 06 Apr 2022 | 8 minutes 11 seconds |
Polymorphism statistics | 10:58:05 06 Apr 2022 | 10:58:05 06 Apr 2022 | 0 seconds |
Output | 10:58:05 06 Apr 2022 | 10:58:18 06 Apr 2022 | 13 seconds |
Total | 23 minutes 30 seconds |