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_122_S110_L001_R1_001.good.fq | 10,200,256 | 1,517,127,327 | 100.0% | 148.7 bases | 150 bases | 95.3% |
errors | Pputida_TALE__HGL_Pputida_122_S110_L001_R2_001.good.fq | 10,200,256 | 1,517,127,327 | 100.0% | 148.7 bases | 150 bases | 94.9% |
total | 20,400,512 | 3,034,254,654 | 100.0% | 148.7 bases | 150 bases | 95.1% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | NC_002947 | 6,181,929 | 439.1 | 6.4 | 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 | 495 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.025 |
reference sequence | pr(no read start) |
---|---|
NC_002947 | 0.41998 |
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 | 23:14:34 29 Mar 2020 | 23:19:56 29 Mar 2020 | 5 minutes 22 seconds |
Read alignment to reference genome | 23:19:56 29 Mar 2020 | 00:07:22 30 Mar 2020 | 47 minutes 26 seconds |
Preprocessing alignments for candidate junction identification | 00:07:22 30 Mar 2020 | 00:13:03 30 Mar 2020 | 5 minutes 41 seconds |
Preliminary analysis of coverage distribution | 00:13:03 30 Mar 2020 | 00:23:02 30 Mar 2020 | 9 minutes 59 seconds |
Identifying junction candidates | 00:23:02 30 Mar 2020 | 00:24:45 30 Mar 2020 | 1 minute 43 seconds |
Re-alignment to junction candidates | 00:24:45 30 Mar 2020 | 00:36:26 30 Mar 2020 | 11 minutes 41 seconds |
Resolving best read alignments | 00:36:26 30 Mar 2020 | 00:46:54 30 Mar 2020 | 10 minutes 28 seconds |
Creating BAM files | 00:46:54 30 Mar 2020 | 00:55:26 30 Mar 2020 | 8 minutes 32 seconds |
Tabulating error counts | 00:55:26 30 Mar 2020 | 01:00:48 30 Mar 2020 | 5 minutes 22 seconds |
Re-calibrating base error rates | 01:00:48 30 Mar 2020 | 01:00:50 30 Mar 2020 | 2 seconds |
Examining read alignment evidence | 01:00:50 30 Mar 2020 | 01:47:43 30 Mar 2020 | 46 minutes 53 seconds |
Polymorphism statistics | 01:47:43 30 Mar 2020 | 01:48:00 30 Mar 2020 | 17 seconds |
Output | 01:48:00 30 Mar 2020 | 01:49:30 30 Mar 2020 | 1 minute 30 seconds |
Total | 2 hours 34 minutes 56 seconds |