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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsGlyA_D15_I0_S2121_L001_R1_001.good.fq1,354,027201,667,048100.0%148.9 bases149 bases98.5%
errorsGlyA_D15_I0_S2121_L001_R2_001.good.fq1,354,027201,667,048100.0%148.9 bases149 bases93.0%
total2,708,054403,334,096100.0%148.9 bases149 bases95.8%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65382.44.9100.0%Escherichia coli str. K-12 sbstr. MG1655, complete genome. Live strain from Systems Biology Research Group
total4,641,653100.0%

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≤ 1000007600
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 ≤ 5000114
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.007

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.79168

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
bowtie22.3.4.3
R3.5.1

Execution Times

stepstartendelapsed
Read and reference sequence file input06:47:52 30 Oct 201806:48:29 30 Oct 201837 seconds
Read alignment to reference genome06:48:29 30 Oct 201806:55:05 30 Oct 20186 minutes 36 seconds
Preprocessing alignments for candidate junction identification06:55:05 30 Oct 201806:55:40 30 Oct 201835 seconds
Preliminary analysis of coverage distribution06:55:40 30 Oct 201806:57:25 30 Oct 20181 minute 45 seconds
Identifying junction candidates06:57:25 30 Oct 201806:57:25 30 Oct 20180 seconds
Re-alignment to junction candidates06:57:25 30 Oct 201806:58:41 30 Oct 20181 minute 16 seconds
Resolving best read alignments06:58:41 30 Oct 201806:59:37 30 Oct 201856 seconds
Creating BAM files06:59:37 30 Oct 201807:01:15 30 Oct 20181 minute 38 seconds
Tabulating error counts07:01:15 30 Oct 201807:01:46 30 Oct 201831 seconds
Re-calibrating base error rates07:01:46 30 Oct 201807:01:47 30 Oct 20181 second
Examining read alignment evidence07:01:47 30 Oct 201807:40:44 30 Oct 201838 minutes 57 seconds
Polymorphism statistics07:40:44 30 Oct 201807:40:44 30 Oct 20180 seconds
Output07:40:44 30 Oct 201807:40:54 30 Oct 201810 seconds
Total 53 minutes 2 seconds