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breseq version 0.28.1 revision 52323b585d6f
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
read file | reads | bases | passed filters | average | longest | mapped | |
---|---|---|---|---|---|---|---|
errors | ALE-IL19_S27_L001_R1_001 | 2,232,806 | 336,108,059 | 99.7% | 150.5 bases | 151 bases | 99.2% |
errors | ALE-IL19_S27_L001_R2_001 | 2,232,326 | 336,020,781 | 99.7% | 150.5 bases | 151 bases | 97.7% |
errors | ALE-IL19_S27_L002_R1_001 | 2,218,455 | 333,965,986 | 99.7% | 150.5 bases | 151 bases | 99.2% |
errors | ALE-IL19_S27_L002_R2_001 | 2,217,498 | 333,808,006 | 99.7% | 150.5 bases | 151 bases | 97.7% |
errors | ALE-IL19_S27_L003_R1_001 | 2,257,233 | 339,815,470 | 99.8% | 150.5 bases | 151 bases | 99.0% |
errors | ALE-IL19_S27_L003_R2_001 | 2,255,699 | 339,543,900 | 99.8% | 150.5 bases | 151 bases | 97.4% |
errors | ALE-IL19_S27_L004_R1_001 | 2,250,543 | 338,826,053 | 99.8% | 150.6 bases | 151 bases | 99.1% |
errors | ALE-IL19_S27_L004_R2_001 | 2,248,317 | 338,462,254 | 99.7% | 150.5 bases | 151 bases | 97.9% |
total | 17,912,877 | 2,696,550,509 | 99.7% | 150.5 bases | 151 bases | 98.4% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | DH1 | 4,630,707 | 570.5 | 3.8 | 98.2% | Escherichia coli DH1, complete genome. |
total | 4,630,707 | 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 | 14291 |
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 | 174 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.012 |
reference sequence | pr(no read start) |
---|---|
DH1 | 0.26075 |
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 | 0.8 |
Consensus minimum coverage each strand | OFF |
Polymorphism E-value cutoff | 10 |
Polymorphism frequency cutoff | 0.2 |
Polymorphism minimum coverage each strand | 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 |
step | start | end | elapsed |
---|---|---|---|
Read and reference sequence file input | 15:17:45 18 Oct 2016 | 15:27:49 18 Oct 2016 | 10 minutes 4 seconds |
Read alignment to reference genome | 15:27:50 18 Oct 2016 | 17:25:32 18 Oct 2016 | 1 hour 57 minutes 42 seconds |
Preprocessing alignments for candidate junction identification | 17:25:32 18 Oct 2016 | 17:57:57 18 Oct 2016 | 32 minutes 25 seconds |
Preliminary analysis of coverage distribution | 17:57:57 18 Oct 2016 | 18:43:20 18 Oct 2016 | 45 minutes 23 seconds |
Identifying junction candidates | 18:43:20 18 Oct 2016 | 18:44:01 18 Oct 2016 | 41 seconds |
Re-alignment to junction candidates | 18:44:01 18 Oct 2016 | 19:14:50 18 Oct 2016 | 30 minutes 49 seconds |
Resolving alignments with junction candidates | 19:14:50 18 Oct 2016 | 19:59:55 18 Oct 2016 | 45 minutes 5 seconds |
Creating BAM files | 19:59:55 18 Oct 2016 | 20:14:36 18 Oct 2016 | 14 minutes 41 seconds |
Tabulating error counts | 20:14:36 18 Oct 2016 | 20:36:25 18 Oct 2016 | 21 minutes 49 seconds |
Re-calibrating base error rates | 20:36:25 18 Oct 2016 | 20:36:27 18 Oct 2016 | 2 seconds |
Examining read alignment evidence | 20:36:27 18 Oct 2016 | 23:05:28 18 Oct 2016 | 2 hours 29 minutes 1 second |
Polymorphism statistics | 23:05:28 18 Oct 2016 | 23:05:35 18 Oct 2016 | 7 seconds |
Output | 23:05:35 18 Oct 2016 | 23:10:44 18 Oct 2016 | 5 minutes 9 seconds |
Total | 7 hours 52 minutes 58 seconds |