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 | SRR22894666_R1.good.fq | 2,574,056 | 332,564,200 | 100.0% | 129.2 bases | 135 bases | 99.6% |
errors | SRR22894666_R2.good.fq | 2,574,056 | 332,569,475 | 100.0% | 129.2 bases | 135 bases | 98.7% |
total | 5,148,112 | 665,133,675 | 100.0% | 129.2 bases | 135 bases | 99.2% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | Annotation_U21_Trimmed_contig_1 | 491,259 | 271.6 | 4.2 | 20.2% | Pediococcus pentosaceus P. pentosaceus_U21 |
coverage | distribution | Annotation_U21_Trimmed_contig_2 | 375,970 | 446.9 | 12.0 | 25.2% | Pediococcus pentosaceus P. pentosaceus_U21 |
coverage | distribution | Annotation_U21_Trimmed_contig_3 | 367,983 | 345.3 | 6.3 | 19.2% | Pediococcus pentosaceus P. pentosaceus_U21 |
coverage | distribution | Annotation_U21_Trimmed_contig_4 | 286,779 | 316.9 | 4.9 | 13.7% | Pediococcus pentosaceus P. pentosaceus_U21 |
coverage | distribution | Annotation_U21_Trimmed_contig_5 | 139,689 | 441.2 | 6.3 | 9.3% | Pediococcus pentosaceus P. pentosaceus_U21 |
coverage | distribution | Annotation_U21_Trimmed_contig_6 | 62,195 | 210.3 | 6.8 | 1.9% | Pediococcus pentosaceus P. pentosaceus_U21 |
coverage | distribution | Annotation_U21_Trimmed_contig_7 | 60,419 | 479.1 | 6.0 | 4.4% | Pediococcus pentosaceus P. pentosaceus_U21 |
coverage | distribution | Annotation_U21_Trimmed_contig_8 | 48,531 | 272.9 | 3.9 | 2.0% | Pediococcus pentosaceus P. pentosaceus_U21 |
coverage | distribution | Annotation_U21_Trimmed_contig_9 | 10,661 | 1668.3 | 17.0 | 2.7% | Pediococcus pentosaceus P. pentosaceus_U21 |
coverage | distribution | Annotation_U21_Trimmed_contig_10 | 3,297 | 1881.1 | 21.3 | 0.9% | Pediococcus pentosaceus P. pentosaceus_U21 |
coverage | distribution | Annotation_U21_Trimmed_contig_11 | 1,711 | 1853.3 | 18.2 | 0.4% | Pediococcus pentosaceus P. pentosaceus_U21 |
coverage | distribution | Annotation_U21_Trimmed_contig_12 | 1,004 | 280.5 | 2.9 | 0.0% | Pediococcus pentosaceus P. pentosaceus_U21 |
coverage | distribution | Annotation_U21_Trimmed_contig_13 | 479 | 321.6 | 8.0 | 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 | 4799 |
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 | 88 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.013 |
reference sequence | pr(no read start) |
---|---|
Annotation_U21_Trimmed_contig_1 | 0.68953 |
Annotation_U21_Trimmed_contig_2 | 0.61870 |
Annotation_U21_Trimmed_contig_3 | 0.65369 |
Annotation_U21_Trimmed_contig_4 | 0.66527 |
Annotation_U21_Trimmed_contig_5 | 0.61781 |
Annotation_U21_Trimmed_contig_6 | 0.72831 |
Annotation_U21_Trimmed_contig_7 | 0.60681 |
Annotation_U21_Trimmed_contig_8 | 0.68764 |
Annotation_U21_Trimmed_contig_9 | 0.43217 |
Annotation_U21_Trimmed_contig_10 | 0.41705 |
Annotation_U21_Trimmed_contig_11 | 0.42577 |
Annotation_U21_Trimmed_contig_12 | 0.70539 |
Annotation_U21_Trimmed_contig_13 | 0.74018 |
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 | 14:04:22 19 Apr 2023 | 14:06:08 19 Apr 2023 | 1 minute 46 seconds |
Read alignment to reference genome | 14:06:08 19 Apr 2023 | 14:21:06 19 Apr 2023 | 14 minutes 58 seconds |
Preprocessing alignments for candidate junction identification | 14:21:06 19 Apr 2023 | 14:22:30 19 Apr 2023 | 1 minute 24 seconds |
Preliminary analysis of coverage distribution | 14:22:30 19 Apr 2023 | 14:24:57 19 Apr 2023 | 2 minutes 27 seconds |
Identifying junction candidates | 14:24:57 19 Apr 2023 | 14:24:59 19 Apr 2023 | 2 seconds |
Re-alignment to junction candidates | 14:24:59 19 Apr 2023 | 14:27:34 19 Apr 2023 | 2 minutes 35 seconds |
Resolving best read alignments | 14:27:34 19 Apr 2023 | 14:29:01 19 Apr 2023 | 1 minute 27 seconds |
Creating BAM files | 14:29:01 19 Apr 2023 | 14:30:58 19 Apr 2023 | 1 minute 57 seconds |
Tabulating error counts | 14:30:58 19 Apr 2023 | 14:31:52 19 Apr 2023 | 54 seconds |
Re-calibrating base error rates | 14:31:52 19 Apr 2023 | 14:31:58 19 Apr 2023 | 6 seconds |
Examining read alignment evidence | 14:31:58 19 Apr 2023 | 14:43:59 19 Apr 2023 | 12 minutes 1 second |
Polymorphism statistics | 14:43:59 19 Apr 2023 | 14:44:00 19 Apr 2023 | 1 second |
Output | 14:44:00 19 Apr 2023 | 14:44:15 19 Apr 2023 | 15 seconds |
Total | 39 minutes 53 seconds |