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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsJ17-F1_S124_R1_001.good.fq3,863,507237,095,997100.0%61.4 bases71 bases93.7%
total3,863,507237,095,997100.0%61.4 bases71 bases93.7%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionExported2,987,94274.87.1100.0%Escherichia coli str. K-12 substr. W3110 DNA, complete genome.
total2,987,942100.0%

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≤ 10000016469
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 ≤ 5000284
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.014

Junction Skew Score Calculation

reference sequencepr(no read start)
Exported0.70909

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 input12:48:17 28 Jun 201912:48:55 28 Jun 201938 seconds
Read alignment to reference genome12:48:55 28 Jun 201912:53:55 28 Jun 20195 minutes 0 seconds
Preprocessing alignments for candidate junction identification12:53:55 28 Jun 201912:54:37 28 Jun 201942 seconds
Preliminary analysis of coverage distribution12:54:37 28 Jun 201912:55:45 28 Jun 20191 minute 8 seconds
Identifying junction candidates12:55:45 28 Jun 201912:55:46 28 Jun 20191 second
Re-alignment to junction candidates12:55:46 28 Jun 201912:57:08 28 Jun 20191 minute 22 seconds
Resolving best read alignments12:57:08 28 Jun 201912:58:12 28 Jun 20191 minute 4 seconds
Creating BAM files12:58:12 28 Jun 201912:59:14 28 Jun 20191 minute 2 seconds
Tabulating error counts12:59:14 28 Jun 201912:59:34 28 Jun 201920 seconds
Re-calibrating base error rates12:59:34 28 Jun 201912:59:34 28 Jun 20190 seconds
Examining read alignment evidence12:59:34 28 Jun 201913:05:34 28 Jun 20196 minutes 0 seconds
Polymorphism statistics13:05:34 28 Jun 201913:05:34 28 Jun 20190 seconds
Output13:05:34 28 Jun 201913:05:42 28 Jun 20198 seconds
Total 17 minutes 25 seconds