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 | Pputida_PALE__HGL_Pputida_171_S159_L001_R1_001.good.fq | 5,428,034 | 795,994,413 | 100.0% | 146.6 bases | 150 bases | 96.3% |
errors | Pputida_PALE__HGL_Pputida_171_S159_L001_R2_001.good.fq | 5,428,034 | 795,994,413 | 100.0% | 146.6 bases | 150 bases | 95.8% |
total | 10,856,068 | 1,591,988,826 | 100.0% | 146.6 bases | 150 bases | 96.0% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | NC_002947 | 6,183,858 | 246.9 | 4.1 | 100.0% | na |
total | 6,183,858 | 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 | 100000 |
Coverage evenness (position-hash) score of junction candidates | ≥ 2 | ≥ 3 |
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold | 100 ≤ n ≤ 5000 | 843 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.042 |
reference sequence | pr(no read start) |
---|---|
NC_002947 | 0.55305 |
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 | 23:00:52 07 Apr 2020 | 23:05:11 07 Apr 2020 | 4 minutes 19 seconds |
Read alignment to reference genome | 23:05:12 07 Apr 2020 | 23:28:48 07 Apr 2020 | 23 minutes 36 seconds |
Preprocessing alignments for candidate junction identification | 23:28:48 07 Apr 2020 | 23:33:28 07 Apr 2020 | 4 minutes 40 seconds |
Preliminary analysis of coverage distribution | 23:33:28 07 Apr 2020 | 23:38:35 07 Apr 2020 | 5 minutes 7 seconds |
Identifying junction candidates | 23:38:35 07 Apr 2020 | 23:46:18 07 Apr 2020 | 7 minutes 43 seconds |
Re-alignment to junction candidates | 23:46:18 07 Apr 2020 | 23:52:58 07 Apr 2020 | 6 minutes 40 seconds |
Resolving best read alignments | 23:52:58 07 Apr 2020 | 00:01:23 08 Apr 2020 | 8 minutes 25 seconds |
Creating BAM files | 00:01:23 08 Apr 2020 | 00:05:31 08 Apr 2020 | 4 minutes 8 seconds |
Tabulating error counts | 00:05:31 08 Apr 2020 | 00:09:38 08 Apr 2020 | 4 minutes 7 seconds |
Re-calibrating base error rates | 00:09:38 08 Apr 2020 | 00:09:39 08 Apr 2020 | 1 second |
Examining read alignment evidence | 00:09:39 08 Apr 2020 | 00:43:12 08 Apr 2020 | 33 minutes 33 seconds |
Polymorphism statistics | 00:43:12 08 Apr 2020 | 00:43:19 08 Apr 2020 | 7 seconds |
Output | 00:43:19 08 Apr 2020 | 00:44:48 08 Apr 2020 | 1 minute 29 seconds |
Total | 1 hour 43 minutes 55 seconds |