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 | ERR1440899_R1.good.fq | 3,030,700 | 293,940,468 | 100.0% | 97.0 bases | 97 bases | 99.7% |
errors | ERR1440899_R2.good.fq | 3,030,699 | 293,940,371 | 100.0% | 97.0 bases | 97 bases | 95.3% |
total | 6,061,399 | 587,880,839 | 100.0% | 97.0 bases | 97 bases | 97.5% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | BX571857 | 2,799,802 | 212.5 | 14.2 | 99.3% | Staphylococcus aureus strain MSSA476, complete genome. |
coverage | distribution | BX571858 | 20,652 | 193.7 | 14.9 | 0.7% | Staphylococcus aureus plasmid pSAS, complete genome. |
total | 2,820,454 | 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 | 848 |
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 | 14 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.001 |
reference sequence | pr(no read start) |
---|---|
BX571857 | 0.45131 |
BX571858 | 0.47993 |
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 | ≤ 0 |
Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction | ≥ 6 |
option | value |
---|---|
Mode | Full Polymorphism |
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 | 2 |
Polymorphism frequency cutoff | 0.05 |
Polymorphism minimum variant coverage each strand | 2 |
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 | ≥3 bases |
Skip base substitutions when they create a homopolymer flanked on each side by | ≥5 bases |
program | version |
---|---|
bowtie2 | 2.3.4.1 |
R | 3.4.4 |
step | start | end | elapsed |
---|---|---|---|
Read and reference sequence file input | 20:20:54 06 Apr 2020 | 20:22:31 06 Apr 2020 | 1 minute 37 seconds |
Read alignment to reference genome | 20:22:32 06 Apr 2020 | 20:32:44 06 Apr 2020 | 10 minutes 12 seconds |
Preprocessing alignments for candidate junction identification | 20:32:44 06 Apr 2020 | 20:34:06 06 Apr 2020 | 1 minute 22 seconds |
Preliminary analysis of coverage distribution | 20:34:06 06 Apr 2020 | 20:36:46 06 Apr 2020 | 2 minutes 40 seconds |
Identifying junction candidates | 20:36:46 06 Apr 2020 | 20:36:46 06 Apr 2020 | 0 seconds |
Re-alignment to junction candidates | 20:36:46 06 Apr 2020 | 20:38:59 06 Apr 2020 | 2 minutes 13 seconds |
Resolving best read alignments | 20:38:59 06 Apr 2020 | 20:41:08 06 Apr 2020 | 2 minutes 9 seconds |
Creating BAM files | 20:41:08 06 Apr 2020 | 20:43:33 06 Apr 2020 | 2 minutes 25 seconds |
Tabulating error counts | 20:43:33 06 Apr 2020 | 20:44:23 06 Apr 2020 | 50 seconds |
Re-calibrating base error rates | 20:44:23 06 Apr 2020 | 20:44:25 06 Apr 2020 | 2 seconds |
Examining read alignment evidence | 20:44:25 06 Apr 2020 | 21:38:51 06 Apr 2020 | 54 minutes 26 seconds |
Polymorphism statistics | 21:38:51 06 Apr 2020 | 21:38:52 06 Apr 2020 | 1 second |
Output | 21:38:52 06 Apr 2020 | 21:39:05 06 Apr 2020 | 13 seconds |
Total | 1 hour 18 minutes 10 seconds |