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 | mix-2_S30_L001_R1_001.good.fq | 211,066 | 30,778,859 | 100.0% | 145.8 bases | 148 bases | 97.2% |
errors | mix-2_S30_L001_R2_001.good.fq | 211,066 | 30,754,187 | 100.0% | 145.7 bases | 148 bases | 96.7% |
errors | mix-2_S30_L002_R1_001.good.fq | 193,954 | 28,276,968 | 100.0% | 145.8 bases | 148 bases | 97.3% |
errors | mix-2_S30_L002_R2_001.good.fq | 193,954 | 28,254,087 | 100.0% | 145.7 bases | 148 bases | 96.6% |
errors | mix-2_S30_L003_R1_001.good.fq | 198,835 | 28,993,323 | 100.0% | 145.8 bases | 148 bases | 97.3% |
errors | mix-2_S30_L003_R2_001.good.fq | 198,835 | 28,969,169 | 100.0% | 145.7 bases | 148 bases | 96.7% |
errors | mix-2_S30_L004_R1_001.good.fq | 187,237 | 27,304,919 | 100.0% | 145.8 bases | 148 bases | 97.3% |
errors | mix-2_S30_L004_R2_001.good.fq | 187,237 | 27,283,630 | 100.0% | 145.7 bases | 148 bases | 96.5% |
total | 1,582,184 | 230,615,142 | 100.0% | 145.8 bases | 148 bases | 97.0% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | NC_002947 | 6,181,873 | 36.4 | 2.1 | 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 | 18810 |
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 | 1241 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.061 |
reference sequence | pr(no read start) |
---|---|
NC_002947 | 0.89328 |
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 | 08:07:10 19 Feb 2020 | 08:07:35 19 Feb 2020 | 25 seconds |
Read alignment to reference genome | 08:07:35 19 Feb 2020 | 08:10:58 19 Feb 2020 | 3 minutes 23 seconds |
Preprocessing alignments for candidate junction identification | 08:10:58 19 Feb 2020 | 08:11:21 19 Feb 2020 | 23 seconds |
Preliminary analysis of coverage distribution | 08:11:21 19 Feb 2020 | 08:12:12 19 Feb 2020 | 51 seconds |
Identifying junction candidates | 08:12:12 19 Feb 2020 | 08:12:22 19 Feb 2020 | 10 seconds |
Re-alignment to junction candidates | 08:12:22 19 Feb 2020 | 08:13:39 19 Feb 2020 | 1 minute 17 seconds |
Resolving best read alignments | 08:13:39 19 Feb 2020 | 08:14:14 19 Feb 2020 | 35 seconds |
Creating BAM files | 08:14:14 19 Feb 2020 | 08:15:02 19 Feb 2020 | 48 seconds |
Tabulating error counts | 08:15:02 19 Feb 2020 | 08:15:18 19 Feb 2020 | 16 seconds |
Re-calibrating base error rates | 08:15:18 19 Feb 2020 | 08:15:21 19 Feb 2020 | 3 seconds |
Examining read alignment evidence | 08:15:21 19 Feb 2020 | 08:18:51 19 Feb 2020 | 3 minutes 30 seconds |
Polymorphism statistics | 08:18:51 19 Feb 2020 | 08:18:52 19 Feb 2020 | 1 second |
Output | 08:18:52 19 Feb 2020 | 08:19:17 19 Feb 2020 | 25 seconds |
Total | 12 minutes 7 seconds |