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 | SRR22894676_R1.good.fq | 3,549,622 | 455,739,766 | 100.0% | 128.4 bases | 135 bases | 99.5% |
errors | SRR22894676_R2.good.fq | 3,549,622 | 455,731,019 | 100.0% | 128.4 bases | 135 bases | 99.0% |
total | 7,099,244 | 911,470,785 | 100.0% | 128.4 bases | 135 bases | 99.3% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | AssemblyC74_contig_1 | 443,529 | 403.1 | 8.0 | 19.8% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_2 | 385,573 | 353.1 | 9.3 | 15.0% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_3 | 255,127 | 278.4 | 5.6 | 7.8% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_4 | 189,292 | 268.7 | 5.5 | 5.6% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_5 | 185,954 | 375.8 | 7.0 | 7.7% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_6 | 168,934 | 321.5 | 7.3 | 6.0% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_7 | 152,772 | 390.6 | 6.9 | 6.6% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_8 | 115,683 | 358.0 | 7.3 | 4.6% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_9 | 104,617 | 292.8 | 6.2 | 3.4% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_10 | 98,564 | 287.8 | 5.9 | 3.1% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_11 | 78,787 | 362.9 | 7.4 | 3.1% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_12 | 59,337 | 393.3 | 6.1 | 2.6% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_13 | 46,240 | 286.0 | 5.4 | 1.5% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_14 | 41,348 | 284.1 | 6.3 | 1.3% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_15 | 36,007 | 269.7 | 5.5 | 1.2% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_16 | 35,103 | 309.4 | 5.5 | 1.2% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_17 | 32,032 | 381.2 | 7.0 | 1.4% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_18 | 27,075 | 390.4 | 6.4 | 1.2% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_19 | 19,031 | 299.2 | 5.9 | 0.6% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_20 | 15,862 | 377.9 | 5.5 | 0.6% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_21 | 10,843 | 292.6 | 7.0 | 0.3% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_22 | 9,537 | 257.5 | 5.7 | 0.3% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_23 | 9,396 | 296.1 | 5.4 | 0.3% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_24 | 8,654 | 363.5 | 8.4 | 0.3% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_25 | 8,555 | 302.3 | 5.3 | 0.3% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_26 | 7,770 | 351.0 | 5.8 | 0.3% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_27 | 7,728 | 259.2 | 6.3 | 0.2% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_28 | 5,975 | 278.1 | 7.9 | 0.2% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_29 | 4,892 | 329.2 | 7.8 | 0.2% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_30 | 4,279 | 230.3 | 7.3 | 0.1% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_31 | 3,396 | 2318.0 | 27.1 | 0.8% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_32 | 3,311 | 272.3 | 5.9 | 0.1% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_33 | 3,075 | 671.3 | 10.6 | 0.2% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_34 | 2,107 | 268.9 | 3.7 | 0.1% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_35 | 2,041 | 217.2 | 5.2 | 0.0% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_36 | 1,754 | 265.4 | 2.4 | 0.0% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_37 | 1,750 | 571.9 | 11.4 | 0.1% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_38 | 1,652 | 601.6 | 29.7 | 0.1% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_39 | 1,643 | 2419.0 | 38.1 | 0.4% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_40 | 1,604 | 308.0 | 4.6 | 0.0% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_41 | 1,330 | 500.6 | 4.5 | 0.1% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_42 | 1,243 | 2629.1 | 43.8 | 0.3% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_43 | 1,217 | 294.1 | 4.2 | 0.0% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_44 | 1,136 | 590.9 | 4.9 | 0.1% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_45 | 1,002 | 1492.5 | 26.8 | 0.1% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_46 | 883 | 296.2 | 24.3 | 0.0% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_47 | 882 | 311.5 | 1.9 | 0.0% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_48 | 844 | 293.9 | 3.4 | 0.0% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_49 | 764 | 639.4 | 9.8 | 0.0% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_50 | 745 | 595.1 | 10.1 | 0.0% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_51 | 723 | 316.7 | 7.1 | 0.0% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_52 | 702 | 546.0 | 7.3 | 0.0% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_53 | 622 | 448.6 | 11.0 | 0.0% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_54 | 611 | 940.3 | 15.5 | 0.0% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_55 | 585 | 327.4 | 7.7 | 0.0% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_56 | 494 | 261.8 | 29.8 | 0.0% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_57 | 493 | 665.0 | 9.1 | 0.0% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_58 | 462 | 421.1 | 2.3 | 0.0% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_59 | 453 | 249.4 | 6.4 | 0.0% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_60 | 439 | 251.8 | 1.9 | 0.0% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_61 | 423 | 583.0 | 2.3 | 0.0% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_62 | 391 | 289.5 | 1.2 | 0.0% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_63 | 383 | 408.6 | 3.5 | 0.0% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_64 | 352 | 566.9 | 3.8 | 0.0% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_65 | 349 | 297.1 | 1.1 | 0.0% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_66 | 349 | 278.9 | 1.2 | 0.0% | Enterococcus faecium AssemblyC74 |
total | 2,608,706 | 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 | 27686 |
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 | 628 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.066 |
reference sequence | pr(no read start) |
---|---|
AssemblyC74_contig_1 | 0.62866 |
AssemblyC74_contig_2 | 0.64701 |
AssemblyC74_contig_3 | 0.68081 |
AssemblyC74_contig_4 | 0.68723 |
AssemblyC74_contig_5 | 0.63859 |
AssemblyC74_contig_6 | 0.66022 |
AssemblyC74_contig_7 | 0.63014 |
AssemblyC74_contig_8 | 0.64585 |
AssemblyC74_contig_9 | 0.67692 |
AssemblyC74_contig_10 | 0.67631 |
AssemblyC74_contig_11 | 0.64526 |
AssemblyC74_contig_12 | 0.63132 |
AssemblyC74_contig_13 | 0.67606 |
AssemblyC74_contig_14 | 0.68059 |
AssemblyC74_contig_15 | 0.68693 |
AssemblyC74_contig_16 | 0.66511 |
AssemblyC74_contig_17 | 0.64060 |
AssemblyC74_contig_18 | 0.62841 |
AssemblyC74_contig_19 | 0.67503 |
AssemblyC74_contig_20 | 0.64116 |
AssemblyC74_contig_21 | 0.68334 |
AssemblyC74_contig_22 | 0.67604 |
AssemblyC74_contig_23 | 0.67999 |
AssemblyC74_contig_24 | 0.64876 |
AssemblyC74_contig_25 | 0.68165 |
AssemblyC74_contig_26 | 0.64723 |
AssemblyC74_contig_27 | 0.70484 |
AssemblyC74_contig_28 | 0.68311 |
AssemblyC74_contig_29 | 0.67263 |
AssemblyC74_contig_30 | 0.71908 |
AssemblyC74_contig_31 | 0.39311 |
AssemblyC74_contig_32 | 0.70734 |
AssemblyC74_contig_33 | 0.55398 |
AssemblyC74_contig_34 | 0.71310 |
AssemblyC74_contig_35 | 0.72650 |
AssemblyC74_contig_36 | 0.70729 |
AssemblyC74_contig_37 | 0.59677 |
AssemblyC74_contig_38 | 0.61199 |
AssemblyC74_contig_39 | 0.37219 |
AssemblyC74_contig_40 | 0.68363 |
AssemblyC74_contig_41 | 0.60376 |
AssemblyC74_contig_42 | 0.40628 |
AssemblyC74_contig_43 | 0.69253 |
AssemblyC74_contig_44 | 0.63155 |
AssemblyC74_contig_45 | 0.47255 |
AssemblyC74_contig_46 | 0.71291 |
AssemblyC74_contig_47 | 0.72727 |
AssemblyC74_contig_48 | 0.73874 |
AssemblyC74_contig_49 | 0.62958 |
AssemblyC74_contig_50 | 0.62685 |
AssemblyC74_contig_51 | 0.75577 |
AssemblyC74_contig_52 | 0.65670 |
AssemblyC74_contig_53 | 0.66720 |
AssemblyC74_contig_54 | 0.53663 |
AssemblyC74_contig_55 | 0.70410 |
AssemblyC74_contig_56 | 0.76721 |
AssemblyC74_contig_57 | 0.65822 |
AssemblyC74_contig_58 | 0.69057 |
AssemblyC74_contig_59 | 0.78366 |
AssemblyC74_contig_60 | 0.82045 |
AssemblyC74_contig_61 | 0.97761 |
AssemblyC74_contig_62 | 0.90370 |
AssemblyC74_contig_63 | 0.68536 |
AssemblyC74_contig_64 | 0.72275 |
AssemblyC74_contig_65 | 0.79897 |
AssemblyC74_contig_66 | 0.70745 |
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 | 14:13:45 19 Apr 2023 | 14:15:59 19 Apr 2023 | 2 minutes 14 seconds |
Read alignment to reference genome | 14:15:59 19 Apr 2023 | 14:30:14 19 Apr 2023 | 14 minutes 15 seconds |
Preprocessing alignments for candidate junction identification | 14:30:14 19 Apr 2023 | 14:31:37 19 Apr 2023 | 1 minute 23 seconds |
Preliminary analysis of coverage distribution | 14:31:37 19 Apr 2023 | 14:35:27 19 Apr 2023 | 3 minutes 50 seconds |
Identifying junction candidates | 14:35:27 19 Apr 2023 | 14:36:31 19 Apr 2023 | 1 minute 4 seconds |
Re-alignment to junction candidates | 14:36:31 19 Apr 2023 | 14:41:57 19 Apr 2023 | 5 minutes 26 seconds |
Resolving best read alignments | 14:41:57 19 Apr 2023 | 14:44:23 19 Apr 2023 | 2 minutes 26 seconds |
Creating BAM files | 14:44:23 19 Apr 2023 | 14:46:59 19 Apr 2023 | 2 minutes 36 seconds |
Tabulating error counts | 14:46:59 19 Apr 2023 | 14:48:17 19 Apr 2023 | 1 minute 18 seconds |
Re-calibrating base error rates | 14:48:17 19 Apr 2023 | 14:48:54 19 Apr 2023 | 37 seconds |
Examining read alignment evidence | 14:48:54 19 Apr 2023 | 15:05:07 19 Apr 2023 | 16 minutes 13 seconds |
Polymorphism statistics | 15:05:07 19 Apr 2023 | 15:05:08 19 Apr 2023 | 1 second |
Output | 15:05:08 19 Apr 2023 | 15:05:51 19 Apr 2023 | 43 seconds |
Total | 52 minutes 6 seconds |