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 | SRR18135096_R1.good.fq | 11,634,069 | 1,756,411,573 | 100.0% | 151.0 bases | 151 bases | 99.9% |
errors | SRR18135096_R2.good.fq | 11,634,069 | 1,756,411,573 | 100.0% | 151.0 bases | 151 bases | 98.6% |
total | 23,268,138 | 3,512,823,146 | 100.0% | 151.0 bases | 151 bases | 99.2% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | NC_008463 | 6,537,648 | 537.2 | 8.1 | 100.0% | Pseudomonas aeruginosa UCBPP-PA14, complete sequence. |
total | 6,537,648 | 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 | 7947 |
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 | 1475 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.070 |
reference sequence | pr(no read start) |
---|---|
NC_008463 | 0.25315 |
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 | 10:41:55 20 Mar 2023 | 10:48:08 20 Mar 2023 | 6 minutes 13 seconds |
Read alignment to reference genome | 10:48:10 20 Mar 2023 | 11:33:57 20 Mar 2023 | 45 minutes 47 seconds |
Preprocessing alignments for candidate junction identification | 11:33:57 20 Mar 2023 | 11:40:08 20 Mar 2023 | 6 minutes 11 seconds |
Preliminary analysis of coverage distribution | 11:40:08 20 Mar 2023 | 11:51:12 20 Mar 2023 | 11 minutes 4 seconds |
Identifying junction candidates | 11:51:12 20 Mar 2023 | 11:51:25 20 Mar 2023 | 13 seconds |
Re-alignment to junction candidates | 11:51:25 20 Mar 2023 | 12:07:00 20 Mar 2023 | 15 minutes 35 seconds |
Resolving best read alignments | 12:07:00 20 Mar 2023 | 12:15:09 20 Mar 2023 | 8 minutes 9 seconds |
Creating BAM files | 12:15:09 20 Mar 2023 | 12:24:50 20 Mar 2023 | 9 minutes 41 seconds |
Tabulating error counts | 12:24:50 20 Mar 2023 | 12:29:23 20 Mar 2023 | 4 minutes 33 seconds |
Re-calibrating base error rates | 12:29:23 20 Mar 2023 | 12:29:24 20 Mar 2023 | 1 second |
Examining read alignment evidence | 12:29:24 20 Mar 2023 | 13:30:37 20 Mar 2023 | 1 hour 1 minute 13 seconds |
Polymorphism statistics | 13:30:37 20 Mar 2023 | 13:30:38 20 Mar 2023 | 1 second |
Output | 13:30:38 20 Mar 2023 | 13:32:04 20 Mar 2023 | 1 minute 26 seconds |
Total | 2 hours 50 minutes 7 seconds |