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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-IL42_S50_L001_R1_001 | 1,831,492 | 275,730,399 | 99.4% | 150.5 bases | 151 bases | 99.3% |
errors | ALE-IL42_S50_L001_R2_001 | 1,834,823 | 276,221,773 | 99.6% | 150.5 bases | 151 bases | 97.1% |
errors | ALE-IL42_S50_L002_R1_001 | 1,822,359 | 274,371,317 | 99.4% | 150.6 bases | 151 bases | 99.4% |
errors | ALE-IL42_S50_L002_R2_001 | 1,825,125 | 274,771,874 | 99.6% | 150.5 bases | 151 bases | 97.2% |
errors | ALE-IL42_S50_L003_R1_001 | 1,854,362 | 279,198,684 | 99.6% | 150.6 bases | 151 bases | 99.1% |
errors | ALE-IL42_S50_L003_R2_001 | 1,855,363 | 279,311,843 | 99.7% | 150.5 bases | 151 bases | 96.8% |
errors | ALE-IL42_S50_L004_R1_001 | 1,845,715 | 277,912,083 | 99.7% | 150.6 bases | 151 bases | 99.3% |
errors | ALE-IL42_S50_L004_R2_001 | 1,844,023 | 277,635,580 | 99.7% | 150.6 bases | 151 bases | 97.7% |
total | 14,713,262 | 2,215,153,553 | 99.6% | 150.6 bases | 151 bases | 98.2% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | DH1 | 4,630,707 | 479.3 | 15.4 | 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 | 10134 |
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 | 172 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.012 |
reference sequence | pr(no read start) |
---|---|
DH1 | 0.32652 |
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 | 22:21:04 18 Oct 2016 | 22:36:19 18 Oct 2016 | 15 minutes 15 seconds |
Read alignment to reference genome | 22:36:33 18 Oct 2016 | 00:36:29 19 Oct 2016 | 1 hour 59 minutes 56 seconds |
Preprocessing alignments for candidate junction identification | 00:36:32 19 Oct 2016 | 01:10:22 19 Oct 2016 | 33 minutes 50 seconds |
Preliminary analysis of coverage distribution | 01:10:22 19 Oct 2016 | 01:46:43 19 Oct 2016 | 36 minutes 21 seconds |
Identifying junction candidates | 01:46:43 19 Oct 2016 | 01:47:00 19 Oct 2016 | 17 seconds |
Re-alignment to junction candidates | 01:47:00 19 Oct 2016 | 02:22:26 19 Oct 2016 | 35 minutes 26 seconds |
Resolving alignments with junction candidates | 02:22:26 19 Oct 2016 | 03:34:42 19 Oct 2016 | 1 hour 12 minutes 16 seconds |
Creating BAM files | 03:34:42 19 Oct 2016 | 03:57:51 19 Oct 2016 | 23 minutes 9 seconds |
Tabulating error counts | 03:57:51 19 Oct 2016 | 04:15:06 19 Oct 2016 | 17 minutes 15 seconds |
Re-calibrating base error rates | 04:15:06 19 Oct 2016 | 04:15:11 19 Oct 2016 | 5 seconds |
Examining read alignment evidence | 04:15:11 19 Oct 2016 | 06:43:45 19 Oct 2016 | 2 hours 28 minutes 34 seconds |
Polymorphism statistics | 06:43:45 19 Oct 2016 | 06:43:47 19 Oct 2016 | 2 seconds |
Output | 06:43:47 19 Oct 2016 | 06:46:36 19 Oct 2016 | 2 minutes 49 seconds |
Total | 8 hours 25 minutes 15 seconds |