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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsGLY_34_005_S226_L001_R1_001.good.fq625,35287,493,964100.0%139.9 bases149 bases97.1%
errorsGLY_34_005_S226_L001_R2_001.good.fq625,35287,493,964100.0%139.9 bases149 bases96.9%
errorsGLY_34_005_S226_L002_R1_001.good.fq621,68486,819,849100.0%139.7 bases149 bases96.8%
errorsGLY_34_005_S226_L002_R2_001.good.fq621,68486,819,849100.0%139.7 bases149 bases96.6%
total2,494,072348,627,626100.0%139.8 bases149 bases96.8%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65267.65.6100.0%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≤ 10000013277
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 ≤ 5000125
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.008

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.79904

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 input23:17:28 05 Jan 201923:18:03 05 Jan 201935 seconds
Read alignment to reference genome23:18:03 05 Jan 201923:22:59 05 Jan 20194 minutes 56 seconds
Preprocessing alignments for candidate junction identification23:22:59 05 Jan 201923:23:29 05 Jan 201930 seconds
Preliminary analysis of coverage distribution23:23:29 05 Jan 201923:25:10 05 Jan 20191 minute 41 seconds
Identifying junction candidates23:25:10 05 Jan 201923:25:21 05 Jan 201911 seconds
Re-alignment to junction candidates23:25:21 05 Jan 201923:26:53 05 Jan 20191 minute 32 seconds
Resolving best read alignments23:26:53 05 Jan 201923:27:46 05 Jan 201953 seconds
Creating BAM files23:27:46 05 Jan 201923:29:18 05 Jan 20191 minute 32 seconds
Tabulating error counts23:29:18 05 Jan 201923:29:46 05 Jan 201928 seconds
Re-calibrating base error rates23:29:46 05 Jan 201923:29:47 05 Jan 20191 second
Examining read alignment evidence23:29:47 05 Jan 201923:38:59 05 Jan 20199 minutes 12 seconds
Polymorphism statistics23:38:59 05 Jan 201923:39:01 05 Jan 20192 seconds
Output23:39:01 05 Jan 201923:39:36 05 Jan 201935 seconds
Total 22 minutes 8 seconds