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 | J0-C1_S82_R1_001.good.fq | 4,436,370 | 275,004,191 | 100.0% | 62.0 bases | 71 bases | 97.6% |
total | 4,436,370 | 275,004,191 | 100.0% | 62.0 bases | 71 bases | 97.6% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | W3110S.gb | 4,646,334 | 57.9 | 6.0 | 100.0% | Escherichia coli str. K-12 substr. W3110 DNA, complete genome. |
total | 4,646,334 | 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 | 22235 |
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 | 253 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.008 |
reference sequence | pr(no read start) |
---|---|
W3110S.gb | 0.70901 |
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 | ≤ 0 |
Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction | ≥ 6 |
option | value |
---|---|
Mode | Full Polymorphism |
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 | 2 |
Polymorphism frequency cutoff | 0.05 |
Polymorphism minimum variant coverage each strand | 2 |
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 | ≥3 bases |
Skip base substitutions when they create a homopolymer flanked on each side by | ≥5 bases |
program | version |
---|---|
bowtie2 | 2.3.4.1 |
R | 3.4.4 |
step | start | end | elapsed |
---|---|---|---|
Read and reference sequence file input | 07:41:33 10 Dec 2019 | 07:42:18 10 Dec 2019 | 45 seconds |
Read alignment to reference genome | 07:42:18 10 Dec 2019 | 07:47:31 10 Dec 2019 | 5 minutes 13 seconds |
Preprocessing alignments for candidate junction identification | 07:47:31 10 Dec 2019 | 07:48:33 10 Dec 2019 | 1 minute 2 seconds |
Preliminary analysis of coverage distribution | 07:48:33 10 Dec 2019 | 07:49:59 10 Dec 2019 | 1 minute 26 seconds |
Identifying junction candidates | 07:49:59 10 Dec 2019 | 07:50:03 10 Dec 2019 | 4 seconds |
Re-alignment to junction candidates | 07:50:03 10 Dec 2019 | 07:51:29 10 Dec 2019 | 1 minute 26 seconds |
Resolving best read alignments | 07:51:29 10 Dec 2019 | 07:52:57 10 Dec 2019 | 1 minute 28 seconds |
Creating BAM files | 07:52:57 10 Dec 2019 | 07:54:16 10 Dec 2019 | 1 minute 19 seconds |
Tabulating error counts | 07:54:16 10 Dec 2019 | 07:54:41 10 Dec 2019 | 25 seconds |
Re-calibrating base error rates | 07:54:41 10 Dec 2019 | 07:54:41 10 Dec 2019 | 0 seconds |
Examining read alignment evidence | 07:54:41 10 Dec 2019 | 08:02:21 10 Dec 2019 | 7 minutes 40 seconds |
Polymorphism statistics | 08:02:21 10 Dec 2019 | 08:02:22 10 Dec 2019 | 1 second |
Output | 08:02:22 10 Dec 2019 | 08:02:56 10 Dec 2019 | 34 seconds |
Total | 21 minutes 23 seconds |