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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errors9-Colony-10-22-12_S12_L001_R1_001.good.fq737,074209,153,599100.0%283.8 bases289 bases99.4%
errors9-Colony-10-22-12_S12_L001_R2_001.good.fq737,074209,181,158100.0%283.8 bases289 bases96.2%
total1,474,148418,334,757100.0%283.8 bases289 bases97.8%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65287.73.7100.0%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≤ 1000005441
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 ≤ 5000372
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.047

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.89392

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 input16:52:04 22 May 201916:52:27 22 May 201923 seconds
Read alignment to reference genome16:52:27 22 May 201917:00:19 22 May 20197 minutes 52 seconds
Preprocessing alignments for candidate junction identification17:00:19 22 May 201917:00:44 22 May 201925 seconds
Preliminary analysis of coverage distribution17:00:44 22 May 201917:02:16 22 May 20191 minute 32 seconds
Identifying junction candidates17:02:16 22 May 201917:02:22 22 May 20196 seconds
Re-alignment to junction candidates17:02:22 22 May 201917:04:33 22 May 20192 minutes 11 seconds
Resolving best read alignments17:04:33 22 May 201917:05:18 22 May 201945 seconds
Creating BAM files17:05:18 22 May 201917:06:39 22 May 20191 minute 21 seconds
Tabulating error counts17:06:39 22 May 201917:07:13 22 May 201934 seconds
Re-calibrating base error rates17:07:13 22 May 201917:07:14 22 May 20191 second
Examining read alignment evidence17:07:14 22 May 201917:13:43 22 May 20196 minutes 29 seconds
Polymorphism statistics17:13:43 22 May 201917:13:43 22 May 20190 seconds
Output17:13:43 22 May 201917:13:55 22 May 201912 seconds
Total 21 minutes 51 seconds