mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 | KT2440_Van_A4_F106_I1_R1_S53_L001_R1_001.good.fq | 252,254 | 31,819,052 | 100.0% | 126.1 bases | 136 bases | 92.9% |
| errors | KT2440_Van_A4_F106_I1_R1_S53_L001_R2_001.good.fq | 252,254 | 31,818,695 | 100.0% | 126.1 bases | 136 bases | 90.2% |
| errors | KT2440_Van_A4_F106_I1_R1_S53_L002_R1_001.good.fq | 248,584 | 31,404,779 | 100.0% | 126.3 bases | 136 bases | 94.0% |
| errors | KT2440_Van_A4_F106_I1_R1_S53_L002_R2_001.good.fq | 248,584 | 31,404,180 | 100.0% | 126.3 bases | 136 bases | 92.3% |
| errors | KT2440_Van_A4_F106_I1_R1_S53_L003_R1_001.good.fq | 249,954 | 31,624,047 | 100.0% | 126.5 bases | 136 bases | 92.9% |
| errors | KT2440_Van_A4_F106_I1_R1_S53_L003_R2_001.good.fq | 249,954 | 31,622,971 | 100.0% | 126.5 bases | 136 bases | 90.9% |
| errors | KT2440_Van_A4_F106_I1_R1_S53_L004_R1_001.good.fq | 251,199 | 31,670,283 | 100.0% | 126.1 bases | 136 bases | 94.1% |
| errors | KT2440_Van_A4_F106_I1_R1_S53_L004_R2_001.good.fq | 251,199 | 31,670,091 | 100.0% | 126.1 bases | 136 bases | 92.5% |
| total | 2,003,982 | 253,034,098 | 100.0% | 126.3 bases | 136 bases | 92.5% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | KT2440 | 6,185,276 | 38.3 | 2.5 | 100.0% | tig00000001|arrow. |
| total | 6,185,276 | 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 | 1794 |
| 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 | 95 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.004 |
| reference sequence | pr(no read start) |
|---|---|
| KT2440 | 0.89236 |
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 | 21:59:09 01 May 2023 | 21:59:44 01 May 2023 | 35 seconds |
| Read alignment to reference genome | 21:59:44 01 May 2023 | 22:04:06 01 May 2023 | 4 minutes 22 seconds |
| Preprocessing alignments for candidate junction identification | 22:04:06 01 May 2023 | 22:04:32 01 May 2023 | 26 seconds |
| Preliminary analysis of coverage distribution | 22:04:32 01 May 2023 | 22:05:40 01 May 2023 | 1 minute 8 seconds |
| Identifying junction candidates | 22:05:40 01 May 2023 | 22:05:41 01 May 2023 | 1 second |
| Re-alignment to junction candidates | 22:05:41 01 May 2023 | 22:06:39 01 May 2023 | 58 seconds |
| Resolving best read alignments | 22:06:39 01 May 2023 | 22:07:14 01 May 2023 | 35 seconds |
| Creating BAM files | 22:07:14 01 May 2023 | 22:08:20 01 May 2023 | 1 minute 6 seconds |
| Tabulating error counts | 22:08:20 01 May 2023 | 22:08:41 01 May 2023 | 21 seconds |
| Re-calibrating base error rates | 22:08:41 01 May 2023 | 22:08:44 01 May 2023 | 3 seconds |
| Examining read alignment evidence | 22:08:44 01 May 2023 | 22:13:29 01 May 2023 | 4 minutes 45 seconds |
| Polymorphism statistics | 22:13:29 01 May 2023 | 22:13:29 01 May 2023 | 0 seconds |
| Output | 22:13:29 01 May 2023 | 22:14:04 01 May 2023 | 35 seconds |
| Total | 14 minutes 55 seconds | ||
