breseq  version 0.33.1  revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorspgi-11-4_S22_L001_R1_001.good.fq1,100,776289,447,678100.0%262.9 bases289 bases99.4%
errorspgi-11-4_S22_L001_R2_001.good.fq1,100,776289,857,001100.0%263.3 bases289 bases95.6%
total2,201,552579,304,679100.0%263.1 bases289 bases97.5%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652124.35.8100.0%Escherichia coli str. K-12 substr. MG1655, complete genome.
total4,641,652100.0%

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.

New Junction Evidence

Junction Candidates Tested

optionlimitactual
Number of alignment pairs examined for constructing junction candidates≤ 1000006474
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 threshold100 ≤ n ≤ 5000481
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.061

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.84719

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.

Final Junction Predictions

optionvalue
Coverage evenness (position-hash) score of predicted junctions must be≥ 3
Skew score of predicted junction (−log10 probability of unusual coverage evenness) must be≤ 0
Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction≥ 6

Read Alignment Evidence

optionvalue
ModeFull Polymorphism
Ploidy1 (haploid)
Consensus mutation E-value cutoff10
Consensus frequency cutoff0.75
Consensus minimum variant coverage each strandOFF
Consensus minimum total coverage each strandOFF
Consensus minimum variant coverageOFF
Consensus minimum total coverageOFF
Polymorphism E-value cutoff2
Polymorphism frequency cutoff0.05
Polymorphism minimum variant coverage each strand2
Polymorphism minimum total coverage each strandOFF
Polymorphism minimum variant coverageOFF
Polymorphism minimum total coverageOFF
Polymorphism bias cutoffOFF
Predict indel polymorphismsYES
Skip indel polymorphisms in homopolymers runs of ≥3 bases
Skip base substitutions when they create a homopolymer flanked on each side by ≥5 bases

Software Versions

programversion
bowtie22.3.4.1
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input20:36:29 28 Feb 202020:37:03 28 Feb 202034 seconds
Read alignment to reference genome20:37:04 28 Feb 202020:46:57 28 Feb 20209 minutes 53 seconds
Preprocessing alignments for candidate junction identification20:46:57 28 Feb 202020:47:35 28 Feb 202038 seconds
Preliminary analysis of coverage distribution20:47:35 28 Feb 202020:49:38 28 Feb 20202 minutes 3 seconds
Identifying junction candidates20:49:38 28 Feb 202020:49:50 28 Feb 202012 seconds
Re-alignment to junction candidates20:49:50 28 Feb 202020:52:44 28 Feb 20202 minutes 54 seconds
Resolving best read alignments20:52:44 28 Feb 202020:53:45 28 Feb 20201 minute 1 second
Creating BAM files20:53:45 28 Feb 202020:55:31 28 Feb 20201 minute 46 seconds
Tabulating error counts20:55:31 28 Feb 202020:56:27 28 Feb 202056 seconds
Re-calibrating base error rates20:56:27 28 Feb 202020:56:28 28 Feb 20201 second
Examining read alignment evidence20:56:28 28 Feb 202021:50:30 28 Feb 202054 minutes 2 seconds
Polymorphism statistics21:50:30 28 Feb 202021:50:31 28 Feb 20201 second
Output21:50:31 28 Feb 202021:50:52 28 Feb 202021 seconds
Total 1 hour 14 minutes 22 seconds