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 | SRR22894678_R1.good.fq | 2,458,357 | 318,785,675 | 100.0% | 129.7 bases | 136 bases | 99.5% |
errors | SRR22894678_R2.good.fq | 2,458,357 | 318,781,307 | 100.0% | 129.7 bases | 136 bases | 98.9% |
total | 4,916,714 | 637,566,982 | 100.0% | 129.7 bases | 136 bases | 99.2% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | TrimmedAssembly_T66_contig_1 | 655,835 | 147.7 | 3.5 | 15.5% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_2 | 291,973 | 237.5 | 4.0 | 11.0% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_3 | 262,583 | 230.4 | 4.1 | 9.6% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_4 | 245,870 | 202.3 | 3.6 | 7.9% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_5 | 187,153 | 202.4 | 3.7 | 6.0% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_6 | 156,776 | 186.5 | 3.4 | 4.6% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_7 | 138,687 | 158.8 | 3.5 | 3.5% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_8 | 137,664 | 169.9 | 3.2 | 3.7% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_9 | 133,707 | 214.9 | 3.6 | 4.6% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_10 | 98,898 | 173.2 | 3.4 | 2.7% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_11 | 96,142 | 178.4 | 3.3 | 2.7% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_12 | 94,931 | 163.6 | 3.5 | 2.5% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_13 | 94,334 | 224.8 | 3.6 | 3.4% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_14 | 91,033 | 211.9 | 3.9 | 3.1% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_15 | 90,630 | 218.9 | 4.0 | 3.2% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_16 | 89,249 | 187.2 | 3.0 | 2.7% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_17 | 66,738 | 166.1 | 2.7 | 1.8% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_18 | 53,854 | 181.1 | 3.6 | 1.5% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_19 | 46,603 | 220.7 | 4.2 | 1.6% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_20 | 39,141 | 167.4 | 3.5 | 1.0% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_21 | 29,409 | 310.9 | 6.1 | 1.4% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_22 | 25,952 | 208.1 | 5.1 | 0.8% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_23 | 24,421 | 206.4 | 3.8 | 1.2% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_24 | 19,315 | 219.0 | 3.8 | 0.7% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_25 | 5,544 | 209.3 | 3.8 | 0.2% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_26 | 3,462 | 180.0 | 3.2 | 0.1% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_27 | 3,273 | 206.5 | 3.5 | 0.1% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_28 | 3,183 | 1004.3 | 13.7 | 0.5% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_29 | 2,480 | 168.8 | 2.7 | 0.1% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_30 | 2,023 | 5268.9 | 52.4 | 1.6% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_31 | 1,737 | 169.9 | 1.6 | 0.0% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_32 | 1,640 | 963.8 | 13.8 | 0.2% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_33 | 1,499 | 184.6 | 3.2 | 0.0% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_34 | 1,203 | 384.0 | 6.4 | 0.1% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_35 | 1,096 | 384.7 | 5.9 | 0.1% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_36 | 864 | 1470.7 | 8.6 | 0.2% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_37 | 853 | 434.4 | 9.5 | 0.0% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_38 | 757 | 1447.1 | 50.1 | 0.1% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_39 | 663 | 221.0 | 3.5 | 0.0% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_40 | 631 | 198.2 | 2.4 | 0.0% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_41 | 437 | 465.4 | 9.9 | 0.0% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_42 | 320 | 1257.0 | 24.9 | 0.0% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
total | 3,202,563 | 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 | 10005 |
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 | 145 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.012 |
reference sequence | pr(no read start) |
---|---|
TrimmedAssembly_T66_contig_1 | 0.76925 |
TrimmedAssembly_T66_contig_2 | 0.70673 |
TrimmedAssembly_T66_contig_3 | 0.71078 |
TrimmedAssembly_T66_contig_4 | 0.72794 |
TrimmedAssembly_T66_contig_5 | 0.72773 |
TrimmedAssembly_T66_contig_6 | 0.73847 |
TrimmedAssembly_T66_contig_7 | 0.75970 |
TrimmedAssembly_T66_contig_8 | 0.75029 |
TrimmedAssembly_T66_contig_9 | 0.71810 |
TrimmedAssembly_T66_contig_10 | 0.74993 |
TrimmedAssembly_T66_contig_11 | 0.74349 |
TrimmedAssembly_T66_contig_12 | 0.75819 |
TrimmedAssembly_T66_contig_13 | 0.71342 |
TrimmedAssembly_T66_contig_14 | 0.72321 |
TrimmedAssembly_T66_contig_15 | 0.71784 |
TrimmedAssembly_T66_contig_16 | 0.73863 |
TrimmedAssembly_T66_contig_17 | 0.75412 |
TrimmedAssembly_T66_contig_18 | 0.74292 |
TrimmedAssembly_T66_contig_19 | 0.71716 |
TrimmedAssembly_T66_contig_20 | 0.75043 |
TrimmedAssembly_T66_contig_21 | 0.67118 |
TrimmedAssembly_T66_contig_22 | 0.72785 |
TrimmedAssembly_T66_contig_23 | 0.68854 |
TrimmedAssembly_T66_contig_24 | 0.71916 |
TrimmedAssembly_T66_contig_25 | 0.72965 |
TrimmedAssembly_T66_contig_26 | 0.75422 |
TrimmedAssembly_T66_contig_27 | 0.74269 |
TrimmedAssembly_T66_contig_28 | 0.52655 |
TrimmedAssembly_T66_contig_29 | 0.77871 |
TrimmedAssembly_T66_contig_30 | 0.32823 |
TrimmedAssembly_T66_contig_31 | 0.77438 |
TrimmedAssembly_T66_contig_32 | 0.51463 |
TrimmedAssembly_T66_contig_33 | 0.76785 |
TrimmedAssembly_T66_contig_34 | 0.67456 |
TrimmedAssembly_T66_contig_35 | 0.68704 |
TrimmedAssembly_T66_contig_36 | 0.56704 |
TrimmedAssembly_T66_contig_37 | 0.67175 |
TrimmedAssembly_T66_contig_38 | 0.53104 |
TrimmedAssembly_T66_contig_39 | 0.74684 |
TrimmedAssembly_T66_contig_40 | 0.76673 |
TrimmedAssembly_T66_contig_41 | 0.72998 |
TrimmedAssembly_T66_contig_42 | 0.63906 |
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 | 14:09:03 19 Apr 2023 | 14:10:44 19 Apr 2023 | 1 minute 41 seconds |
Read alignment to reference genome | 14:10:44 19 Apr 2023 | 14:21:46 19 Apr 2023 | 11 minutes 2 seconds |
Preprocessing alignments for candidate junction identification | 14:21:46 19 Apr 2023 | 14:22:44 19 Apr 2023 | 58 seconds |
Preliminary analysis of coverage distribution | 14:22:44 19 Apr 2023 | 14:25:07 19 Apr 2023 | 2 minutes 23 seconds |
Identifying junction candidates | 14:25:07 19 Apr 2023 | 14:25:13 19 Apr 2023 | 6 seconds |
Re-alignment to junction candidates | 14:25:13 19 Apr 2023 | 14:27:46 19 Apr 2023 | 2 minutes 33 seconds |
Resolving best read alignments | 14:27:46 19 Apr 2023 | 14:29:18 19 Apr 2023 | 1 minute 32 seconds |
Creating BAM files | 14:29:18 19 Apr 2023 | 14:31:03 19 Apr 2023 | 1 minute 45 seconds |
Tabulating error counts | 14:31:03 19 Apr 2023 | 14:31:56 19 Apr 2023 | 53 seconds |
Re-calibrating base error rates | 14:31:56 19 Apr 2023 | 14:32:14 19 Apr 2023 | 18 seconds |
Examining read alignment evidence | 14:32:14 19 Apr 2023 | 14:43:31 19 Apr 2023 | 11 minutes 17 seconds |
Polymorphism statistics | 14:43:31 19 Apr 2023 | 14:43:32 19 Apr 2023 | 1 second |
Output | 14:43:32 19 Apr 2023 | 14:44:02 19 Apr 2023 | 30 seconds |
Total | 34 minutes 59 seconds |