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 | Pputida_sub_A1_F37_I1_R1_001.good.fq | 3,208,066 | 425,741,327 | 100.0% | 132.7 bases | 136 bases | 96.7% |
errors | Pputida_sub_A1_F37_I1_R2_001.good.fq | 3,208,066 | 425,741,327 | 100.0% | 132.7 bases | 136 bases | 82.6% |
total | 6,416,132 | 851,482,654 | 100.0% | 132.7 bases | 136 bases | 89.7% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | NC_002947 | 6,183,858 | 134.5 | 8.0 | 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 | 10861 |
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 | 557 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.025 |
reference sequence | pr(no read start) |
---|---|
NC_002947 | 0.77484 |
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 | 04:41:08 03 Feb 2021 | 04:47:15 03 Feb 2021 | 6 minutes 7 seconds |
Read alignment to reference genome | 04:47:16 03 Feb 2021 | 05:38:01 03 Feb 2021 | 50 minutes 45 seconds |
Preprocessing alignments for candidate junction identification | 05:38:01 03 Feb 2021 | 05:43:25 03 Feb 2021 | 5 minutes 24 seconds |
Preliminary analysis of coverage distribution | 05:43:25 03 Feb 2021 | 05:55:54 03 Feb 2021 | 12 minutes 29 seconds |
Identifying junction candidates | 05:55:54 03 Feb 2021 | 05:56:18 03 Feb 2021 | 24 seconds |
Re-alignment to junction candidates | 05:56:18 03 Feb 2021 | 06:10:02 03 Feb 2021 | 13 minutes 44 seconds |
Resolving best read alignments | 06:10:02 03 Feb 2021 | 06:17:00 03 Feb 2021 | 6 minutes 58 seconds |
Creating BAM files | 06:17:00 03 Feb 2021 | 06:28:43 03 Feb 2021 | 11 minutes 43 seconds |
Tabulating error counts | 06:28:43 03 Feb 2021 | 06:32:19 03 Feb 2021 | 3 minutes 36 seconds |
Re-calibrating base error rates | 06:32:19 03 Feb 2021 | 06:32:22 03 Feb 2021 | 3 seconds |
Examining read alignment evidence | 06:32:22 03 Feb 2021 | 07:17:07 03 Feb 2021 | 44 minutes 45 seconds |
Polymorphism statistics | 07:17:07 03 Feb 2021 | 07:17:09 03 Feb 2021 | 2 seconds |
Output | 07:17:09 03 Feb 2021 | 07:18:18 03 Feb 2021 | 1 minute 9 seconds |
Total | 2 hours 37 minutes 9 seconds |