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 | SRR22894674_R1.good.fq | 2,924,254 | 375,960,437 | 100.0% | 128.6 bases | 135 bases | 99.5% |
errors | SRR22894674_R2.good.fq | 2,924,254 | 375,948,641 | 100.0% | 128.6 bases | 135 bases | 99.0% |
total | 5,848,508 | 751,909,078 | 100.0% | 128.6 bases | 135 bases | 99.3% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | AssemblyC74_contig_1 | 443,529 | 314.5 | 4.8 | 18.8% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_2 | 385,573 | 280.4 | 5.0 | 14.5% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_3 | 255,127 | 236.7 | 3.9 | 8.1% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_4 | 189,292 | 244.8 | 4.0 | 6.2% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_5 | 185,954 | 297.1 | 4.7 | 7.4% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_6 | 168,934 | 267.7 | 4.2 | 6.1% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_7 | 152,772 | 321.2 | 4.8 | 6.6% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_8 | 115,683 | 282.6 | 4.4 | 4.4% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_9 | 104,617 | 250.0 | 4.3 | 3.5% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_10 | 98,564 | 240.2 | 4.1 | 3.2% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_11 | 78,787 | 294.2 | 4.4 | 3.1% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_12 | 59,337 | 314.1 | 4.3 | 2.5% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_13 | 46,240 | 248.1 | 3.9 | 1.5% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_14 | 41,348 | 249.9 | 4.1 | 1.4% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_15 | 36,007 | 307.0 | 4.6 | 1.6% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_16 | 35,103 | 259.8 | 4.0 | 1.2% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_17 | 32,032 | 294.4 | 4.6 | 1.3% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_18 | 27,075 | 310.9 | 4.5 | 1.1% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_19 | 19,031 | 262.3 | 4.5 | 0.7% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_20 | 15,862 | 291.4 | 4.7 | 0.6% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_21 | 10,843 | 255.1 | 3.3 | 0.4% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_22 | 9,537 | 284.0 | 4.7 | 0.4% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_23 | 9,396 | 247.3 | 4.3 | 0.3% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_24 | 8,654 | 309.6 | 5.8 | 0.4% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_25 | 8,555 | 257.6 | 4.9 | 0.3% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_26 | 7,770 | 299.7 | 4.8 | 0.3% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_27 | 7,728 | 294.0 | 5.0 | 0.3% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_28 | 5,975 | 308.4 | 6.3 | 0.2% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_29 | 4,892 | 272.6 | 5.6 | 0.2% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_30 | 4,279 | 280.1 | 5.6 | 0.2% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_31 | 3,396 | 1872.7 | 18.3 | 0.8% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_32 | 3,311 | 310.3 | 7.6 | 0.1% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_33 | 3,075 | 523.5 | 7.8 | 0.2% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_34 | 2,107 | 231.5 | 3.1 | 0.1% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_35 | 2,041 | 262.8 | 7.2 | 0.1% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_36 | 1,754 | 309.6 | 4.5 | 0.1% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_37 | 1,750 | 659.0 | 11.3 | 0.1% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_38 | 1,652 | 499.5 | 11.2 | 0.1% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_39 | 1,643 | 1922.9 | 32.4 | 0.4% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_40 | 1,604 | 249.8 | 4.2 | 0.1% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_41 | 1,330 | 574.9 | 4.9 | 0.1% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_42 | 1,243 | 2525.0 | 29.1 | 0.4% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_43 | 1,217 | 327.7 | 3.0 | 0.1% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_44 | 1,136 | 635.7 | 9.5 | 0.1% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_45 | 1,002 | 1326.9 | 14.3 | 0.2% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_46 | 883 | 231.8 | 4.2 | 0.0% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_47 | 882 | 328.4 | 5.1 | 0.0% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_48 | 844 | 326.7 | 2.9 | 0.0% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_49 | 764 | 546.5 | 6.3 | 0.0% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_50 | 745 | 505.8 | 5.1 | 0.0% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_51 | 723 | 324.8 | 2.5 | 0.0% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_52 | 702 | 538.8 | 5.3 | 0.0% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_53 | 622 | 540.1 | 4.4 | 0.0% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_54 | 611 | 706.8 | 6.6 | 0.0% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_55 | 585 | 262.3 | 3.6 | 0.0% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_56 | 494 | 271.9 | 6.2 | 0.0% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_57 | 493 | 538.5 | 5.7 | 0.0% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_58 | 462 | 327.8 | 2.8 | 0.0% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_59 | 453 | 174.0 | 9.5 | 0.0% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_60 | 439 | 295.5 | 1.0 | 0.0% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_61 | 423 | 633.2 | 5.8 | 0.0% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_62 | 391 | 311.9 | 1.2 | 0.0% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_63 | 383 | 337.3 | 1.6 | 0.0% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_64 | 352 | 620.3 | 12.0 | 0.0% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_65 | 349 | [315.3] | [17.0] | 0.0% | Enterococcus faecium AssemblyC74 |
coverage | distribution | AssemblyC74_contig_66 | 349 | 300.8 | 2.7 | 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.
Fit failed Negative binomial fit failed for this reference sequence. It may have an unusual coverage depth distribution. JC and MC predictions may be less accurate.
option | limit | actual |
---|---|---|
Number of alignment pairs examined for constructing junction candidates | ≤ 100000 | 26417 |
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 | 691 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.073 |
reference sequence | pr(no read start) |
---|---|
AssemblyC74_contig_1 | 0.66809 |
AssemblyC74_contig_2 | 0.68323 |
AssemblyC74_contig_3 | 0.70781 |
AssemblyC74_contig_4 | 0.70294 |
AssemblyC74_contig_5 | 0.67563 |
AssemblyC74_contig_6 | 0.69059 |
AssemblyC74_contig_7 | 0.66370 |
AssemblyC74_contig_8 | 0.68564 |
AssemblyC74_contig_9 | 0.70292 |
AssemblyC74_contig_10 | 0.70417 |
AssemblyC74_contig_11 | 0.67976 |
AssemblyC74_contig_12 | 0.66712 |
AssemblyC74_contig_13 | 0.70304 |
AssemblyC74_contig_14 | 0.70367 |
AssemblyC74_contig_15 | 0.67374 |
AssemblyC74_contig_16 | 0.69312 |
AssemblyC74_contig_17 | 0.68330 |
AssemblyC74_contig_18 | 0.66928 |
AssemblyC74_contig_19 | 0.69542 |
AssemblyC74_contig_20 | 0.67978 |
AssemblyC74_contig_21 | 0.70488 |
AssemblyC74_contig_22 | 0.68087 |
AssemblyC74_contig_23 | 0.70634 |
AssemblyC74_contig_24 | 0.67554 |
AssemblyC74_contig_25 | 0.70649 |
AssemblyC74_contig_26 | 0.67375 |
AssemblyC74_contig_27 | 0.68976 |
AssemblyC74_contig_28 | 0.67164 |
AssemblyC74_contig_29 | 0.69627 |
AssemblyC74_contig_30 | 0.70243 |
AssemblyC74_contig_31 | 0.42270 |
AssemblyC74_contig_32 | 0.68864 |
AssemblyC74_contig_33 | 0.60764 |
AssemblyC74_contig_34 | 0.73469 |
AssemblyC74_contig_35 | 0.70076 |
AssemblyC74_contig_36 | 0.67729 |
AssemblyC74_contig_37 | 0.58398 |
AssemblyC74_contig_38 | 0.64588 |
AssemblyC74_contig_39 | 0.40018 |
AssemblyC74_contig_40 | 0.70421 |
AssemblyC74_contig_41 | 0.59474 |
AssemblyC74_contig_42 | 0.40587 |
AssemblyC74_contig_43 | 0.68356 |
AssemblyC74_contig_44 | 0.62058 |
AssemblyC74_contig_45 | 0.47904 |
AssemblyC74_contig_46 | 0.74462 |
AssemblyC74_contig_47 | 0.72118 |
AssemblyC74_contig_48 | 0.72097 |
AssemblyC74_contig_49 | 0.63874 |
AssemblyC74_contig_50 | 0.65705 |
AssemblyC74_contig_51 | 0.72156 |
AssemblyC74_contig_52 | 0.65242 |
AssemblyC74_contig_53 | 0.64469 |
AssemblyC74_contig_54 | 0.58054 |
AssemblyC74_contig_55 | 0.73810 |
AssemblyC74_contig_56 | 0.76012 |
AssemblyC74_contig_57 | 0.68458 |
AssemblyC74_contig_58 | 0.73780 |
AssemblyC74_contig_59 | 0.79691 |
AssemblyC74_contig_60 | 0.80208 |
AssemblyC74_contig_61 | 0.92000 |
AssemblyC74_contig_62 | 0.91791 |
AssemblyC74_contig_63 | 0.72674 |
AssemblyC74_contig_64 | 0.64596 |
AssemblyC74_contig_65 | NA |
AssemblyC74_contig_66 | 0.71429 |
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 | 14:10:48 19 Apr 2023 | 14:12:40 19 Apr 2023 | 1 minute 52 seconds |
Read alignment to reference genome | 14:12:40 19 Apr 2023 | 14:26:45 19 Apr 2023 | 14 minutes 5 seconds |
Preprocessing alignments for candidate junction identification | 14:26:45 19 Apr 2023 | 14:27:52 19 Apr 2023 | 1 minute 7 seconds |
Preliminary analysis of coverage distribution | 14:27:52 19 Apr 2023 | 14:31:19 19 Apr 2023 | 3 minutes 27 seconds |
Identifying junction candidates | 14:31:19 19 Apr 2023 | 14:32:38 19 Apr 2023 | 1 minute 19 seconds |
Re-alignment to junction candidates | 14:32:38 19 Apr 2023 | 14:37:36 19 Apr 2023 | 4 minutes 58 seconds |
Resolving best read alignments | 14:37:36 19 Apr 2023 | 14:39:35 19 Apr 2023 | 1 minute 59 seconds |
Creating BAM files | 14:39:35 19 Apr 2023 | 14:41:45 19 Apr 2023 | 2 minutes 10 seconds |
Tabulating error counts | 14:41:45 19 Apr 2023 | 14:42:48 19 Apr 2023 | 1 minute 3 seconds |
Re-calibrating base error rates | 14:42:48 19 Apr 2023 | 14:43:24 19 Apr 2023 | 36 seconds |
Examining read alignment evidence | 14:43:24 19 Apr 2023 | 14:56:46 19 Apr 2023 | 13 minutes 22 seconds |
Polymorphism statistics | 14:56:46 19 Apr 2023 | 14:56:47 19 Apr 2023 | 1 second |
Output | 14:56:47 19 Apr 2023 | 14:57:30 19 Apr 2023 | 43 seconds |
Total | 46 minutes 42 seconds |