breseq  version 0.30.0  revision f53f5bf51c1f
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errors1Glu_S1_L001_R2_0011,547,177428,705,760100.0%277.1 bases301 bases83.4%
errors1Glu_S1_L001_R1_0011,547,221425,639,170100.0%275.1 bases301 bases93.6%
total3,094,398854,344,930100.0%276.1 bases301 bases88.5%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652165.34.7100.0%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≤ 1000002877
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 ≤ 5000279
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.037

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.84831

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 cutoffOFF
Consensus minimum coverage each strandOFF
Polymorphism E-value cutoff2
Polymorphism frequency cutoff0.05
Polymorphism minimum coverage each strand2
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
R3.3.1

Execution Times

stepstartendelapsed
Read and reference sequence file input14:43:45 13 Apr 201714:44:55 13 Apr 20171 minute 10 seconds
Read alignment to reference genome14:44:55 13 Apr 201714:53:10 13 Apr 20178 minutes 15 seconds
Preprocessing alignments for candidate junction identification14:53:10 13 Apr 201714:55:02 13 Apr 20171 minute 52 seconds
Preliminary analysis of coverage distribution14:55:02 13 Apr 201714:58:09 13 Apr 20173 minutes 7 seconds
Identifying junction candidates14:58:09 13 Apr 201714:58:25 13 Apr 201716 seconds
Re-alignment to junction candidates14:58:25 13 Apr 201714:59:12 13 Apr 201747 seconds
Resolving alignments with junction candidates14:59:12 13 Apr 201715:02:33 13 Apr 20173 minutes 21 seconds
Creating BAM files15:02:33 13 Apr 201715:04:12 13 Apr 20171 minute 39 seconds
Tabulating error counts15:04:12 13 Apr 201715:07:49 13 Apr 20173 minutes 37 seconds
Re-calibrating base error rates15:07:49 13 Apr 201715:07:49 13 Apr 20170 seconds
Examining read alignment evidence15:07:49 13 Apr 201718:27:52 13 Apr 20173 hours 20 minutes 3 seconds
Polymorphism statistics18:27:52 13 Apr 201718:27:52 13 Apr 20170 seconds
Output18:27:52 13 Apr 201718:28:36 13 Apr 201744 seconds
Total 3 hours 44 minutes 51 seconds