breseq  version 0.35.4  revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsAA_PAL019_S19_R1_001.good.fq1,187,401176,518,726100.0%148.7 bases149 bases98.3%
errorsAA_PAL019_S19_R2_001.good.fq1,187,401176,518,726100.0%148.7 bases149 bases96.3%
total2,374,802353,037,452100.0%148.7 bases149 bases97.3%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65268.82.7100.0%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≤ 10000013987
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 ≤ 5000441
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.029

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.80522

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
Minimum probablilty assigned that no mapped read will start at a given position and strand for junction prediction0.1
Junction allow suboptimal matchesFALSE
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
bowtie22.2.6
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input20:08:25 15 Apr 202120:09:08 15 Apr 202143 seconds
Read alignment to reference genome20:09:08 15 Apr 202120:15:27 15 Apr 20216 minutes 19 seconds
Preprocessing alignments for candidate junction identification20:15:27 15 Apr 202120:15:56 15 Apr 202129 seconds
Preliminary analysis of coverage distribution20:15:56 15 Apr 202120:17:57 15 Apr 20212 minutes 1 second
Identifying junction candidates20:17:57 15 Apr 202120:18:03 15 Apr 20216 seconds
Re-alignment to junction candidates20:18:03 15 Apr 202120:19:27 15 Apr 20211 minute 24 seconds
Resolving best read alignments20:19:27 15 Apr 202120:20:10 15 Apr 202143 seconds
Creating BAM files20:20:10 15 Apr 202120:22:05 15 Apr 20211 minute 55 seconds
Tabulating error counts20:22:05 15 Apr 202120:22:37 15 Apr 202132 seconds
Re-calibrating base error rates20:22:37 15 Apr 202120:22:37 15 Apr 20210 seconds
Examining read alignment evidence20:22:37 15 Apr 202121:02:36 15 Apr 202139 minutes 59 seconds
Polymorphism statistics21:02:36 15 Apr 202121:02:37 15 Apr 20211 second
Output21:02:37 15 Apr 202121:03:06 15 Apr 202129 seconds
Total 54 minutes 41 seconds