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 | Pputida_TALE__HGL_Pputida_136_S124_L001_R1_001.good.fq | 6,907,717 | 1,022,632,798 | 100.0% | 148.0 bases | 150 bases | 96.1% |
errors | Pputida_TALE__HGL_Pputida_136_S124_L001_R2_001.good.fq | 6,907,717 | 1,022,632,798 | 100.0% | 148.0 bases | 150 bases | 95.5% |
total | 13,815,434 | 2,045,265,596 | 100.0% | 148.0 bases | 150 bases | 95.8% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | NC_002947 | 6,181,929 | 315.6 | 5.8 | 100.0% | Pseudomonas putida KT2440 chromosome, complete genome. |
total | 6,181,929 | 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 | 100000 |
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 | 1092 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.055 |
reference sequence | pr(no read start) |
---|---|
NC_002947 | 0.49874 |
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 | 06:53:18 30 Mar 2020 | 06:56:54 30 Mar 2020 | 3 minutes 36 seconds |
Read alignment to reference genome | 06:56:54 30 Mar 2020 | 07:27:28 30 Mar 2020 | 30 minutes 34 seconds |
Preprocessing alignments for candidate junction identification | 07:27:28 30 Mar 2020 | 07:30:48 30 Mar 2020 | 3 minutes 20 seconds |
Preliminary analysis of coverage distribution | 07:30:48 30 Mar 2020 | 07:37:04 30 Mar 2020 | 6 minutes 16 seconds |
Identifying junction candidates | 07:37:04 30 Mar 2020 | 07:42:55 30 Mar 2020 | 5 minutes 51 seconds |
Re-alignment to junction candidates | 07:42:55 30 Mar 2020 | 07:51:18 30 Mar 2020 | 8 minutes 23 seconds |
Resolving best read alignments | 07:51:18 30 Mar 2020 | 07:57:46 30 Mar 2020 | 6 minutes 28 seconds |
Creating BAM files | 07:57:46 30 Mar 2020 | 08:03:13 30 Mar 2020 | 5 minutes 27 seconds |
Tabulating error counts | 08:03:13 30 Mar 2020 | 08:06:19 30 Mar 2020 | 3 minutes 6 seconds |
Re-calibrating base error rates | 08:06:19 30 Mar 2020 | 08:06:21 30 Mar 2020 | 2 seconds |
Examining read alignment evidence | 08:06:21 30 Mar 2020 | 08:36:13 30 Mar 2020 | 29 minutes 52 seconds |
Polymorphism statistics | 08:36:13 30 Mar 2020 | 08:36:25 30 Mar 2020 | 12 seconds |
Output | 08:36:25 30 Mar 2020 | 08:37:35 30 Mar 2020 | 1 minute 10 seconds |
Total | 1 hour 44 minutes 17 seconds |