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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorspgi-15-3_S31_L001_R1_001.good.fq819,034223,159,134100.0%272.5 bases289 bases99.6%
errorspgi-15-3_S31_L001_R2_001.good.fq819,034223,273,059100.0%272.6 bases289 bases95.7%
total1,638,068446,432,193100.0%272.5 bases289 bases97.7%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65295.74.0100.0%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≤ 1000004038
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 ≤ 5000261
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.033

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.87915

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 input12:29:20 25 Feb 202012:29:47 25 Feb 202027 seconds
Read alignment to reference genome12:29:47 25 Feb 202012:37:59 25 Feb 20208 minutes 12 seconds
Preprocessing alignments for candidate junction identification12:37:59 25 Feb 202012:38:28 25 Feb 202029 seconds
Preliminary analysis of coverage distribution12:38:28 25 Feb 202012:40:05 25 Feb 20201 minute 37 seconds
Identifying junction candidates12:40:05 25 Feb 202012:40:10 25 Feb 20205 seconds
Re-alignment to junction candidates12:40:10 25 Feb 202012:42:18 25 Feb 20202 minutes 8 seconds
Resolving best read alignments12:42:18 25 Feb 202012:43:06 25 Feb 202048 seconds
Creating BAM files12:43:06 25 Feb 202012:44:50 25 Feb 20201 minute 44 seconds
Tabulating error counts12:44:50 25 Feb 202012:45:35 25 Feb 202045 seconds
Re-calibrating base error rates12:45:35 25 Feb 202012:45:36 25 Feb 20201 second
Examining read alignment evidence12:45:36 25 Feb 202013:24:41 25 Feb 202039 minutes 5 seconds
Polymorphism statistics13:24:41 25 Feb 202013:24:42 25 Feb 20201 second
Output13:24:42 25 Feb 202013:25:01 25 Feb 202019 seconds
Total 55 minutes 41 seconds