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 | ERR1579184_R1.good.fq | 2,685,840 | 260,495,740 | 100.0% | 97.0 bases | 97 bases | 99.7% |
errors | ERR1579184_R2.good.fq | 2,685,840 | 260,495,740 | 100.0% | 97.0 bases | 97 bases | 96.3% |
total | 5,371,680 | 520,991,480 | 100.0% | 97.0 bases | 97 bases | 98.0% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | BX571857 | 2,799,802 | 184.5 | 5.9 | 98.8% | Staphylococcus aureus strain MSSA476, complete genome. |
coverage | distribution | BX571858 | 20,652 | 293.7 | 9.6 | 1.2% | 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 | 4003 |
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 | 94 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.007 |
reference sequence | pr(no read start) |
---|---|
BX571857 | 0.46739 |
BX571858 | 0.32670 |
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 | 04:16:39 07 Apr 2020 | 04:18:01 07 Apr 2020 | 1 minute 22 seconds |
Read alignment to reference genome | 04:18:01 07 Apr 2020 | 04:26:48 07 Apr 2020 | 8 minutes 47 seconds |
Preprocessing alignments for candidate junction identification | 04:26:48 07 Apr 2020 | 04:28:00 07 Apr 2020 | 1 minute 12 seconds |
Preliminary analysis of coverage distribution | 04:28:00 07 Apr 2020 | 04:30:17 07 Apr 2020 | 2 minutes 17 seconds |
Identifying junction candidates | 04:30:17 07 Apr 2020 | 04:30:18 07 Apr 2020 | 1 second |
Re-alignment to junction candidates | 04:30:18 07 Apr 2020 | 04:32:19 07 Apr 2020 | 2 minutes 1 second |
Resolving best read alignments | 04:32:19 07 Apr 2020 | 04:34:20 07 Apr 2020 | 2 minutes 1 second |
Creating BAM files | 04:34:20 07 Apr 2020 | 04:36:25 07 Apr 2020 | 2 minutes 5 seconds |
Tabulating error counts | 04:36:25 07 Apr 2020 | 04:37:10 07 Apr 2020 | 45 seconds |
Re-calibrating base error rates | 04:37:10 07 Apr 2020 | 04:37:11 07 Apr 2020 | 1 second |
Examining read alignment evidence | 04:37:11 07 Apr 2020 | 04:45:41 07 Apr 2020 | 8 minutes 30 seconds |
Polymorphism statistics | 04:45:41 07 Apr 2020 | 04:45:42 07 Apr 2020 | 1 second |
Output | 04:45:42 07 Apr 2020 | 04:45:54 07 Apr 2020 | 12 seconds |
Total | 29 minutes 15 seconds |