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 | SRR22894667_R1.good.fq | 2,894,227 | 375,286,918 | 100.0% | 129.7 bases | 135 bases | 99.5% |
errors | SRR22894667_R2.good.fq | 2,894,227 | 375,280,838 | 100.0% | 129.7 bases | 135 bases | 99.0% |
total | 5,788,454 | 750,567,756 | 100.0% | 129.7 bases | 135 bases | 99.3% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | Annotation_U21_Trimmed_contig_1 | 491,259 | 314.6 | 4.4 | 20.7% | Pediococcus pentosaceus P. pentosaceus_U21 |
coverage | distribution | Annotation_U21_Trimmed_contig_2 | 375,970 | 494.0 | 13.7 | 24.6% | Pediococcus pentosaceus P. pentosaceus_U21 |
coverage | distribution | Annotation_U21_Trimmed_contig_3 | 367,983 | 386.1 | 7.9 | 19.0% | Pediococcus pentosaceus P. pentosaceus_U21 |
coverage | distribution | Annotation_U21_Trimmed_contig_4 | 286,779 | 357.1 | 5.6 | 13.8% | Pediococcus pentosaceus P. pentosaceus_U21 |
coverage | distribution | Annotation_U21_Trimmed_contig_5 | 139,689 | 488.7 | 7.2 | 9.2% | Pediococcus pentosaceus P. pentosaceus_U21 |
coverage | distribution | Annotation_U21_Trimmed_contig_6 | 62,195 | 201.2 | 6.3 | 1.7% | Pediococcus pentosaceus P. pentosaceus_U21 |
coverage | distribution | Annotation_U21_Trimmed_contig_7 | 60,419 | 534.0 | 6.6 | 4.3% | Pediococcus pentosaceus P. pentosaceus_U21 |
coverage | distribution | Annotation_U21_Trimmed_contig_8 | 48,531 | 320.5 | 4.3 | 2.1% | Pediococcus pentosaceus P. pentosaceus_U21 |
coverage | distribution | Annotation_U21_Trimmed_contig_9 | 10,661 | 2294.3 | 20.6 | 3.3% | Pediococcus pentosaceus P. pentosaceus_U21 |
coverage | distribution | Annotation_U21_Trimmed_contig_10 | 3,297 | 2136.7 | 20.5 | 0.9% | Pediococcus pentosaceus P. pentosaceus_U21 |
coverage | distribution | Annotation_U21_Trimmed_contig_11 | 1,711 | 2168.9 | 22.1 | 0.5% | Pediococcus pentosaceus P. pentosaceus_U21 |
coverage | distribution | Annotation_U21_Trimmed_contig_12 | 1,004 | 336.8 | 3.5 | 0.0% | Pediococcus pentosaceus P. pentosaceus_U21 |
coverage | distribution | Annotation_U21_Trimmed_contig_13 | 479 | 369.5 | 5.0 | 0.0% | Pediococcus pentosaceus P. pentosaceus_U21 |
total | 1,849,977 | 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 | 5453 |
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 | 95 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.014 |
reference sequence | pr(no read start) |
---|---|
Annotation_U21_Trimmed_contig_1 | 0.66950 |
Annotation_U21_Trimmed_contig_2 | 0.60435 |
Annotation_U21_Trimmed_contig_3 | 0.63951 |
Annotation_U21_Trimmed_contig_4 | 0.64823 |
Annotation_U21_Trimmed_contig_5 | 0.60377 |
Annotation_U21_Trimmed_contig_6 | 0.73349 |
Annotation_U21_Trimmed_contig_7 | 0.59295 |
Annotation_U21_Trimmed_contig_8 | 0.66664 |
Annotation_U21_Trimmed_contig_9 | 0.38518 |
Annotation_U21_Trimmed_contig_10 | 0.40127 |
Annotation_U21_Trimmed_contig_11 | 0.40970 |
Annotation_U21_Trimmed_contig_12 | 0.67235 |
Annotation_U21_Trimmed_contig_13 | 0.74016 |
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 | 14:11:30 19 Apr 2023 | 14:13:19 19 Apr 2023 | 1 minute 49 seconds |
Read alignment to reference genome | 14:13:20 19 Apr 2023 | 14:24:32 19 Apr 2023 | 11 minutes 12 seconds |
Preprocessing alignments for candidate junction identification | 14:24:32 19 Apr 2023 | 14:25:39 19 Apr 2023 | 1 minute 7 seconds |
Preliminary analysis of coverage distribution | 14:25:39 19 Apr 2023 | 14:28:16 19 Apr 2023 | 2 minutes 37 seconds |
Identifying junction candidates | 14:28:16 19 Apr 2023 | 14:28:17 19 Apr 2023 | 1 second |
Re-alignment to junction candidates | 14:28:17 19 Apr 2023 | 14:31:22 19 Apr 2023 | 3 minutes 5 seconds |
Resolving best read alignments | 14:31:22 19 Apr 2023 | 14:33:04 19 Apr 2023 | 1 minute 42 seconds |
Creating BAM files | 14:33:04 19 Apr 2023 | 14:35:13 19 Apr 2023 | 2 minutes 9 seconds |
Tabulating error counts | 14:35:13 19 Apr 2023 | 14:36:15 19 Apr 2023 | 1 minute 2 seconds |
Re-calibrating base error rates | 14:36:15 19 Apr 2023 | 14:36:22 19 Apr 2023 | 7 seconds |
Examining read alignment evidence | 14:36:22 19 Apr 2023 | 14:49:52 19 Apr 2023 | 13 minutes 30 seconds |
Polymorphism statistics | 14:49:52 19 Apr 2023 | 14:49:53 19 Apr 2023 | 1 second |
Output | 14:49:53 19 Apr 2023 | 14:50:10 19 Apr 2023 | 17 seconds |
Total | 38 minutes 39 seconds |