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_tpIsolate_AEvo01EP_Isolate_2_S1598_L005_R1_001.good.fq527,86975,386,189100.0%142.8 bases143 bases95.7%
errorsCCK_tpIsolate_AEvo01EP_Isolate_2_S1598_L005_R2_001.good.fq527,86975,386,189100.0%142.8 bases143 bases83.7%
total1,055,738150,772,378100.0%142.8 bases143 bases89.7%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65229.01.4100.0%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≤ 1000005493
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 ≤ 500080
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.005

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.91784

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 input22:21:45 27 Feb 202022:22:02 27 Feb 202017 seconds
Read alignment to reference genome22:22:02 27 Feb 202022:25:27 27 Feb 20203 minutes 25 seconds
Preprocessing alignments for candidate junction identification22:25:27 27 Feb 202022:25:42 27 Feb 202015 seconds
Preliminary analysis of coverage distribution22:25:42 27 Feb 202022:26:16 27 Feb 202034 seconds
Identifying junction candidates22:26:16 27 Feb 202022:26:18 27 Feb 20202 seconds
Re-alignment to junction candidates22:26:18 27 Feb 202022:27:05 27 Feb 202047 seconds
Resolving best read alignments22:27:05 27 Feb 202022:27:27 27 Feb 202022 seconds
Creating BAM files22:27:27 27 Feb 202022:27:58 27 Feb 202031 seconds
Tabulating error counts22:27:58 27 Feb 202022:28:08 27 Feb 202010 seconds
Re-calibrating base error rates22:28:08 27 Feb 202022:28:09 27 Feb 20201 second
Examining read alignment evidence22:28:09 27 Feb 202022:30:35 27 Feb 20202 minutes 26 seconds
Polymorphism statistics22:30:35 27 Feb 202022:30:36 27 Feb 20201 second
Output22:30:36 27 Feb 202022:30:46 27 Feb 202010 seconds
Total 9 minutes 1 second