breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
read file | reads | bases | passed filters | average | longest | mapped | |
---|---|---|---|---|---|---|---|
errors | ALE-84_S84_L001_R1_001.good.fq | 424,024 | 59,598,899 | 100.0% | 140.6 bases | 148 bases | 98.2% |
errors | ALE-84_S84_L001_R2_001.good.fq | 424,024 | 59,635,424 | 100.0% | 140.6 bases | 148 bases | 97.1% |
errors | ALE-84_S84_L002_R1_001.good.fq | 422,605 | 59,204,247 | 100.0% | 140.1 bases | 147 bases | 98.3% |
errors | ALE-84_S84_L002_R2_001.good.fq | 422,605 | 59,087,097 | 100.0% | 139.8 bases | 147 bases | 97.5% |
errors | ALE-84_S84_L003_R1_001.good.fq | 428,510 | 59,938,695 | 100.0% | 139.9 bases | 147 bases | 98.3% |
errors | ALE-84_S84_L003_R2_001.good.fq | 428,510 | 59,790,935 | 100.0% | 139.5 bases | 147 bases | 98.2% |
errors | ALE-84_S84_L004_R1_001.good.fq | 401,469 | 56,305,153 | 100.0% | 140.2 bases | 148 bases | 99.1% |
errors | ALE-84_S84_L004_R2_001.good.fq | 401,469 | 56,353,084 | 100.0% | 140.4 bases | 148 bases | 97.1% |
total | 3,353,216 | 469,913,534 | 100.0% | 140.1 bases | 148 bases | 98.0% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | NC_002947 | 6,181,873 | 79.3 | 10.8 | 100.0% | Pseudomonas putida KT2440 chromosome, complete genome. |
total | 6,181,873 | 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 | 16403 |
Coverage evenness (position-hash) score of junction candidates | ≥ 2 | ≥ 3 |
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold | 100 ≤ n ≤ 5000 | 97 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.005 |
reference sequence | pr(no read start) |
---|---|
NC_002947 | 0.78360 |
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 |
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 | 2.3.4.1 |
R | 3.4.4 |
step | start | end | elapsed |
---|---|---|---|
Read and reference sequence file input | 09:43:57 18 Feb 2020 | 09:44:47 18 Feb 2020 | 50 seconds |
Read alignment to reference genome | 09:44:47 18 Feb 2020 | 09:51:38 18 Feb 2020 | 6 minutes 51 seconds |
Preprocessing alignments for candidate junction identification | 09:51:38 18 Feb 2020 | 09:52:23 18 Feb 2020 | 45 seconds |
Preliminary analysis of coverage distribution | 09:52:23 18 Feb 2020 | 09:54:17 18 Feb 2020 | 1 minute 54 seconds |
Identifying junction candidates | 09:54:17 18 Feb 2020 | 09:55:04 18 Feb 2020 | 47 seconds |
Re-alignment to junction candidates | 09:55:04 18 Feb 2020 | 09:57:06 18 Feb 2020 | 2 minutes 2 seconds |
Resolving best read alignments | 09:57:06 18 Feb 2020 | 09:58:17 18 Feb 2020 | 1 minute 11 seconds |
Creating BAM files | 09:58:17 18 Feb 2020 | 10:00:03 18 Feb 2020 | 1 minute 46 seconds |
Tabulating error counts | 10:00:03 18 Feb 2020 | 10:00:39 18 Feb 2020 | 36 seconds |
Re-calibrating base error rates | 10:00:39 18 Feb 2020 | 10:00:41 18 Feb 2020 | 2 seconds |
Examining read alignment evidence | 10:00:41 18 Feb 2020 | 10:07:40 18 Feb 2020 | 6 minutes 59 seconds |
Polymorphism statistics | 10:07:40 18 Feb 2020 | 10:07:40 18 Feb 2020 | 0 seconds |
Output | 10:07:40 18 Feb 2020 | 10:08:01 18 Feb 2020 | 21 seconds |
Total | 24 minutes 4 seconds |