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 | SRR22894672_R1.good.fq | 2,850,563 | 372,730,761 | 100.0% | 130.8 bases | 136 bases | 98.8% |
errors | SRR22894672_R2.good.fq | 2,850,563 | 372,717,599 | 100.0% | 130.8 bases | 136 bases | 98.2% |
total | 5,701,126 | 745,448,360 | 100.0% | 130.8 bases | 136 bases | 98.5% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | TrimmedAssembly_T66_contig_1 | 655,835 | 170.9 | 3.6 | 15.4% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_2 | 291,973 | 309.5 | 4.7 | 12.4% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_3 | 262,583 | 286.5 | 4.8 | 10.3% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_4 | 245,870 | 233.0 | 3.8 | 7.8% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_5 | 187,153 | 231.9 | 3.9 | 6.0% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_6 | 156,776 | 213.2 | 3.7 | 4.6% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_7 | 138,687 | 177.1 | 3.2 | 3.4% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_8 | 137,664 | 192.5 | 3.5 | 3.6% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_9 | 133,707 | 253.6 | 3.5 | 4.6% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_10 | 98,898 | 198.5 | 3.7 | 2.7% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_11 | 96,142 | 202.0 | 3.4 | 2.7% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_12 | 94,931 | 185.6 | 3.6 | 2.4% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_13 | 94,334 | 277.2 | 4.1 | 3.6% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_14 | 91,033 | 257.5 | 3.9 | 3.2% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_15 | 90,630 | 252.5 | 4.2 | 3.1% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_16 | 89,249 | 213.7 | 3.5 | 2.6% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_17 | 66,738 | 183.7 | 3.3 | 1.7% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_18 | 53,854 | 205.5 | 3.5 | 1.5% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_19 | 46,603 | 264.9 | 3.7 | 1.7% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_20 | 39,141 | 188.6 | 3.3 | 1.0% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_21 | 29,409 | 211.3 | 3.9 | 0.8% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_22 | 25,952 | 184.5 | 3.9 | 0.6% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_23 | 24,421 | 162.5 | 3.7 | 0.7% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_24 | 19,315 | 257.2 | 3.7 | 0.7% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_25 | 5,544 | 185.5 | 3.7 | 0.1% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_26 | 3,462 | 118.4 | 1.8 | 0.1% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_27 | 3,273 | 250.5 | 3.7 | 0.1% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_28 | 3,183 | 1172.2 | 15.3 | 0.5% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_29 | 2,480 | 117.2 | 1.9 | 0.0% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_30 | 2,023 | 4989.2 | 40.0 | 1.3% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_31 | 1,737 | 205.2 | 1.3 | 0.0% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_32 | 1,640 | 1107.7 | 18.9 | 0.2% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_33 | 1,499 | 202.4 | 8.3 | 0.0% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_34 | 1,203 | 484.5 | 13.1 | 0.1% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_35 | 1,096 | 452.5 | 3.5 | 0.1% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_36 | 864 | 1622.7 | 9.7 | 0.2% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_37 | 853 | 404.9 | 7.1 | 0.0% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_38 | 757 | 1663.7 | 37.2 | 0.1% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_39 | 663 | 196.2 | 3.0 | 0.0% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_40 | 631 | 240.1 | 1.9 | 0.0% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_41 | 437 | 504.5 | 5.0 | 0.0% | Lactiplantibacillus plantarum Lactobacillus plantarum_DTU |
coverage | distribution | TrimmedAssembly_T66_contig_42 | 320 | 1478.6 | 22.4 | 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 | 10885 |
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 | 150 |
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 | 0.75506 |
TrimmedAssembly_T66_contig_2 | 0.67441 |
TrimmedAssembly_T66_contig_3 | 0.68601 |
TrimmedAssembly_T66_contig_4 | 0.71339 |
TrimmedAssembly_T66_contig_5 | 0.71384 |
TrimmedAssembly_T66_contig_6 | 0.72437 |
TrimmedAssembly_T66_contig_7 | 0.74927 |
TrimmedAssembly_T66_contig_8 | 0.73853 |
TrimmedAssembly_T66_contig_9 | 0.70028 |
TrimmedAssembly_T66_contig_10 | 0.73699 |
TrimmedAssembly_T66_contig_11 | 0.72997 |
TrimmedAssembly_T66_contig_12 | 0.74607 |
TrimmedAssembly_T66_contig_13 | 0.69001 |
TrimmedAssembly_T66_contig_14 | 0.70172 |
TrimmedAssembly_T66_contig_15 | 0.70435 |
TrimmedAssembly_T66_contig_16 | 0.72680 |
TrimmedAssembly_T66_contig_17 | 0.74359 |
TrimmedAssembly_T66_contig_18 | 0.73429 |
TrimmedAssembly_T66_contig_19 | 0.69546 |
TrimmedAssembly_T66_contig_20 | 0.73816 |
TrimmedAssembly_T66_contig_21 | 0.72963 |
TrimmedAssembly_T66_contig_22 | 0.75265 |
TrimmedAssembly_T66_contig_23 | 0.73402 |
TrimmedAssembly_T66_contig_24 | 0.70308 |
TrimmedAssembly_T66_contig_25 | 0.75506 |
TrimmedAssembly_T66_contig_26 | 0.81040 |
TrimmedAssembly_T66_contig_27 | 0.71920 |
TrimmedAssembly_T66_contig_28 | 0.50141 |
TrimmedAssembly_T66_contig_29 | 0.80904 |
TrimmedAssembly_T66_contig_30 | 0.33836 |
TrimmedAssembly_T66_contig_31 | 0.74611 |
TrimmedAssembly_T66_contig_32 | 0.51341 |
TrimmedAssembly_T66_contig_33 | 0.76885 |
TrimmedAssembly_T66_contig_34 | 0.65170 |
TrimmedAssembly_T66_contig_35 | 0.67108 |
TrimmedAssembly_T66_contig_36 | 0.54336 |
TrimmedAssembly_T66_contig_37 | 0.68816 |
TrimmedAssembly_T66_contig_38 | 0.52312 |
TrimmedAssembly_T66_contig_39 | 0.76646 |
TrimmedAssembly_T66_contig_40 | 0.75277 |
TrimmedAssembly_T66_contig_41 | 0.74027 |
TrimmedAssembly_T66_contig_42 | 0.62969 |
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 | 14:11:01 19 Apr 2023 | 14:12:52 19 Apr 2023 | 1 minute 51 seconds |
Read alignment to reference genome | 14:12:52 19 Apr 2023 | 14:24:38 19 Apr 2023 | 11 minutes 46 seconds |
Preprocessing alignments for candidate junction identification | 14:24:38 19 Apr 2023 | 14:25:45 19 Apr 2023 | 1 minute 7 seconds |
Preliminary analysis of coverage distribution | 14:25:45 19 Apr 2023 | 14:28:37 19 Apr 2023 | 2 minutes 52 seconds |
Identifying junction candidates | 14:28:37 19 Apr 2023 | 14:28:44 19 Apr 2023 | 7 seconds |
Re-alignment to junction candidates | 14:28:44 19 Apr 2023 | 14:31:44 19 Apr 2023 | 3 minutes 0 seconds |
Resolving best read alignments | 14:31:44 19 Apr 2023 | 14:33:30 19 Apr 2023 | 1 minute 46 seconds |
Creating BAM files | 14:33:30 19 Apr 2023 | 14:35:41 19 Apr 2023 | 2 minutes 11 seconds |
Tabulating error counts | 14:35:41 19 Apr 2023 | 14:36:43 19 Apr 2023 | 1 minute 2 seconds |
Re-calibrating base error rates | 14:36:43 19 Apr 2023 | 14:37:01 19 Apr 2023 | 18 seconds |
Examining read alignment evidence | 14:37:01 19 Apr 2023 | 14:50:09 19 Apr 2023 | 13 minutes 8 seconds |
Polymorphism statistics | 14:50:09 19 Apr 2023 | 14:50:10 19 Apr 2023 | 1 second |
Output | 14:50:10 19 Apr 2023 | 14:50:41 19 Apr 2023 | 31 seconds |
Total | 39 minutes 40 seconds |