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 | ERR1351683_R1.good.fq | 3,432,515 | 432,320,498 | 100.0% | 125.9 bases | 126 bases | 99.8% |
errors | ERR1351683_R2.good.fq | 3,432,515 | 432,320,498 | 100.0% | 125.9 bases | 126 bases | 99.6% |
total | 6,865,030 | 864,640,996 | 100.0% | 125.9 bases | 126 bases | 99.7% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | CP009273 | 4,631,469 | 181.5 | 2.6 | 97.9% | Escherichia coli BW25113, complete genome. |
coverage | distribution | KX077536 | 8,187 | 2515.8 | 27.8 | 2.1% | Vector pCBB, complete sequence. |
total | 4,639,656 | 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 | 6726 |
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 | 48 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.003 |
reference sequence | pr(no read start) |
---|---|
CP009273 | 0.50370 |
KX077536 | 0.01306 |
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 | 12:37:04 30 Mar 2021 | 12:38:58 30 Mar 2021 | 1 minute 54 seconds |
Read alignment to reference genome | 12:38:59 30 Mar 2021 | 12:52:56 30 Mar 2021 | 13 minutes 57 seconds |
Preprocessing alignments for candidate junction identification | 12:52:56 30 Mar 2021 | 12:54:32 30 Mar 2021 | 1 minute 36 seconds |
Preliminary analysis of coverage distribution | 12:54:32 30 Mar 2021 | 12:58:03 30 Mar 2021 | 3 minutes 31 seconds |
Identifying junction candidates | 12:58:03 30 Mar 2021 | 12:58:04 30 Mar 2021 | 1 second |
Re-alignment to junction candidates | 12:58:04 30 Mar 2021 | 13:01:44 30 Mar 2021 | 3 minutes 40 seconds |
Resolving best read alignments | 13:01:44 30 Mar 2021 | 13:03:42 30 Mar 2021 | 1 minute 58 seconds |
Creating BAM files | 13:03:42 30 Mar 2021 | 13:06:48 30 Mar 2021 | 3 minutes 6 seconds |
Tabulating error counts | 13:06:48 30 Mar 2021 | 13:08:11 30 Mar 2021 | 1 minute 23 seconds |
Re-calibrating base error rates | 13:08:11 30 Mar 2021 | 13:08:13 30 Mar 2021 | 2 seconds |
Examining read alignment evidence | 13:08:13 30 Mar 2021 | 13:22:59 30 Mar 2021 | 14 minutes 46 seconds |
Polymorphism statistics | 13:22:59 30 Mar 2021 | 13:22:59 30 Mar 2021 | 0 seconds |
Output | 13:22:59 30 Mar 2021 | 13:23:23 30 Mar 2021 | 24 seconds |
Total | 46 minutes 18 seconds |