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 | SRR22894670_R1.good.fq | 2,566,888 | 337,178,897 | 100.0% | 131.4 bases | 136 bases | 99.6% |
errors | SRR22894670_R2.good.fq | 2,566,888 | 337,175,785 | 100.0% | 131.4 bases | 136 bases | 99.0% |
total | 5,133,776 | 674,354,682 | 100.0% | 131.4 bases | 136 bases | 99.3% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | TrimmedAssembly_T66_contig_1 | 655,835 | 156.2 | 3.2 | 15.5% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_2 | 291,973 | 279.8 | 4.3 | 12.3% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_3 | 262,583 | 258.4 | 4.4 | 10.2% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_4 | 245,870 | 213.2 | 3.5 | 7.9% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_5 | 187,153 | 211.6 | 3.4 | 6.0% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_6 | 156,776 | 194.7 | 3.3 | 4.6% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_7 | 138,687 | 162.2 | 3.1 | 3.4% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_8 | 137,664 | 177.4 | 3.0 | 3.7% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_9 | 133,707 | 228.3 | 3.3 | 4.6% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_10 | 98,898 | 180.2 | 3.3 | 2.7% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_11 | 96,142 | 183.6 | 2.8 | 2.6% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_12 | 94,931 | 171.4 | 3.1 | 2.4% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_13 | 94,334 | 251.9 | 3.8 | 3.5% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_14 | 91,033 | 233.8 | 3.6 | 3.2% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_15 | 90,630 | 233.8 | 3.8 | 3.2% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_16 | 89,249 | 195.7 | 3.1 | 2.6% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_17 | 66,738 | 168.5 | 2.9 | 1.7% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_18 | 53,854 | 188.9 | 3.3 | 1.5% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_19 | 46,603 | 241.1 | 4.0 | 1.7% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_20 | 39,141 | 173.7 | 3.1 | 1.0% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_21 | 29,409 | 218.6 | 4.0 | 0.9% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_22 | 25,952 | 172.6 | 3.8 | 0.6% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_23 | 24,421 | 158.3 | 4.2 | 0.7% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_24 | 19,315 | 232.5 | 3.0 | 0.7% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_25 | 5,544 | 167.6 | 2.6 | 0.1% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_26 | 3,462 | 108.9 | 2.2 | 0.1% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_27 | 3,273 | 226.2 | 2.8 | 0.1% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_28 | 3,183 | 1030.1 | 11.5 | 0.5% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_29 | 2,480 | 114.6 | 1.6 | 0.0% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_30 | 2,023 | 4455.5 | 29.4 | 1.3% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_31 | 1,737 | 177.0 | 1.9 | 0.0% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_32 | 1,640 | 1000.5 | 19.9 | 0.2% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_33 | 1,499 | 191.6 | 2.5 | 0.0% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_34 | 1,203 | 415.2 | 4.8 | 0.1% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_35 | 1,096 | 402.0 | 3.2 | 0.1% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_36 | 864 | 1508.0 | 4.6 | 0.2% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_37 | 853 | 359.2 | 5.2 | 0.0% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_38 | 757 | 1537.2 | 29.8 | 0.1% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_39 | 663 | 175.3 | 1.3 | 0.0% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_40 | 631 | 215.7 | 6.5 | 0.0% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_41 | 437 | 486.2 | 3.5 | 0.0% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_42 | 320 | 1414.9 | 20.2 | 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 | 10336 |
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 | 156 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.013 |
reference sequence | pr(no read start) |
---|---|
TrimmedAssembly_T66_contig_1 | 0.76710 |
TrimmedAssembly_T66_contig_2 | 0.69135 |
TrimmedAssembly_T66_contig_3 | 0.70207 |
TrimmedAssembly_T66_contig_4 | 0.72771 |
TrimmedAssembly_T66_contig_5 | 0.72762 |
TrimmedAssembly_T66_contig_6 | 0.73877 |
TrimmedAssembly_T66_contig_7 | 0.76150 |
TrimmedAssembly_T66_contig_8 | 0.74987 |
TrimmedAssembly_T66_contig_9 | 0.71820 |
TrimmedAssembly_T66_contig_10 | 0.75081 |
TrimmedAssembly_T66_contig_11 | 0.74514 |
TrimmedAssembly_T66_contig_12 | 0.75649 |
TrimmedAssembly_T66_contig_13 | 0.70667 |
TrimmedAssembly_T66_contig_14 | 0.71759 |
TrimmedAssembly_T66_contig_15 | 0.71602 |
TrimmedAssembly_T66_contig_16 | 0.74099 |
TrimmedAssembly_T66_contig_17 | 0.75740 |
TrimmedAssembly_T66_contig_18 | 0.74502 |
TrimmedAssembly_T66_contig_19 | 0.70948 |
TrimmedAssembly_T66_contig_20 | 0.75258 |
TrimmedAssembly_T66_contig_21 | 0.72848 |
TrimmedAssembly_T66_contig_22 | 0.76291 |
TrimmedAssembly_T66_contig_23 | 0.75079 |
TrimmedAssembly_T66_contig_24 | 0.71747 |
TrimmedAssembly_T66_contig_25 | 0.76687 |
TrimmedAssembly_T66_contig_26 | 0.81603 |
TrimmedAssembly_T66_contig_27 | 0.73591 |
TrimmedAssembly_T66_contig_28 | 0.52655 |
TrimmedAssembly_T66_contig_29 | 0.81963 |
TrimmedAssembly_T66_contig_30 | 0.35344 |
TrimmedAssembly_T66_contig_31 | 0.77231 |
TrimmedAssembly_T66_contig_32 | 0.52561 |
TrimmedAssembly_T66_contig_33 | 0.76818 |
TrimmedAssembly_T66_contig_34 | 0.66708 |
TrimmedAssembly_T66_contig_35 | 0.69708 |
TrimmedAssembly_T66_contig_36 | 0.54097 |
TrimmedAssembly_T66_contig_37 | 0.71571 |
TrimmedAssembly_T66_contig_38 | 0.54359 |
TrimmedAssembly_T66_contig_39 | 0.78664 |
TrimmedAssembly_T66_contig_40 | 0.75217 |
TrimmedAssembly_T66_contig_41 | 0.74027 |
TrimmedAssembly_T66_contig_42 | 0.63438 |
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 | 14:08:43 19 Apr 2023 | 14:10:23 19 Apr 2023 | 1 minute 40 seconds |
Read alignment to reference genome | 14:10:23 19 Apr 2023 | 14:24:58 19 Apr 2023 | 14 minutes 35 seconds |
Preprocessing alignments for candidate junction identification | 14:24:58 19 Apr 2023 | 14:25:58 19 Apr 2023 | 1 minute 0 seconds |
Preliminary analysis of coverage distribution | 14:25:58 19 Apr 2023 | 14:28:33 19 Apr 2023 | 2 minutes 35 seconds |
Identifying junction candidates | 14:28:33 19 Apr 2023 | 14:28:41 19 Apr 2023 | 8 seconds |
Re-alignment to junction candidates | 14:28:41 19 Apr 2023 | 14:31:33 19 Apr 2023 | 2 minutes 52 seconds |
Resolving best read alignments | 14:31:33 19 Apr 2023 | 14:33:07 19 Apr 2023 | 1 minute 34 seconds |
Creating BAM files | 14:33:07 19 Apr 2023 | 14:35:06 19 Apr 2023 | 1 minute 59 seconds |
Tabulating error counts | 14:35:06 19 Apr 2023 | 14:36:03 19 Apr 2023 | 57 seconds |
Re-calibrating base error rates | 14:36:03 19 Apr 2023 | 14:36:26 19 Apr 2023 | 23 seconds |
Examining read alignment evidence | 14:36:26 19 Apr 2023 | 14:48:32 19 Apr 2023 | 12 minutes 6 seconds |
Polymorphism statistics | 14:48:32 19 Apr 2023 | 14:48:33 19 Apr 2023 | 1 second |
Output | 14:48:33 19 Apr 2023 | 14:49:02 19 Apr 2023 | 29 seconds |
Total | 40 minutes 19 seconds |