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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsDRR021342_R1.good.fq1,956,085444,590,934100.0%227.3 bases239 bases99.1%
errorsDRR021342_R2.good.fq1,956,085445,784,377100.0%227.9 bases239 bases84.5%
total3,912,170890,375,311100.0%227.6 bases239 bases91.8%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0077794,646,332183.68.2100.0%Escherichia coli str. K-12 substr. W3110, complete sequence.
total4,646,332100.0%

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≤ 10000035727
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 3
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 5000127
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.013

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0077790.78890

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 input17:36:26 17 Mar 202017:37:23 17 Mar 202057 seconds
Read alignment to reference genome17:37:23 17 Mar 202017:52:35 17 Mar 202015 minutes 12 seconds
Preprocessing alignments for candidate junction identification17:52:35 17 Mar 202017:53:37 17 Mar 20201 minute 2 seconds
Preliminary analysis of coverage distribution17:53:37 17 Mar 202017:56:45 17 Mar 20203 minutes 8 seconds
Identifying junction candidates17:56:45 17 Mar 202017:58:13 17 Mar 20201 minute 28 seconds
Re-alignment to junction candidates17:58:13 17 Mar 202018:02:22 17 Mar 20204 minutes 9 seconds
Resolving best read alignments18:02:22 17 Mar 202018:04:03 17 Mar 20201 minute 41 seconds
Creating BAM files18:04:03 17 Mar 202018:06:51 17 Mar 20202 minutes 48 seconds
Tabulating error counts18:06:51 17 Mar 202018:07:56 17 Mar 20201 minute 5 seconds
Re-calibrating base error rates18:07:56 17 Mar 202018:07:57 17 Mar 20201 second
Examining read alignment evidence18:07:57 17 Mar 202019:36:58 17 Mar 20201 hour 29 minutes 1 second
Polymorphism statistics19:36:58 17 Mar 202019:37:00 17 Mar 20202 seconds
Output19:37:00 17 Mar 202019:38:27 17 Mar 20201 minute 27 seconds
Total 2 hours 2 minutes 1 second