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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsCCK_pgIsolate_Evo04EP_Isolate_1_S1621_L005_R1_001.good.fq1,451,929207,044,293100.0%142.6 bases143 bases96.2%
errorsCCK_pgIsolate_Evo04EP_Isolate_1_S1621_L005_R2_001.good.fq1,451,929207,044,293100.0%142.6 bases143 bases87.6%
total2,903,858414,088,586100.0%142.6 bases143 bases91.9%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65282.11.9100.0%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≤ 10000015520
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 ≤ 5000305
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.019

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.79190

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≤ 3
Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction≥ 1

Read Alignment Evidence

optionvalue
ModeConsensus/Mixed Base
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 cutoff10
Polymorphism frequency cutoff0.2
Polymorphism minimum variant coverage each strandOFF
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 ofOFF
Skip base substitutions when they create a homopolymer flanked on each side byOFF

Software Versions

programversion
bowtie22.3.4.1
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input07:17:11 25 Feb 202007:17:55 25 Feb 202044 seconds
Read alignment to reference genome07:17:55 25 Feb 202007:27:08 25 Feb 20209 minutes 13 seconds
Preprocessing alignments for candidate junction identification07:27:08 25 Feb 202007:27:50 25 Feb 202042 seconds
Preliminary analysis of coverage distribution07:27:50 25 Feb 202007:29:34 25 Feb 20201 minute 44 seconds
Identifying junction candidates07:29:34 25 Feb 202007:29:39 25 Feb 20205 seconds
Re-alignment to junction candidates07:29:39 25 Feb 202007:32:05 25 Feb 20202 minutes 26 seconds
Resolving best read alignments07:32:05 25 Feb 202007:33:07 25 Feb 20201 minute 2 seconds
Creating BAM files07:33:07 25 Feb 202007:34:43 25 Feb 20201 minute 36 seconds
Tabulating error counts07:34:43 25 Feb 202007:35:14 25 Feb 202031 seconds
Re-calibrating base error rates07:35:14 25 Feb 202007:35:15 25 Feb 20201 second
Examining read alignment evidence07:35:15 25 Feb 202007:41:40 25 Feb 20206 minutes 25 seconds
Polymorphism statistics07:41:40 25 Feb 202007:41:40 25 Feb 20200 seconds
Output07:41:40 25 Feb 202007:41:57 25 Feb 202017 seconds
Total 24 minutes 46 seconds